High Pressure X-Ray Crystallography With the Diamond Cell at NIST/NBS

PubMed Central

Piermarini, Gasper J.

2001-01-01

Scientists in the Crystallography Section at NIST/NBS made several outstanding contributions which greatly promoted the development and advancement of high pressure x-ray crystallography during the second-half of the 20th century. These milestone achievements or “firsts” included: (1) the invention of the lever-arm type diamond anvil cell (DAC) in 1958; (2) the development of DAC technology for powder x-ray diffraction at high pressure in 1960; (3) the introduction of DAC methodology for single crystal x-ray diffraction at high pressure in 1964; (4) the invention of the optical fluorescence ruby method of pressure measurement in 1971; and (5) the discovery of hydrostatic pressure-transmitting media useful to unprecedented pressures for that time. These achievements provided the spark that ignited the explosion of activity in high pressure research that occurred in laboratories throughout the world during the latter part of the 20th century. It is still going on, unabated, today. An estimated 5000 DACs were built during the last 40 years. PMID:27500054

Probing the Complex Architecture of Multimodular Carbohydrate-Active Enzymes Using a Combination of Small Angle X-Ray Scattering and X-Ray Crystallography.

PubMed

Czjzek, Mirjam; Ficko-Blean, Elizabeth

2017-01-01

The various modules in multimodular carbohydrate-active enzymes (CAZymes) may function in catalysis, carbohydrate binding, protein-protein interactions or as linkers. Here, we describe how combining the biophysical techniques of Small Angle X-ray Scattering (SAXS) and macromolecular X-ray crystallography (XRC) provides a powerful tool for examination into questions related to overall structural organization of ultra multimodular CAZymes.

A Compact X-Ray System for Macromolecular Crystallography

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Gibson, Walter; Joy, Marshall

2000-01-01

We describe the design and performance of a high flux x-ray system for a macromolecular crystallography that combines a microfocus x-ray generator (40 micrometer full width at half maximum spot size at a power level of 46.5 W) and a collimating polycapillary optic. The Cu Ka lpha x-ray flux produced by this optimized system through a 500,um diam orifice is 7.0 times greater than the x-ray flux previously reported by Gubarev et al. [M. Gubarev et al., J. Appl. Crystallogr. 33, 882 (2000)]. The x-ray flux from the microfocus system is also 2.6 times higher than that produced by a rotating anode generator equipped with a graded multilayer monochromator (green optic, Osmic Inc. CMF24-48-Cu6) and 40% less than that produced by a rotating anode generator with the newest design of graded multilayer monochromator (blue optic, Osmic, Inc. CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 W, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42 540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym)=5.0% for data extending to 1.70 A, and 4.8% for the complete set of data to 1.85 A. The amplitudes of the observed reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

A Compact X-Ray System for Macromolecular Crystallography. 5

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Joy, Marshall

2000-01-01

We describe the design and performance of a high flux x-ray system for macromolecular crystallography that combines a microfocus x-ray generator (40 gm FWHM spot size at a power level of 46.5Watts) and a 5.5 mm focal distance polycapillary optic. The Cu K(sub alpha) X-ray flux produced by this optimized system is 7.0 times above the X-ray flux previously reported. The X-ray flux from the microfocus system is also 3.2 times higher than that produced by the rotating anode generator equipped with a long focal distance graded multilayer monochromator (Green optic; CMF24-48-Cu6) and 30% less than that produced by the rotating anode generator with the newest design of graded multilayer monochromator (Blue optic; CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 Watts, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42,540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym) 5.0% for the data extending to 1.7A, and 4.8% for the complete set of data to 1.85A. The amplitudes of the reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

Time-Resolved Macromolecular Crystallography at Modern X-Ray Sources.

PubMed

Schmidt, Marius

2017-01-01

Time-resolved macromolecular crystallography unifies protein structure determination with chemical kinetics. With the advent of fourth generation X-ray sources the time-resolution can be on the order of 10-40 fs, which opens the ultrafast time scale to structure determination. Fundamental motions and transitions associated with chemical reactions in proteins can now be observed. Moreover, new experimental approaches at synchrotrons allow for the straightforward investigation of all kind of reactions in biological macromolecules. Here, recent developments in the field are reviewed.

A convolutional neural network-based screening tool for X-ray serial crystallography

PubMed Central

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.; Ushizima, Daniela; Yang, Chao; Sauter, Nicholas K.

2018-01-01

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization. PMID:29714177

A convolutional neural network-based screening tool for X-ray serial crystallography.

PubMed

Ke, Tsung Wei; Brewster, Aaron S; Yu, Stella X; Ushizima, Daniela; Yang, Chao; Sauter, Nicholas K

2018-05-01

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization. open access.

A convolutional neural network-based screening tool for X-ray serial crystallography

DOE PAGES

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.; ...

2018-04-24

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization.

A convolutional neural network-based screening tool for X-ray serial crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization.

100 Years Later: Celebrating the Contributions of X-ray Crystallography to Allergy and Clinical Immunology

PubMed Central

Pomés, Anna; Chruszcz, Maksymilian; Gustchina, Alla; Minor, Wladek; Mueller, Geoffrey A.; Pedersen, Lars C.; Wlodawer, Alexander; Chapman, Martin D.

2015-01-01

Current knowledge of molecules involved in immunology and allergic disease results from significant contributions of X-ray crystallography, a discipline that just celebrated its 100th anniversary. The histories of allergens and X-ray crystallography are intimately intertwined. The first enzyme structure to be determined was lysozyme, also known as the chicken food allergen Gal d 4. Crystallography determines the exact three-dimensional positions of atoms in molecules. Structures of molecular complexes in the disciplines of immunology and allergy have revealed the atoms involved in molecular interactions and in mechanisms of disease. These complexes include peptides presented by MHC class II molecules, cytokines bound to their receptors, allergen-antibody complexes, and innate immune receptors with their ligands. The information derived from crystallographic studies provides insights into the function of molecules. Allergen function is one of the determinants of environmental exposure, which is essential for IgE sensitization. Proteolytic activity of allergens or their capacity to bind lipopolysaccharides may also contribute to allergenicity. The atomic positions define the molecular surface that is accessible to antibodies. This surface in turn determines antibody specificity and cross-reactivity that are important factors for the selection of allergen panels used for molecular diagnosis and for the interpretation of clinical symptoms. This review celebrates the contributions of X-ray crystallography to clinical immunology and allergy, focusing on new molecular perspectives that influence the diagnosis and treatment of allergic diseases. PMID:26145985

100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology.

PubMed

Pomés, Anna; Chruszcz, Maksymilian; Gustchina, Alla; Minor, Wladek; Mueller, Geoffrey A; Pedersen, Lars C; Wlodawer, Alexander; Chapman, Martin D

2015-07-01

Current knowledge of molecules involved in immunology and allergic disease results from the significant contributions of x-ray crystallography, a discipline that just celebrated its 100th anniversary. The histories of allergens and x-ray crystallography are intimately intertwined. The first enzyme structure to be determined was lysozyme, also known as the chicken food allergen Gal d 4. Crystallography determines the exact 3-dimensional positions of atoms in molecules. Structures of molecular complexes in the disciplines of immunology and allergy have revealed the atoms involved in molecular interactions and mechanisms of disease. These complexes include peptides presented by MHC class II molecules, cytokines bound to their receptors, allergen-antibody complexes, and innate immune receptors with their ligands. The information derived from crystallographic studies provides insights into the function of molecules. Allergen function is one of the determinants of environmental exposure, which is essential for IgE sensitization. Proteolytic activity of allergens or their capacity to bind LPSs can also contribute to allergenicity. The atomic positions define the molecular surface that is accessible to antibodies. In turn, this surface determines antibody specificity and cross-reactivity, which are important factors for the selection of allergen panels used for molecular diagnosis and the interpretation of clinical symptoms. This review celebrates the contributions of x-ray crystallography to clinical immunology and allergy, focusing on new molecular perspectives that influence the diagnosis and treatment of allergic diseases. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. All rights reserved.

Protein crystallization: Eluding the bottleneck of X-ray crystallography

PubMed Central

Holcomb, Joshua; Spellmon, Nicholas; Zhang, Yingxue; Doughan, Maysaa; Li, Chunying; Yang, Zhe

2017-01-01

To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins. PMID:29051919

X-ray crystallography

NASA Technical Reports Server (NTRS)

2001-01-01

X-rays diffracted from a well-ordered protein crystal create sharp patterns of scattered light on film. A computer can use these patterns to generate a model of a protein molecule. To analyze the selected crystal, an X-ray crystallographer shines X-rays through the crystal. Unlike a single dental X-ray, which produces a shadow image of a tooth, these X-rays have to be taken many times from different angles to produce a pattern from the scattered light, a map of the intensity of the X-rays after they diffract through the crystal. The X-rays bounce off the electron clouds that form the outer structure of each atom. A flawed crystal will yield a blurry pattern; a well-ordered protein crystal yields a series of sharp diffraction patterns. From these patterns, researchers build an electron density map. With powerful computers and a lot of calculations, scientists can use the electron density patterns to determine the structure of the protein and make a computer-generated model of the structure. The models let researchers improve their understanding of how the protein functions. They also allow scientists to look for receptor sites and active areas that control a protein's function and role in the progress of diseases. From there, pharmaceutical researchers can design molecules that fit the active site, much like a key and lock, so that the protein is locked without affecting the rest of the body. This is called structure-based drug design.

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature.

PubMed

Tsujino, Soichiro; Tomizaki, Takashi

2016-05-06

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

NASA Astrophysics Data System (ADS)

Tsujino, Soichiro; Tomizaki, Takashi

2016-05-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

PubMed Central

Tsujino, Soichiro; Tomizaki, Takashi

2016-01-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography. PMID:27150272

In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?

PubMed

Gallat, François-Xavier; Matsugaki, Naohiro; Coussens, Nathan P; Yagi, Koichiro J; Boudes, Marion; Higashi, Tetsuya; Tsuji, Daisuke; Tatano, Yutaka; Suzuki, Mamoru; Mizohata, Eiichi; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Park, Jaehyun; Song, Changyong; Hatsui, Takaki; Yabashi, Makina; Nango, Eriko; Itoh, Kohji; Coulibaly, Fasséli; Tobe, Stephen; Ramaswamy, S; Stay, Barbara; Iwata, So; Chavas, Leonard M G

2014-07-17

The serendipitous discovery of the spontaneous growth of protein crystals inside cells has opened the field of crystallography to chemically unmodified samples directly available from their natural environment. On the one hand, through in vivo crystallography, protocols for protein crystal preparation can be highly simplified, although the technique suffers from difficulties in sampling, particularly in the extraction of the crystals from the cells partly due to their small sizes. On the other hand, the extremely intense X-ray pulses emerging from X-ray free-electron laser (XFEL) sources, along with the appearance of serial femtosecond crystallography (SFX) is a milestone for radiation damage-free protein structural studies but requires micrometre-size crystals. The combination of SFX with in vivo crystallography has the potential to boost the applicability of these techniques, eventually bringing the field to the point where in vitro sample manipulations will no longer be required, and direct imaging of the crystals from within the cells will be achievable. To fully appreciate the diverse aspects of sample characterization, handling and analysis, SFX experiments at the Japanese SPring-8 angstrom compact free-electron laser were scheduled on various types of in vivo grown crystals. The first experiments have demonstrated the feasibility of the approach and suggest that future in vivo crystallography applications at XFELs will be another alternative to nano-crystallography. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

UV-Visible Absorption Spectroscopy Enhanced X-ray Crystallography at Synchrotron and X-ray Free Electron Laser Sources.

PubMed

Cohen, Aina E; Doukov, Tzanko; Soltis, Michael S

2016-01-01

This review describes the use of single crystal UV-Visible Absorption micro-Spectrophotometry (UV-Vis AS) to enhance the design and execution of X-ray crystallography experiments for structural investigations of reaction intermediates of redox active and photosensitive proteins. Considerations for UV-Vis AS measurements at the synchrotron and associated instrumentation are described. UV-Vis AS is useful to verify the intermediate state of an enzyme and to monitor the progression of reactions within crystals. Radiation induced redox changes within protein crystals may be monitored to devise effective diffraction data collection strategies. An overview of the specific effects of radiation damage on macromolecular crystals is presented along with data collection strategies that minimize these effects by combining data from multiple crystals used at the synchrotron and with the X-ray free electron laser.

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

PubMed Central

van Thor, Jasper J.; Madsen, Anders

2015-01-01

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse. PMID:26798786

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

van Thor, Jasper J.; Madsen, Anders

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

DOE PAGES

van Thor, Jasper J.; Madsen, Anders

2015-01-01

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

Using X-Ray Crystallography to Simplify and Accelerate Biologics Drug Development.

PubMed

Brader, Mark L; Baker, Edward N; Dunn, Michael F; Laue, Thomas M; Carpenter, John F

2017-02-01

Every major biopharmaceutical company incorporates a protein crystallography unit that is central to its structure-based drug discovery efforts. Yet these capabilities are rarely leveraged toward the formal higher order structural characterization that is so challenging but integral to large-scale biologics manufacturing. Although the biotech industry laments the shortcomings of its favored biophysical techniques, x-ray crystallography is not even considered for drug development. Why not? We suggest that this is due, at least in part, to outdated thinking (for a recent industry-wide survey, see Gabrielson JP, Weiss IV WF. Technical decision-making with higher order structure data: starting a new dialogue. J Pharm Sci. 2015;104(4):1240-1245). We examine some myths surrounding protein crystallography and highlight the inherent properties of protein crystals (molecular identity, biochemical purity, conformational uniformity, and macromolecular crowding) as having practicable commonalities with today's patient-focused liquid drug products. In the new millennium, protein crystallography has become essentially a routine analytical test. Its application may aid the identification of better candidate molecules that are more amenable to high-concentration processing, formulation, and analysis thereby helping to make biologics drug development quicker, simpler, and cheaper. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography.

PubMed

Gicquel, Yannig; Schubert, Robin; Kapis, Svetlana; Bourenkov, Gleb; Schneider, Thomas; Perbandt, Markus; Betzel, Christian; Chapman, Henry N; Heymann, Michael

2018-04-24

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 µm grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography

Curved position-sensitive detector for X-ray crystallography

NASA Astrophysics Data System (ADS)

Izumi, T.

1980-11-01

A new curved position-sensitive proportional detector has been constructed for X-ray crystallography. A very hard steel wire 0.2 mm in diameter was used as a single anode wire. It was bent to a radius of 6.5 cm and was suspended elastically in a wide 160° 2θ angular aperture. An amplifier and ADC-per-cathode strip system was made in order to encode the position. The spatial resolution is better than 0.37 mm (fwhm) along the curved anode wire, and this value corresponds to an angular resolution of 0.28° in 2θ. It is shown that a thick hard anode wire is quite suitable for use as a curved position-sensitive detector.

Automated identification of functional dynamic networks from X-ray crystallography

PubMed Central

van den Bedem, Henry; Bhabha, Gira; Yang, Kun; Wright, Peter E.; Fraser, James S.

2013-01-01

Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active site conformations and consequently alter protein function. In addition to comparing independently determined X-ray crystal structures, alternative conformations observed at low levels of electron density have the potential to provide mechanistic insights into conformational dynamics. Here, we report a new multi-conformer contact network algorithm (CONTACT) that identifies networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. Contact networks in Escherichia coli dihydrofolate reductase (ecDHFR) predict the long-range pattern of NMR chemical shift perturbations of an allosteric mutation. A comparison of contact networks in wild type and mutant ecDHFR suggests how mutations that alter optimized networks of coordinated motions can impair catalytic function. Thus, CONTACT-guided mutagenesis will allow the structure-dynamics-function relationship to be exploited in protein engineering and design. PMID:23913260

X-ray crystallography, an essential tool for the determination of thermodynamic relationships between crystalline polymorphs.

PubMed

Céolin, R; Rietveld, I-B

2016-01-01

After a short review of the controversies surrounding the discovery of crystalline polymorphism in relation to our present day understanding, the methods of how to solve the stability hierarchy of different polymorphs will be briefly discussed. They involve either theoretical calculations, or, more commonly, experimental methods based on classical thermodynamics. The experimental approach is mainly carried out using heat-exchange data associated to the transition of one form into another. It will be demonstrated that work-related data associated to the phase transition should be taken into account and the role of X-ray crystallography therein will be discussed. X-ray crystallography has become increasingly precise and can nowadays provide specific volumes and their differences as a function of temperature, and also as a function of pressure, humidity, and time. Copyright © 2015 Académie Nationale de Pharmacie. Published by Elsevier Masson SAS. All rights reserved.

Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

DOE PAGES

Kern, Jan; Yachandra, Vittal K.; Yano, Junko

2015-09-02

We have studied the structure of enzymes and the chemistry at the catalytic sites, intensively and have acquired an understanding of the atomic-scale chemistry which requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the samplemore » is destroyed. Our review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.« less

Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kern, Jan; Yachandra, Vittal K.; Yano, Junko

We have studied the structure of enzymes and the chemistry at the catalytic sites, intensively and have acquired an understanding of the atomic-scale chemistry which requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the samplemore » is destroyed. Our review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.« less

Femtosecond crystallography with ultrabright electrons and x-rays: capturing chemistry in action.

PubMed

Miller, R J Dwayne

2014-03-07

With the recent advances in ultrabright electron and x-ray sources, it is now possible to extend crystallography to the femtosecond time domain to literally light up atomic motions involved in the primary processes governing structural transitions. This review chronicles the development of brighter and brighter electron and x-ray sources that have enabled atomic resolution to structural dynamics for increasingly complex systems. The primary focus is on achieving sufficient brightness using pump-probe protocols to resolve the far-from-equilibrium motions directing chemical processes that in general lead to irreversible changes in samples. Given the central importance of structural transitions to conceptualizing chemistry, this emerging field has the potential to significantly improve our understanding of chemistry and its connection to driving biological processes.

Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography.

PubMed

Yefanov, Oleksandr; Gati, Cornelius; Bourenkov, Gleb; Kirian, Richard A; White, Thomas A; Spence, John C H; Chapman, Henry N; Barty, Anton

2014-07-17

Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 µm in size. This manuscript describes an alternative way of handling diffraction data recorded by serial femtosecond crystallography, by mapping the diffracted intensities into three-dimensional reciprocal space rather than integrating each image in two dimensions as in the classical approach. We call this procedure 'three-dimensional merging'. This procedure retains information about asymmetry in Bragg peaks and diffracted intensities between Bragg spots. This intensity distribution can be used to extract reflection intensities for structure determination and opens up novel avenues for post-refinement, while observed intensity between Bragg peaks and peak asymmetry are of potential use in novel direct phasing strategies.

Coded diffraction system in X-ray crystallography using a boolean phase coded aperture approximation

NASA Astrophysics Data System (ADS)

Pinilla, Samuel; Poveda, Juan; Arguello, Henry

2018-03-01

Phase retrieval is a problem present in many applications such as optics, astronomical imaging, computational biology and X-ray crystallography. Recent work has shown that the phase can be better recovered when the acquisition architecture includes a coded aperture, which modulates the signal before diffraction, such that the underlying signal is recovered from coded diffraction patterns. Moreover, this type of modulation effect, before the diffraction operation, can be obtained using a phase coded aperture, just after the sample under study. However, a practical implementation of a phase coded aperture in an X-ray application is not feasible, because it is computationally modeled as a matrix with complex entries which requires changing the phase of the diffracted beams. In fact, changing the phase implies finding a material that allows to deviate the direction of an X-ray beam, which can considerably increase the implementation costs. Hence, this paper describes a low cost coded X-ray diffraction system based on block-unblock coded apertures that enables phase reconstruction. The proposed system approximates the phase coded aperture with a block-unblock coded aperture by using the detour-phase method. Moreover, the SAXS/WAXS X-ray crystallography software was used to simulate the diffraction patterns of a real crystal structure called Rhombic Dodecahedron. Additionally, several simulations were carried out to analyze the performance of block-unblock approximations in recovering the phase, using the simulated diffraction patterns. Furthermore, the quality of the reconstructions was measured in terms of the Peak Signal to Noise Ratio (PSNR). Results show that the performance of the block-unblock phase coded apertures approximation decreases at most 12.5% compared with the phase coded apertures. Moreover, the quality of the reconstructions using the boolean approximations is up to 2.5 dB of PSNR less with respect to the phase coded aperture reconstructions.

Accessing protein conformational ensembles using room-temperature X-ray crystallography

PubMed Central

Fraser, James S.; van den Bedem, Henry; Samelson, Avi J.; Lang, P. Therese; Holton, James M.; Echols, Nathaniel; Alber, Tom

2011-01-01

Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation. PMID:21918110

Apparatus and method for nanoflow liquid jet and serial femtosecond x-ray protein crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bogan, Michael J.; Laksmono, Hartawan; Sierra, Raymond G.

Techniques for nanoflow serial femtosecond x-ray protein crystallography include providing a sample fluid by mixing a plurality of a first target of interest with a carrier fluid and injecting the sample fluid into a vacuum chamber at a rate less than about 4 microliters per minute. In some embodiments, the carrier fluid has a viscosity greater than about 3 centipoise.

Cell-free protein synthesis for structure determination by X-ray crystallography.

PubMed

Watanabe, Miki; Miyazono, Ken-ichi; Tanokura, Masaru; Sawasaki, Tatsuya; Endo, Yaeta; Kobayashi, Ichizo

2010-01-01

Structure determination has been difficult for those proteins that are toxic to the cells and cannot be prepared in a large amount in vivo. These proteins, even when biologically very interesting, tend to be left uncharacterized in the structural genomics projects. Their cell-free synthesis can bypass the toxicity problem. Among the various cell-free systems, the wheat-germ-based system is of special interest due to the following points: (1) Because the gene is placed under a plant translational signal, its toxic expression in a bacterial host is reduced. (2) It has only little codon preference and, especially, little discrimination between methionine and selenomethionine (SeMet), which allows easy preparation of selenomethionylated proteins for crystal structure determination by SAD and MAD methods. (3) Translation is uncoupled from transcription, so that the toxicity of the translation product on DNA and its transcription, if any, can be bypassed. We have shown that the wheat-germ-based cell-free protein synthesis is useful for X-ray crystallography of one of the 4-bp cutter restriction enzymes, which are expected to be very toxic to all forms of cells retaining the genome. Our report on its structure represents the first report of structure determination by X-ray crystallography using protein overexpressed with the wheat-germ-based cell-free protein expression system. This will be a method of choice for cytotoxic proteins when its cost is not a problem. Its use will become popular when the crystal structure determination technology has evolved to require only a tiny amount of protein.

In meso in situ serial X-ray crystallography of soluble and membrane proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Chia-Ying; Olieric, Vincent; Ma, Pikyee

A method for performing high-throughput in situ serial X-ray crystallography with soluble and membrane proteins in the lipid cubic phase is described. It works with microgram quantities of protein and lipid (and ligand when present) and is compatible with the most demanding sulfur SAD phasing. The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins,more » including the β{sub 2}-adrenoreceptor–G{sub s} protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at

Suite of three protein crystallography beamlines with single superconducting bend magnet as the source.

PubMed

MacDowell, Alastair A; Celestre, Rich S; Howells, Malcolm; McKinney, Wayne; Krupnick, James; Cambie, Daniella; Domning, Edward E; Duarte, Robert M; Kelez, Nicholas; Plate, David W; Cork, Carl W; Earnest, Thomas N; Dickert, Jeffery; Meigs, George; Ralston, Corie; Holton, James M; Alber, Tom; Berger, James M; Agard, David A; Padmore, Howard A

2004-11-01

At the Advanced Light Source, three protein crystallography beamlines have been built that use as a source one of the three 6 T single-pole superconducting bending magnets (superbends) that were recently installed in the ring. The use of such single-pole superconducting bend magnets enables the development of a hard X-ray program on a relatively low-energy 1.9 GeV ring without taking up insertion-device straight sections. The source is of relatively low power but, owing to the small electron beam emittance, it has high brightness. X-ray optics are required to preserve the brightness and to match the illumination requirements for protein crystallography. This was achieved by means of a collimating premirror bent to a plane parabola, a double-crystal monochromator followed by a toroidal mirror that focuses in the horizontal direction with a 2:1 demagnification. This optical arrangement partially balances aberrations from the collimating and toroidal mirrors such that a tight focused spot size is achieved. The optical properties of the beamline are an excellent match to those required by the small protein crystals that are typically measured. The design and performance of these new beamlines are described.

FreeDam - A webtool for free-electron laser-induced damage in femtosecond X-ray crystallography

NASA Astrophysics Data System (ADS)

Jönsson, H. Olof; Östlin, Christofer; Scott, Howard A.; Chapman, Henry N.; Aplin, Steve J.; Tîmneanu, Nicuşor; Caleman, Carl

2018-03-01

Over the last decade X-ray free-electron laser (XFEL) sources have been made available to the scientific community. One of the most successful uses of these new machines has been protein crystallography. When samples are exposed to the intense short X-ray pulses provided by the XFELs, the sample quickly becomes highly ionized and the atomic structure is affected. Here we present a webtool dubbed FreeDam based on non-thermal plasma simulations, for estimation of radiation damage in free-electron laser experiments in terms of ionization, temperatures and atomic displacements. The aim is to make this tool easily accessible to scientists who are planning and performing experiments at XFELs.

Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission.

PubMed

Jönsson, H Olof; Caleman, Carl; Andreasson, Jakob; Tîmneanu, Nicuşor

2017-11-01

Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

X-Ray Lasers

ERIC Educational Resources Information Center

Chapline, George; Wood, Lowell

1975-01-01

Outlines the prospects of generating coherent x rays using high-power lasers and indentifies problem areas in their development. Indicates possible applications for coherent x rays in the fields of chemistry, biology, and crystallography. (GS)

X-ray Structure of Native Scorpion Toxin BmBKTx1 by Racemic Protein Crystallography Using Direct Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mandal, Kalyaneswar; Pentelute, Brad L.; Tereshko, Valentina

2009-04-08

Racemic protein crystallography, enabled by total chemical synthesis, has allowed us to determine the X-ray structure of native scorpion toxin BmBKTx1; direct methods were used for phase determination. This is the first example of a protein racemate that crystallized in space group I41/a.

Synthesis and structure elucidation of a series of pyranochromene chalcones and flavanones using 1D and 2D NMR spectroscopy and X-ray crystallography.

PubMed

Pawar, Sunayna S; Koorbanally, Neil A

2014-06-01

A series of novel pyranochromene chalcones and corresponding flavanones were synthesized. This is the first report on the confirmation of the absolute configuration of chromene-based flavanones using X-ray crystallography. These compounds were characterized by 2D NMR spectroscopy, and their assignments are reported herein. The 3D structure of the chalcone 3b and flavanone 4g was determined by X-ray crystallography, and the structure of the flavanone was confirmed to be in the S configuration at C-2. Copyright © 2014 John Wiley & Sons, Ltd.

X-rays from Magnetic B-type Stars

NASA Astrophysics Data System (ADS)

Fletcher, Corinne; Petit, Véronique; Caballero-Nieves, Saida Maria; Nazé, Yaël; Owocki, Stan; Wade, Gregg; Cohen, David; Townsend, Richard; David-Uraz, Alexandre; Shultz, Matt

2018-01-01

Recent surveys have found that ~10% of OB-type stars host strong (~1kG), mostly dipolar magnetic fields. The prominent idea describing the interaction between the stellar winds and the magnetic field is the magnetically confined wind shock model. In this model, the ionized wind material is forced to move along the closed magnetic field loops and collides at the magnetic equator creating a shock. As the shocked material cools radiatively it will emit X-rays. Therefore, X-ray spectroscopy is a key tool in detecting and characterizing the wind material confined by the magnetic fields of these stars. Some of these magnetic B-type stars are found to have very short rotational periods. The effects of the rapid rotation on the X-ray production within the magnetosphere have yet to be explored in detail. The added centrifugal force is predicted to cause faster wind outflows along the field lines, which could lead to higher shock temperatures and harder X-rays. However, this is not observed in all rapidly rotating magnetic B-type stars. In order to address this question from a theoretical point of view, we use the X-ray Analytical Dynamical Magnetosphere model, developed for slow rotators and implement the physics of rapid rotation. Using X-ray spectroscopy from ESA’s XMM-Newton space telescope, we observed 5 rapidly rotating B-types stars to add to the previous list of observations. Comparing the observed X-ray luminosity and hardness ratio to that predicted by the XADM allows us to determine the role an added centrifugal acceleration plays in the magnetospheres of these stars.

X-Ray Crystallography Reagent

NASA Technical Reports Server (NTRS)

Morrison, Dennis R. (Inventor); Mosier, Benjamin (Inventor)

2003-01-01

Microcapsules prepared by encapsulating an aqueous solution of a protein, drug or other bioactive substance inside a semi-permeable membrane by are disclosed. The microcapsules are formed by interfacial coacervation under conditions where the shear forces are limited to 0-100 dynes per square centimeter at the interface. By placing the microcapsules in a high osmotic dewatering solution. the protein solution is gradually made saturated and then supersaturated. and the controlled nucleation and crystallization of the protein is achieved. The crystal-filled microcapsules prepared by this method can be conveniently harvested and stored while keeping the encapsulated crystals in essentially pristine condition due to the rugged. protective membrane. Because the membrane components themselves are x-ray transparent, large crystal-containing microcapsules can be individually selected, mounted in x-ray capillary tubes and subjected to high energy x-ray diffraction studies to determine the 3-D smucture of the protein molecules. Certain embodiments of the microcapsules of the invention have composite polymeric outer membranes which are somewhat elastic, water insoluble, permeable only to water, salts, and low molecular weight molecules and are structurally stable in fluid shear forces typically encountered in the human vascular system.

The high-field magnet endstation for X-ray magnetic dichroism experiments at ESRF soft X-ray beamline ID32.

PubMed

Kummer, K; Fondacaro, A; Jimenez, E; Velez-Fort, E; Amorese, A; Aspbury, M; Yakhou-Harris, F; van der Linden, P; Brookes, N B

2016-03-01

A new high-field magnet endstation for X-ray magnetic dichroism experiments has been installed and commissioned at the ESRF soft X-ray beamline ID32. The magnet consists of two split-pairs of superconducting coils which can generate up to 9 T along the beam and up to 4 T orthogonal to the beam. It is connected to a cluster of ultra-high-vacuum chambers that offer a comprehensive set of surface preparation and characterization techniques. The endstation and the beam properties have been designed to provide optimum experimental conditions for X-ray magnetic linear and circular dichroism experiments in the soft X-ray range between 400 and 1600 eV photon energy. User operation started in November 2014.

A rapid alternative to X-ray crystallography for chiral determination: case studies of vibrational circular dichroism (VCD) to advance drug discovery projects.

PubMed

Wesolowski, Steven S; Pivonka, Don E

2013-07-15

The absolute stereochemistry of chiral drugs is usually established via X-ray crystallography. However, vibrational circular dichroism (VCD) spectroscopy coupled with quantum mechanics simulations offers a rapid alternative to crystallography and is readily applied to both crystalline and non-crystalline samples. VCD is an effective complement to X-ray analysis of drug candidates, and it can be used as a high-throughput means of assessing absolute stereochemistry at all phases of the discovery process (hundreds of assignments per year). The practical implementation (or fee-for-service outsourcing) of VCD and selected case studies are illustrated with an emphasis on providing utility and impact to pharmaceutical discovery programs. Copyright © 2013 Elsevier Ltd. All rights reserved.

Molecular structure in the solid state by X-ray crystallography and SSNMR and in solution by NMR of two 1,4-diazepines

NASA Astrophysics Data System (ADS)

Nieto, Carla I.; Sanz, Dionisia; Claramunt, Rosa M.; Torralba, M. Carmen; Torres, M. Rosario; Alkorta, Ibon; Elguero, José

2018-03-01

The crystals of two 1,4-diazepines prepared from curcuminoid β-diketones and ethylenediamine were studied by X-ray crystallography and NMR. Their tautomerism, intramolecular hydrogen bonds and conformation were determined.

Extending X-Ray Crystallography to Allow the Imaging of Noncrystalline Materials, Cells, and Single Protein Complexes

NASA Astrophysics Data System (ADS)

Miao, Jianwei; Ishikawa, Tetsuya; Shen, Qun; Earnest, Thomas

2008-05-01

In 1999, researchers extended X-ray crystallography to allow the imaging of noncrystalline specimens by measuring the X-ray diffraction pattern of a noncrystalline specimen and then directly phasing it using the oversampling method with iterative algorithms. Since then, the field has evolved moving in three important directions. The first is the 3D structural determination of noncrystalline materials, which includes the localization of the defects and strain field inside nanocrystals, and quantitative 3D imaging of disordered materials such as nanoparticles and biomaterials. The second is the 3D imaging of frozen-hydrated whole cells at a resolution of 10 nm or better. A main thrust is to localize specific multiprotein complexes inside cells. The third is the potential of imaging single large protein complexes using extremely intense and ultrashort X-ray pulses. In this article, we review the principles of this methodology, summarize recent developments in each of the three directions, and illustrate a few examples.

X-ray tube with magnetic electron steering

DOEpatents

Reed, Kim W.; Turman, Bobby N.; Kaye, Ronald J.; Schneider, Larry X.

2000-01-01

An X-ray tube uses a magnetic field to steer electrons. The magnetic field urges electrons toward the anode, increasing the proportion of electrons emitted from the cathode that reach desired portions of the anode and consequently contribute to X-ray production. The magnetic field also urges electrons reflected from the anode back to the anode, further increasing the efficiency of the tube.

Theory of magnetic cataclysmic binary X-ray sources

NASA Technical Reports Server (NTRS)

Lamb, Don Q.

1988-01-01

The theory of magnetic cataclysmic binary X-ray sources is reviewed. The physics of the accretion torque for disk and for stream accretion is described, and the magnetic field strengths of DQ Her stars inferred from their spin behavior and of AM Her stars from direct measurement are discussed. The implications of disk and stream accretion for the geometry of the emission region and for the X-ray pulse profiles are considered. The physicl properties of the X-ray emission region and the expected infrared, optical, soft X-ray, and hard X-ray spectra are described. The orientations of the magnetic moment in AM Her stars inferred from the circular and linear polarization of the optical light and the optical light curve are commented on.

High-throughput plasmid construction using homologous recombination in yeast: its mechanisms and application to protein production for X-ray crystallography.

PubMed

Mizutani, Kimihiko

2015-01-01

Homologous recombination is a system for repairing the broken genomes of living organisms by connecting two DNA strands at their homologous sequences. Today, homologous recombination in yeast is used for plasmid construction as a substitute for traditional methods using restriction enzymes and ligases. This method has various advantages over the traditional method, including flexibility in the position of DNA insertion and ease of manipulation. Recently, the author of this review reported the construction of plasmids by homologous recombination in the methanol-utilizing yeast Pichia pastoris, which is known to be an excellent expression host for secretory proteins and membrane proteins. The method enabled high-throughput construction of expression systems of proteins using P. pastoris; the constructed expression systems were used to investigate the expression conditions of membrane proteins and to perform X-ray crystallography of secretory proteins. This review discusses the mechanisms and applications of homologous recombination, including the production of proteins for X-ray crystallography.

X-ray free electron lasers motivate bioanalytical characterization of protein nanocrystals: serial femtosecond crystallography.

PubMed

Bogan, Michael J

2013-04-02

Atomic resolution structures of large biomacromolecular complexes can now be recorded at room temperature from crystals with submicrometer dimensions using intense femtosecond pulses delivered by the world's largest and most powerful X-ray machine, a laser called the Linac Coherent Light Source. Abundant opportunities exist for the bioanalytical sciences to help extend this revolutionary advance in structural biology to the ultimate goal of recording molecular-movies of noncrystalline biomacromolecules. This Feature will introduce the concept of serial femtosecond crystallography to the nonexpert, briefly review progress to date, and highlight some potential contributions from the analytical sciences.

X-RAY EMISSION FROM MAGNETIC MASSIVE STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nazé, Yaël; Petit, Véronique; Rinbrand, Melanie

2014-11-01

Magnetically confined winds of early-type stars are expected to be sources of bright and hard X-rays. To clarify the systematics of the observed X-ray properties, we have analyzed a large series of Chandra and XMM-Newton observations, corresponding to all available exposures of known massive magnetic stars (over 100 exposures covering ∼60% of stars compiled in the catalog of Petit et al.). We show that the X-ray luminosity is strongly correlated with the stellar wind mass-loss rate, with a power-law form that is slightly steeper than linear for the majority of the less luminous, lower- M-dot B stars and flattens formore » the more luminous, higher- M-dot O stars. As the winds are radiatively driven, these scalings can be equivalently written as relations with the bolometric luminosity. The observed X-ray luminosities, and their trend with mass-loss rates, are well reproduced by new MHD models, although a few overluminous stars (mostly rapidly rotating objects) exist. No relation is found between other X-ray properties (plasma temperature, absorption) and stellar or magnetic parameters, contrary to expectations (e.g., higher temperature for stronger mass-loss rate). This suggests that the main driver for the plasma properties is different from the main determinant of the X-ray luminosity. Finally, variations of the X-ray hardnesses and luminosities, in phase with the stellar rotation period, are detected for some objects and they suggest that some temperature stratification exists in massive stars' magnetospheres.« less

Study on four polymorphs of bifendate based on X-ray crystallography.

PubMed

Nie, Jinju; Yang, Dezhi; Hu, Kun; Lu, Yang

2016-05-01

Bifendate, a synthetic anti-hepatitis drug, exhibits polycrystalline mode phenomena with 2 polymorphs reported (forms A and B). Single crystals of the known crystalline form B and 3 new crystallosolvates involving bifendate solvated with tetrahydrofuran (C), dioxane (D), and pyridine (E) in a stoichiometric ratio of 1:1 were obtained and characterized by X-ray crystallography, thermal analysis, and Fourier transform infrared (FT-IR) spectroscopy. The differences in molecular conformation, intermolecular interaction and crystal packing arrangement for the four polymorphs were determined and the basis for the polymorphisms was investigated. The rotation of single bonds resulted in different orientations for the biphenyl, methyl ester and methoxyl groups. All guest solvent molecules interacted with the host molecule via an interesting intercalative mode along the [1 0 0] direction in the channel formed by the host molecules through weak aromatic stacking interactions or non-classical hydrogen bonds, of which the volume and planarity played an important role in the intercalation of the host with the guest. The incorporation of solvent-augmented rotation of the C-C bond of the biphenyl group had a striking effect on the host molecular conformation and contributed to the formation of bifendate polymorphs. Moreover, the simulated powder X-ray diffraction (PXRD) patterns for each form were calculated on the basis of the single-crystal data and proved to be unique. The single-crystal structures of the four crystalline forms are reported in this paper.

The Relationship Between X-Ray Radiance and Magnetic Flux

NASA Astrophysics Data System (ADS)

Pevtsov, Alexei A.; Fisher, George H.; Acton, Loren W.; Longcope, Dana W.; Johns-Krull, Christopher M.; Kankelborg, Charles C.; Metcalf, Thomas R.

2003-12-01

We use soft X-ray and magnetic field observations of the Sun (quiet Sun, X-ray bright points, active regions, and integrated solar disk) and active stars (dwarf and pre-main-sequence) to study the relationship between total unsigned magnetic flux, Φ, and X-ray spectral radiance, LX. We find that Φ and LX exhibit a very nearly linear relationship over 12 orders of magnitude, albeit with significant levels of scatter. This suggests a universal relationship between magnetic flux and the power dissipated through coronal heating. If the relationship can be assumed linear, it is consistent with an average volumetric heating rate Q~B/L, where B is the average field strength along a closed field line and L is its length between footpoints. The Φ-LX relationship also indicates that X-rays provide a useful proxy for the magnetic flux on stars when magnetic measurements are unavailable.

Watching proteins function with 150-ps time-resolved X-ray crystallography

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2007-03-01

We have used time-resolved Laue crystallography to characterize ligand migration pathways and dynamics in wild-type and several mutant forms of myoglobin (Mb), a ligand-binding heme protein found in muscle tissue. In these pump-probe experiments, which were conducted on the ID09B time-resolved beamline at the European Synchrotron and Radiation Facility, a laser pulse photodissociates CO from an MbCO crystal and a suitably delayed X-ray pulse probes its structure via Laue diffraction. Single-site mutations in the vicinity of the heme pocket docking site were found to have a dramatic effect on ligand migration. To visualize this process, time-resolved electron density maps were stitched together into movies that unveil with <2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration. These studies help to illustrate at an atomic level relationships between protein structure, dynamics, and function.

Substrate specificity of pyrimidine nucleoside phosphorylases of NP-II family probed by X-ray crystallography and molecular modeling

NASA Astrophysics Data System (ADS)

Balaev, V. V.; Lashkov, A. A.; Prokofev, I. I.; Gabdulkhakov, A. G.; Seregina, T. A.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

2016-09-01

Pyrimidine nucleoside phosphorylases, which are widely used in the biotechnological production of nucleosides, have different substrate specificity for pyrimidine nucleosides. An interesting feature of these enzymes is that the three-dimensional structure of thymidine-specific nucleoside phosphorylase is similar to the structure of nonspecific pyrimidine nucleoside phosphorylase. The three-dimensional structures of thymidine phosphorylase from Salmonella typhimurium and nonspecific pyrimidine nucleoside phosphorylase from Bacillus subtilis in complexes with a sulfate anion were determined for the first time by X-ray crystallography. An analysis of the structural differences between these enzymes demonstrated that Lys108, which is involved in the phosphate binding in pyrimidine nucleoside phosphorylase, corresponds to Met111 in thymidine phosphorylases. This difference results in a decrease in the charge on one of the hydroxyl oxygens of the phosphate anion in thymidine phosphorylase and facilitates the catalysis through SN2 nucleophilic substitution. Based on the results of X-ray crystallography, the virtual screening was performed for identifying a potent inhibitor (anticancer agent) of nonspecific pyrimidine nucleoside phosphorylase, which does not bind to thymidine phosphorylase. The molecular dynamics simulation revealed the stable binding of the discovered compound—2-pyrimidin-2-yl-1H-imidazole-4-carboxylic acid—to the active site of pyrimidine nucleoside phosphorylase.

Magnetic x-ray dichroism in ultrathin epitaxial films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tobin, J.G.; Goodman, K.W.; Cummins, T.R.

1997-04-01

The authors have used Magnetic X-ray Linear Dichroism (MXLD) and Magnetic X-ray Circular Dichroism (MXCD) to study the magnetic properties of epitaxial overlayers in an elementally specific fashion. Both MXLD and MXCD Photoelectron Spectroscopy were performed in a high resolution mode at the Spectromicroscopy Facility of the ALS. Circular Polarization was obtained via the utilization of a novel phase retarder (soft x-ray quarter wave plate) based upon transmission through a multilayer film. The samples were low temperature Fe overlayers, magnetic alloy films of NiFe and CoNi, and Gd grown on Y. The authors results include a direct comparison of highmore » resolution angle resolved Photoelectron Spectroscopy performed in MXLD and MXCD modes as well as structural studies with photoelectron diffraction.« less

Magnetic Untwisting in Most Solar X-Ray Jets

NASA Technical Reports Server (NTRS)

Moore, Ronald; Sterling, Alphonse; Falconer, David; Robe, Dominic

2013-01-01

From 54 X-ray jets observed in the polar coronal holes by Hinode's X-Ray Telescope (XRT) during coverage in movies from Solar Dynamic Observatory's Atmospheric Imaging Assembly (AIA) taken in its He II 304 Å band at a cadence of 12 s, we have established a basic characteristic of solar X-ray jets: untwisting motion in the spire. In this presentation, we show the progression of few of these X-ray jets in XRT images and track their untwisting in AIA He II images. From their structure displayed in their XRT movies, 19 jets were evidently standard jets made by interchange reconnection of the magnetic-arcade base with ambient open field, 32 were evidently blowout jets made by blowout eruption of the base arcade, and 3 were of ambiguous form. As was anticipated from the >10,000 km span of the base arcade in most polar X-ray jets and from the disparity of standard jets and blowout jets in their magnetic production, few of the standard X-ray jets (3 of 19) but nearly all of the blowout X-ray jets (29 of 32) carried enough cool (T is approximately 105 K) plasma to be seen in their He II movies. In the 32 X-ray jets that showed a cool component, the He II movies show 10-100 km/s untwisting motions about the axis of the spire in all 3 standard jets and in 26 of the 29 blowout jets. Evidently, the open magnetic field in nearly all blowout X-ray jets and probably in most standard X-ray jets carries transient twist. This twist apparently relaxes by propagating out along the open field as a torsional wave. High-resolution spectrograms and Dopplergrams have shown that most Type-II spicules have torsional motions of 10-30 km/s. Our observation of similar torsional motion in X-ray jets strengthens the case for Type-II spicules being made in the same way as X-ray jets, by blowout eruption of a twisted magnetic arcade in the spicule base and/or by interchange reconnection of the twisted base arcade with the ambient open field. This work was funded by NASA's Heliophysics Division

Protein Crystallography from the Perspective of Technology Developments

PubMed Central

Su, Xiao-Dong; Zhang, Heng; Terwilliger, Thomas C.; Liljas, Anders; Xiao, Junyu; Dong, Yuhui

2015-01-01

Early on, crystallography was a domain of mineralogy and mathematics and dealt mostly with symmetry properties and imaginary crystal lattices. This changed when Wilhelm Conrad Röntgen discovered X-rays in 1895, and in 1912 Max von Laue and his associates discovered X-ray irradiated salt crystals would produce diffraction patterns that could reveal the internal atomic periodicity of the crystals. In the same year the father-and-son team, Henry and Lawrence Bragg successfully solved the first crystal structure of sodium chloride and the era of modern crystallography began. Protein crystallography (PX) started some 20 years later with the pioneering work of British crystallographers. In the past 50-60 years, the achievements of modern crystallography and particularly those in protein crystallography have been due to breakthroughs in theoretical and technical advancements such as phasing and direct methods; to more powerful X-ray sources such as synchrotron radiation (SR); to more sensitive and efficient X-ray detectors; to ever faster computers and to improvements in software. The exponential development of protein crystallography has been accelerated by the invention and applications of recombinant DNA technology that can yield nearly any protein of interest in large amounts and with relative ease. Novel methods, informatics platforms, and technologies for automation and high-throughput have allowed the development of large-scale, high efficiency macromolecular crystallography efforts in the field of structural genomics (SG). Very recently, the X-ray free-electron laser (XFEL) sources and its applications in protein crystallography have shown great potential for revolutionizing the whole field again in the near future. PMID:25983389

X-Ray Crystallography: One Century of Nobel Prizes

ERIC Educational Resources Information Center

Galli, Simona

2014-01-01

In 2012, the United Nations General Assembly declared 2014 the International Year of Crystallography. Throughout the year 2014 and beyond, all the crystallographic associations and societies active all over the world are organizing events to attract the wider public toward crystallography and the numerous topics to which it is deeply interlinked.…

Combining NMR and X-ray crystallography in fragment-based drug discovery: discovery of highly potent and selective BACE-1 inhibitors.

PubMed

Wyss, Daniel F; Wang, Yu-Sen; Eaton, Hugh L; Strickland, Corey; Voigt, Johannes H; Zhu, Zhaoning; Stamford, Andrew W

2012-01-01

Fragment-based drug discovery (FBDD) has become increasingly popular over the last decade. We review here how we have used highly structure-driven fragment-based approaches to complement more traditional lead discovery to tackle high priority targets and those struggling for leads. Combining biomolecular nuclear magnetic resonance (NMR), X-ray crystallography, and molecular modeling with structure-assisted chemistry and innovative biology as an integrated approach for FBDD can solve very difficult problems, as illustrated in this chapter. Here, a successful FBDD campaign is described that has allowed the development of a clinical candidate for BACE-1, a challenging CNS drug target. Crucial to this achievement were the initial identification of a ligand-efficient isothiourea fragment through target-based NMR screening and the determination of its X-ray crystal structure in complex with BACE-1, which revealed an extensive H-bond network with the two active site aspartate residues. This detailed 3D structural information then enabled the design and validation of novel, chemically stable and accessible heterocyclic acylguanidines as aspartic acid protease inhibitor cores. Structure-assisted fragment hit-to-lead optimization yielded iminoheterocyclic BACE-1 inhibitors that possess desirable molecular properties as potential therapeutic agents to test the amyloid hypothesis of Alzheimer's disease in a clinical setting.

Microfabrication of High Resolution X-ray Magnetic Calorimeters

NASA Astrophysics Data System (ADS)

Hsieh, Wen-Ting; Bandler, Simon R.; Kelly, Daniel P.; Porst, Jan P.; Rotzinger, Hannes; Seidel, George M.; Stevenson, Thomas R.

2009-12-01

Metallic magnetic calorimeter (MMC) is one of the most promising x-ray detector technologies for providing the very high energy resolution needed for future astronomical x-ray imaging spectroscopy. For this purpose, we have developed micro-fabricated 5×5 arrays of MMC of which each individual pixel has excellent energy resolution as good as 3.4 eV at 6 keV x-ray. Here we report on the fabrication techniques developed to achieve good resolution and high efficiency. These include: processing of a thin insulation layer for strong magnetic coupling between the AuEr sensor film and the niobium pick-up coil; production of overhanging absorbers for enhanced efficiency of x-ray absorption; fabrication on SiN membranes to minimize the effects on energy resolution from athermal phonon loss. We have also improved the deposition of the magnetic sensor film such that the film magnetization is nearly completely that is expected from the AuEr sputter target bulk material. In addition, we have included a study of a positional sensitive design, the Hydra design, which allows thermal coupling of four absorbers to a common MMC sensor and circuit.

X-ray magnetic circular dichroism and hard X-ray photoelectron spectroscopy of tetragonal Mn72Ge28 epitaxial thin film

NASA Astrophysics Data System (ADS)

Kim, Jinhyeok; Mizuguchi, Masaki; Inami, Nobuhito; Ueno, Tetsuro; Ueda, Shigenori; Takanashi, Koki

2018-04-01

An epitaxially grown Mn72Ge28 film with a tetragonal crystal structure was fabricated. It was clarified that the film had a perpendicular magnetization and a high perpendicular magnetic anisotropy energy of 14.3 Merg/cm3. The electronic structure was investigated by X-ray magnetic circular dichroism and hard X-ray photoelectron spectroscopy. The obtained X-ray magnetic circular dichroism spectrum revealed that the Mn orbital magnetic moment governed the magnetocrystalline anisotropy of the Mn72Ge28 film. A doublet structure was observed for the Mn 2p3/2 peak of hard X-ray photoelectron spectrum, indicating the spin exchange interaction between the 2p core-hole and 3d valence electrons.

Synthesis, X-ray crystallography, and computational analysis of 1-azafenestranes.

PubMed

Denmark, Scott E; Montgomery, Justin I; Kramps, Laurenz A

2006-09-06

The tandem [4+2]/[3+2] cycloaddition of nitroalkenes has been employed in the synthesis of 1-azafenestranes, molecules of theoretical interest because of planarizing distortion of their central carbon atoms. The synthesis of c,c,c,c-[5.5.5.5]-1-azafenestrane was completed in good yield from a substituted nitrocyclopentene, and its borane adduct was analyzed through X-ray crystallography, which showed a moderate distortion from ideal tetrahedral geometry. The syntheses of two members of the [4.5.5.5] family of 1-azafenestranes are also reported, including one with a trans fusion at a bicyclic ring junction which brings about considerable planarization of one of the central angles (16.8 degrees deviation from tetrahedral geometry). While investigating the [4.5.5.5]-1-azafenestranes, a novel dyotropic rearrangement that converts nitroso acetals into tetracyclic aminals was discovered. Through conformational analysis, a means to prevent this molecular reorganization was formulated and realized experimentally with the use of a bulky vinyl ether in the key [4+2] cycloaddition reaction. Finally, DFT calculations on relative strain energy for the 1-azafenestranes, as well as their predicted central angles, are disclosed.

A combined solid-state NMR and X-ray crystallography study of the bromide ion environments in triphenylphosphonium bromides.

PubMed

Burgess, Kevin M N; Korobkov, Ilia; Bryce, David L

2012-04-27

Multinuclear ((31)P and (79/81)Br), multifield (9.4, 11.75, and 21.1 T) solid-state nuclear magnetic resonance experiments are performed for seven phosphonium bromides bearing the triphenylphosphonium cation, a molecular scaffold found in many applications in chemistry. This is undertaken to fully characterise their bromine electric field gradient (EFG) tensors, as well as the chemical shift (CS) tensors of both the halogen and the phosphorus nuclei, providing a rare and novel insight into the local electronic environments surrounding them. New crystal structures, obtained from single-crystal X-ray diffraction, are reported for six compounds to aid in the interpretation of the NMR data. Among them is a new structure of BrPPh(4), because the previously reported one was inconsistent with our magnetic resonance data, thereby demonstrating how NMR data of non-standard nuclei can correct or improve X-ray diffraction data. Our results indicate that, despite sizable quadrupolar interactions, (79/81)Br magnetic resonance spectroscopy is a powerful characterisation tool that allows for the differentiation between chemically similar bromine sites, as shown through the range in the characteristic NMR parameters. (35/37)Cl solid-state NMR data, obtained for an analogous phosphonium chloride sample, provide insight into the relationship between unit cell volume, nuclear quadrupolar coupling constants, and Sternheimer antishielding factors. The experimental findings are complemented by gauge-including projector-augmented wave (GIPAW) DFT calculations, which substantiate our experimentally determined strong dependence of the largest component of the bromine CS tensor, δ(11), on the shortest Br-P distance in the crystal structure, a finding that has possible application in the field of NMR crystallography. This trend is explained in terms of Ramsey's theory on paramagnetic shielding. Overall, this work demonstrates how careful NMR studies of underexploited exotic nuclides, such

Frontiers in imaging magnetism with polarized x-rays

DOE PAGES

Fischer, Peter

2015-01-08

Although magnetic imaging with polarized x-rays is a rather young scientific discipline, the various types of established x-ray microscopes have already taken an important role in state-of-the-art characterization of the properties and behavior of spin textures in advanced materials. Furthermore, the opportunities ahead will be to obtain in a unique way indispensable multidimensional information of the structure, dynamics and composition of scientifically interesting and technologically relevant magnetic materials.

Phosphor Scanner For Imaging X-Ray Diffraction

NASA Technical Reports Server (NTRS)

Carter, Daniel C.; Hecht, Diana L.; Witherow, William K.

1992-01-01

Improved optoelectronic scanning apparatus generates digitized image of x-ray image recorded in phosphor. Scanning fiber-optic probe supplies laser light stimulating luminescence in areas of phosphor exposed to x rays. Luminescence passes through probe and fiber to integrating sphere and photomultiplier. Sensitivity and resolution exceed previously available scanners. Intended for use in x-ray crystallography, medical radiography, and molecular biology.

Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction

PubMed Central

Heymann, Michael; Opthalage, Achini; Wierman, Jennifer L.; Akella, Sathish; Szebenyi, Doletha M. E.; Gruner, Sol M.; Fraden, Seth

2014-01-01

An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation. PMID:25295176

Developing advanced X-ray scattering methods combined with crystallography and computation.

PubMed

Perry, J Jefferson P; Tainer, John A

2013-03-01

The extensive use of small angle X-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered

The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data.

PubMed

Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

2017-01-17

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4 O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S 1 state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal

Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams.

PubMed

Botha, Sabine; Nass, Karol; Barends, Thomas R M; Kabsch, Wolfgang; Latz, Beatrice; Dworkowski, Florian; Foucar, Lutz; Panepucci, Ezequiel; Wang, Meitian; Shoeman, Robert L; Schlichting, Ilme; Doak, R Bruce

2015-02-01

Recent advances in synchrotron sources, beamline optics and detectors are driving a renaissance in room-temperature data collection. The underlying impetus is the recognition that conformational differences are observed in functionally important regions of structures determined using crystals kept at ambient as opposed to cryogenic temperature during data collection. In addition, room-temperature measurements enable time-resolved studies and eliminate the need to find suitable cryoprotectants. Since radiation damage limits the high-resolution data that can be obtained from a single crystal, especially at room temperature, data are typically collected in a serial fashion using a number of crystals to spread the total dose over the entire ensemble. Several approaches have been developed over the years to efficiently exchange crystals for room-temperature data collection. These include in situ collection in trays, chips and capillary mounts. Here, the use of a slowly flowing microscopic stream for crystal delivery is demonstrated, resulting in extremely high-throughput delivery of crystals into the X-ray beam. This free-stream technology, which was originally developed for serial femtosecond crystallography at X-ray free-electron lasers, is here adapted to serial crystallography at synchrotrons. By embedding the crystals in a high-viscosity carrier stream, high-resolution room-temperature studies can be conducted at atmospheric pressure using the unattenuated X-ray beam, thus permitting the analysis of small or weakly scattering crystals. The high-viscosity extrusion injector is described, as is its use to collect high-resolution serial data from native and heavy-atom-derivatized lysozyme crystals at the Swiss Light Source using less than half a milligram of protein crystals. The room-temperature serial data allow de novo structure determination. The crystal size used in this proof-of-principle experiment was dictated by the available flux density. However, upcoming

Understanding pre-mRNA splicing through crystallography.

PubMed

Espinosa, Sara; Zhang, Lingdi; Li, Xueni; Zhao, Rui

2017-08-01

Crystallography is a powerful tool to determine the atomic structures of proteins and RNAs. X-ray crystallography has been used to determine the structure of many splicing related proteins and RNAs, making major contributions to our understanding of the molecular mechanism and regulation of pre-mRNA splicing. Compared to other structural methods, crystallography has its own advantage in the high-resolution structural information it can provide and the unique biological questions it can answer. In addition, two new crystallographic methods - the serial femtosecond crystallography and 3D electron crystallography - were developed to overcome some of the limitations of traditional X-ray crystallography and broaden the range of biological problems that crystallography can solve. This review discusses the theoretical basis, instrument requirements, troubleshooting, and exciting potential of these crystallographic methods to further our understanding of pre-mRNA splicing, a critical event in gene expression of all eukaryotes. Copyright © 2017 Elsevier Inc. All rights reserved.

Combined analysis of 1,3-benzodioxoles by crystalline sponge X-ray crystallography and laser desorption ionization mass spectrometry.

PubMed

Hayashi, Yukako; Ohara, Kazuaki; Taki, Rika; Saeki, Tomomi; Yamaguchi, Kentaro

2018-03-12

The crystalline sponge (CS) method, which employs single-crystal X-ray diffraction to determine the structure of an analyte present as a liquid or an oil and having a low melting point, was used in combination with laser desorption ionization mass spectrometry (LDI-MS). 1,3-Benzodioxole derivatives were encapsulated in CS and their structures were determined by combining X-ray crystallography and MS. After the X-ray analysis, the CS was subjected to imaging mass spectrometry (IMS) with an LDI spiral-time-of-flight mass spectrometer (TOF-MS). The ion detection area matched the microscopic image of the encapsulated CS. In addition, the accumulated 1D mass spectra showed that fragmentation of the guest molecule (hereafter, guest) can be easily visualized without any interference from the fragment ions of CS except for two strong ion peaks derived from the tridentate ligand TPT (2,4,6-tris(4-pyridyl)-1,3,5-triazine) of the CS and its fragment. X-ray analysis clearly showed the presence of the guest as well as the π-π, CH-halogen, and CH-O interactions between the guest and the CS framework. However, some guests remained randomly diffused in the nanopores of CS. In addition, the detection limit was less than sub-pmol order based on the weight and density of CS determined by X-ray analysis. Spectroscopic data, such as UV-vis and NMR, also supported the encapsulation of the guest through the interaction between the guest and CS components. The results denote that the CS-LDI-MS method, which combines CS, X-ray analysis and LDI-MS, is effective for structure determination.

Pink-beam serial crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meents, A.; Wiedorn, M. O.; Srajer, V.

Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, “pink”, beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized formore » very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.« less

Pink-beam serial crystallography

DOE PAGES

Meents, A.; Wiedorn, M. O.; Srajer, V.; ...

2017-11-03

Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, “pink”, beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized formore » very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.« less

From lows to highs: using low-resolution models to phase X-ray data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stuart, David I.; Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot; Abrescia, Nicola G. A., E-mail: nabrescia@cicbiogune.es

2013-11-01

An unusual example of how virus structure determination pushes the limits of the molecular replacement method is presented. The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here,more » the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.« less

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

High-Resolution Detector For X-Ray Diffraction

NASA Technical Reports Server (NTRS)

Carter, Daniel C.; Withrow, William K.; Pusey, Marc L.; Yost, Vaughn H.

1988-01-01

Proposed x-ray-sensitive imaging detector offers superior spatial resolution, counting-rate capacity, and dynamic range. Instrument based on laser-stimulated luminescence and reusable x-ray-sensitive film. Detector scans x-ray film line by line. Extracts latent image in film and simultaneously erases film for reuse. Used primarily for protein crystallography. Principle adapted to imaging detectors for electron microscopy and fluorescence spectroscopy and general use in astronomy, engineering, and medicine.

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

DOE PAGES

Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

2015-07-30

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism.

PubMed

Fan, Tingting; Grychtol, Patrik; Knut, Ronny; Hernández-García, Carlos; Hickstein, Daniel D; Zusin, Dmitriy; Gentry, Christian; Dollar, Franklin J; Mancuso, Christopher A; Hogle, Craig W; Kfir, Ofer; Legut, Dominik; Carva, Karel; Ellis, Jennifer L; Dorney, Kevin M; Chen, Cong; Shpyrko, Oleg G; Fullerton, Eric E; Cohen, Oren; Oppeneer, Peter M; Milošević, Dejan B; Becker, Andreas; Jaroń-Becker, Agnieszka A; Popmintchev, Tenio; Murnane, Margaret M; Kapteyn, Henry C

2015-11-17

We demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 µm, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantum trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N4,5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform.

Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism

PubMed Central

Fan, Tingting; Grychtol, Patrik; Knut, Ronny; Hernández-García, Carlos; Hickstein, Daniel D.; Zusin, Dmitriy; Gentry, Christian; Dollar, Franklin J.; Mancuso, Christopher A.; Hogle, Craig W.; Kfir, Ofer; Legut, Dominik; Carva, Karel; Ellis, Jennifer L.; Dorney, Kevin M.; Chen, Cong; Shpyrko, Oleg G.; Fullerton, Eric E.; Cohen, Oren; Oppeneer, Peter M.; Milošević, Dejan B.; Becker, Andreas; Jaroń-Becker, Agnieszka A.; Popmintchev, Tenio; Murnane, Margaret M.; Kapteyn, Henry C.

2015-01-01

We demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 µm, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantum trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N4,5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform. PMID:26534992

Soft x-ray coherent diffraction imaging on magnetic nanostructures

NASA Astrophysics Data System (ADS)

Shi, Xiaowen; Lee, James; Mishra, Shrawan; Parks, Daniel; Tyliszczak, Tolek; Shapiro, David; Roy, Sujoy; Kevan, Steve; Stxm Team At Als Collaboration; Soft X-Ray Microscopy Group At Als Collaboration; Soft X-ray scattering at ALS, LBL Team

2014-03-01

Coherent soft X-rays diffraction imaging enable coherent magnetic resonance scattering at transition metal L-edge to be probed so that magnetic domains could be imaged with very high spatial resolution with phase contrast, reaching sub-10nm. One of the overwhelming advantages of using coherent X-rays is the ability to resolve phase contrast images with linearly polarized light with both phase and absorption contrast comparing to real-space imaging, which can only be studied with circularly polarized light with absorption contrast only. Here we report our first results on high-resolution of magnetic domains imaging of CoPd multilayer thin film with coherent soft X-ray ptychography method. We are aiming to resolve and understand magnetic domain wall structures with the highest obtainable resolution here at Advanced Light Source. In principle types of magnetic domain walls could be studied so that Neel or Bloch walls can be distinguished by imaging. This work at LBNL was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy (contract no. DE-AC02- 05CH11231).

Small-Angle X-ray Scattering (SAXS) Instrument Performance and Validation Using Silver Nanoparticles

DTIC Science & Technology

2016-12-01

Intercalibration of small-angle X- Ray and neutron-scattering data. Journal of Applied Crystallography . 1988;21:629–638. 7. Zhang F, Ilavsky J, Long GG...Materials Transactions A. 2009;41:1151–1158. 8. Kusz J, Bohm H. Performance of a confocal multilayer X-ray optic. Journal of Applied Crystallography ...Journal of Applied Crystallography . 2004;37:369–380. 10. Orthaber D, Bergmann A, Glatter O. SAXS experiments on absolute scale with Kratky systems using

Small Angle X ray Scattering (SAXS) Instrument Performance and Validation Using Silver Nanoparticles

DTIC Science & Technology

2016-12-01

Intercalibration of small-angle X- Ray and neutron-scattering data. Journal of Applied Crystallography . 1988;21:629–638. 7. Zhang F, Ilavsky J, Long GG...Materials Transactions A. 2009;41:1151–1158. 8. Kusz J, Bohm H. Performance of a confocal multilayer X-ray optic. Journal of Applied Crystallography ...Journal of Applied Crystallography . 2004;37:369–380. 10. Orthaber D, Bergmann A, Glatter O. SAXS experiments on absolute scale with Kratky systems using

Liquid sample delivery techniques for serial femtosecond crystallography

PubMed Central

Weierstall, Uwe

2014-01-01

X-ray free-electron lasers overcome the problem of radiation damage in protein crystallography and allow structure determination from micro- and nanocrystals at room temperature. To ensure that consecutive X-ray pulses do not probe previously exposed crystals, the sample needs to be replaced with the X-ray repetition rate, which ranges from 120 Hz at warm linac-based free-electron lasers to 1 MHz at superconducting linacs. Liquid injectors are therefore an essential part of a serial femtosecond crystallography experiment at an X-ray free-electron laser. Here, we compare different techniques of injecting microcrystals in solution into the pulsed X-ray beam in vacuum. Sample waste due to mismatch of the liquid flow rate to the X-ray repetition rate can be addressed through various techniques. PMID:24914163

The X-ray corona and the photospheric magnetic field.

NASA Technical Reports Server (NTRS)

Krieger, A. S.; Vaiana, G. S.; Van Speybroeck, L. P.

1971-01-01

Soft X-ray photographs of the solar corona have been obtained on four flights of a rocket-borne grazing incidence telescope having a resolution of a few arc sec. The configuration of the X-ray emitting structures in the corona has been compared to the magnetic field distribution measured by photospheric longitudinal magnetograms. The X-ray structures trace the three-dimensional configuration of the magnetic field through the lower corona. Active regions in the corona take the form of tubular structures connecting regions of opposite magnetic polarity within the same or adjacent chromospheric active regions. Higher, larger structures link widely separated active regions into complexes of activity covering substantial fractions of the disk. The complexes are separated by areas of low average field in the photosphere. Interconnections across the solar equator appear to originate over areas of preceding polarity.

Bringing diffuse X-ray scattering into focus

DOE PAGES

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

2018-02-16

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Bringing diffuse X-ray scattering into focus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Resonant magnetic scattering of polarized soft x rays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sacchi, M.; Hague, C.F.; Gullikson, E.M.

1997-04-01

Magnetic effects on X-ray scattering (Bragg diffraction, specular reflectivity or diffuse scattering) are a well known phenomenon, and they also represent a powerful tool for investigating magnetic materials since it was shown that they are strongly enhanced when the photon energy is tuned across an absorption edge (resonant process). The resonant enhancement of the magnetic scattering has mainly been investigated at high photon energies, in order to match the Bragg law for the typical lattice spacings of crystals. In the soft X-ray range, even larger effects are expected, working for instance at the 2p edges of transition metals of themore » first row or at the 3d edges of rare earths (300-1500 eV), but the corresponding long wavelengths prevent the use of single crystals. Two approaches have been recently adopted in this energy range: (i) the study of the Bragg diffraction from artificial structures of appropriate 2d spacing; (ii) the analysis of the specular reflectivity, which contains analogous information but has no constraints related to the lattice spacing. Both approaches have their own specific advantages: for instance, working under Bragg conditions provides information about the (magnetic) periodicity in ordered structures, while resonant reflectivity can easily be related to electronic properties and absorption spectra. An important aspect common to all the resonant X-ray scattering techniques is the element selectivity inherent to the fact of working at a specific absorption edge: under these conditions, X-ray scattering becomes in fact a spectroscopy. Results are presented for films of iron and cobalt.« less

Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100K

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerlits, Oksana O.; Keen, David A.; Blakeley, Matthew P.

HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly altermore » the drug–enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.« less

Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100K

DOE PAGES

Gerlits, Oksana O.; Keen, David A.; Blakeley, Matthew P.; ...

2017-02-14

HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly altermore » the drug–enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.« less

Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism

DOE PAGES

Fan, Tingting; Grychtol, Patrik; Knut, Ronny; ...

2015-11-03

Here, we demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 µm, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantummore » trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N 4,5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform.« less

Accounting for partiality in serial crystallography using ray-tracing principles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kroon-Batenburg, Loes M. J., E-mail: l.m.j.kroon-batenburg@uu.nl; Schreurs, Antoine M. M.; Ravelli, Raimond B. G.

Serial crystallography generates partial reflections from still diffraction images. Partialities are estimated with EVAL ray-tracing simulations, thereby improving merged reflection data to a similar quality as conventional rotation data. Serial crystallography generates ‘still’ diffraction data sets that are composed of single diffraction images obtained from a large number of crystals arbitrarily oriented in the X-ray beam. Estimation of the reflection partialities, which accounts for the expected observed fractions of diffraction intensities, has so far been problematic. In this paper, a method is derived for modelling the partialities by making use of the ray-tracing diffraction-integration method EVAL. The method estimates partialitiesmore » based on crystal mosaicity, beam divergence, wavelength dispersion, crystal size and the interference function, accounting for crystallite size. It is shown that modelling of each reflection by a distribution of interference-function weighted rays yields a ‘still’ Lorentz factor. Still data are compared with a conventional rotation data set collected from a single lysozyme crystal. Overall, the presented still integration method improves the data quality markedly. The R factor of the still data compared with the rotation data decreases from 26% using a Monte Carlo approach to 12% after applying the Lorentz correction, to 5.3% when estimating partialities by EVAL and finally to 4.7% after post-refinement. The merging R{sub int} factor of the still data improves from 105 to 56% but remains high. This suggests that the accuracy of the model parameters could be further improved. However, with a multiplicity of around 40 and an R{sub int} of ∼50% the merged still data approximate the quality of the rotation data. The presented integration method suitably accounts for the partiality of the observed intensities in still diffraction data, which is a critical step to improve data quality in serial crystallography.« less

Life in the fast lane for protein crystallization and X-ray crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2005-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2004-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from

Polarization Radiation with Turbulent Magnetic Fields from X-Ray Binaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jian-Fu; Xiang, Fu-Yuan; Lu, Ju-Fu, E-mail: jfzhang@xtu.edu.cn, E-mail: fyxiang@xtu.edu.cn, E-mail: lujf@xmu.edu.cn

2017-02-10

We study the properties of polarized radiation in turbulent magnetic fields from X-ray binary jets. These turbulent magnetic fields are composed of large- and small-scale configurations, which result in the polarized jitter radiation when the characteristic length of turbulence is less than the non-relativistic Larmor radius. On the contrary, the polarized synchrotron emission occurs, corresponding to a large-scale turbulent environment. We calculate the spectral energy distributions and the degree of polarization for a general microquasar. Numerical results show that turbulent magnetic field configurations can indeed provide a high degree of polarization, which does not mean that a uniform, large-scale magneticmore » field structure exists. The model is applied to investigate the properties of polarized radiation of the black-hole X-ray binary Cygnus X-1. Under the constraint of multiband observations of this source, our studies demonstrate that the model can explain the high polarization degree at the MeV tail and predict the highly polarized properties at the high-energy γ -ray region, and that the dominant small-scale turbulent magnetic field plays an important role for explaining the highly polarized observation at hard X-ray/soft γ -ray bands. This model can be tested by polarization observations of upcoming polarimeters at high-energy γ -ray bands.« less

The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

DOE PAGES

Askerka, Mikhail; Brudvig, Gary W.; Batista, Victor S.

2016-12-21

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage “S” states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves throughmore » the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/ MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional Xray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this

The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Askerka, Mikhail; Brudvig, Gary W.; Batista, Victor S.

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage “S” states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves throughmore » the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/ MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional Xray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this

a-Si:H TFT-silicon hybrid low-energy x-ray detector

DOE PAGES

Shin, Kyung -Wook; Karim, Karim S.

2017-03-15

Direct conversion crystalline silicon X-ray imagers are used for low-energy X-ray photon (4-20 keV) detection in scientific research applications such as protein crystallography. In this paper, we demonstrate a novel pixel architecture that integrates a crystalline silicon X-ray detector with a thin-film transistor amorphous silicon pixel readout circuit. We describe a simplified two-mask process to fabricate a complete imaging array and present preliminary results that show the fabricated pixel to be sensitive to 5.89-keV photons from a low activity Fe-55 gamma source. Furthermore, this paper presented can expedite the development of high spatial resolution, low cost, direct conversion imagers formore » X-ray diffraction and crystallography applications.« less

The future of crystallography in drug discovery

PubMed Central

Zheng, Heping; Hou, Jing; Zimmerman, Matthew D; Wlodawer, Alexander; Minor, Wladek

2014-01-01

Introduction X-ray crystallography plays an important role in structure-based drug design (SBDD), and accurate analysis of crystal structures of target macromolecules and macromolecule–ligand complexes is critical at all stages. However, whereas there has been significant progress in improving methods of structural biology, particularly in X-ray crystallography, corresponding progress in the development of computational methods (such as in silico high-throughput screening) is still on the horizon. Crystal structures can be overinterpreted and thus bias hypotheses and follow-up experiments. As in any experimental science, the models of macromolecular structures derived from X-ray diffraction data have their limitations, which need to be critically evaluated and well understood for structure-based drug discovery. Areas covered This review describes how the validity, accuracy and precision of a protein or nucleic acid structure determined by X-ray crystallography can be evaluated from three different perspectives: i) the nature of the diffraction experiment; ii) the interpretation of an electron density map; and iii) the interpretation of the structural model in terms of function and mechanism. The strategies to optimally exploit a macromolecular structure are also discussed in the context of ‘Big Data’ analysis, biochemical experimental design and structure-based drug discovery. Expert opinion Although X-ray crystallography is one of the most detailed ‘microscopes’ available today for examining macromolecular structures, the authors would like to re-emphasize that such structures are only simplified models of the target macromolecules. The authors also wish to reinforce the idea that a structure should not be thought of as a set of precise coordinates but rather as a framework for generating hypotheses to be explored. Numerous biochemical and biophysical experiments, including new diffraction experiments, can and should be performed to verify or falsify

Characterization of X-Ray Diffraction System with a Microfocus X-Ray Source and a Polycapillary Optic

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail; Marshall, Joy K.; Ciszak, Ewa; Ponomarev, Igor

2000-01-01

We present here an optimized microfocus x-ray source and polycapillary optic system designed for diffraction of small protein crystals. The x-ray beam is formed by a 5.5mm focal length capillary collimator coupled with a 40 micron x-ray source operating at 46Watts. Measurements of the x-ray flux, the divergence and the spectral characteristics of the beam are presented, This optimized system provides a seven fold greater flux than our recently reported configuration [M. Gubarev, et al., J. of Applied Crystallography (2000) 33, in press]. We now make a comparison with a 5kWatts rotating anode generator (Rigaku) coupled with confocal multilayer focusing mirrors (Osmic, CMF12- 38Cu6). The microfocus x-ray source and polycapillary collimator system delivers 60% of the x-ray flux from the rotating anode system. Additional ways to improve our microfocus x-ray system, and thus increase the x-ray flux will be discussed.

Femtosecond X-ray protein nanocrystallography

PubMed Central

Chapman, Henry N.; Fromme, Petra; Barty, Anton; White, Thomas A.; Kirian, Richard A.; Aquila, Andrew; Hunter, Mark S.; Schulz, Joachim; DePonte, Daniel P.; Weierstall, Uwe; Doak, R. Bruce; Maia, Filipe R. N. C.; Martin, Andrew V.; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L.; Epp, Sascha W.; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J.; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D.; Hau-Riege, Stefan P.; Frank, Matthias; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Williams, Garth J.; Hajdu, Janos; Timneanu, Nicusor; Seibert, M. Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E.; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M.; Barends, Thomas R. M.; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C. H.

2012-01-01

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage. PMID:21293373

Femtosecond X-ray protein nanocrystallography.

PubMed

Chapman, Henry N; Fromme, Petra; Barty, Anton; White, Thomas A; Kirian, Richard A; Aquila, Andrew; Hunter, Mark S; Schulz, Joachim; DePonte, Daniel P; Weierstall, Uwe; Doak, R Bruce; Maia, Filipe R N C; Martin, Andrew V; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L; Epp, Sascha W; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D; Hau-Riege, Stefan P; Frank, Matthias; Hampton, Christina Y; Sierra, Raymond G; Starodub, Dmitri; Williams, Garth J; Hajdu, Janos; Timneanu, Nicusor; Seibert, M Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M; Barends, Thomas R M; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C H

2011-02-03

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

Formation of X-ray emitting stationary shocks in magnetized protostellar jets

NASA Astrophysics Data System (ADS)

Ustamujic, S.; Orlando, S.; Bonito, R.; Miceli, M.; Gómez de Castro, A. I.; López-Santiago, J.

2016-12-01

Context. X-ray observations of protostellar jets show evidence of strong shocks heating the plasma up to temperatures of a few million degrees. In some cases, the shocked features appear to be stationary. They are interpreted as shock diamonds. Aims: We investigate the physics that guides the formation of X-ray emitting stationary shocks in protostellar jets; the role of the magnetic field in determining the location, stability, and detectability in X-rays of these shocks; and the physical properties of the shocked plasma. Methods: We performed a set of 2.5-dimensional magnetohydrodynamic numerical simulations that modelled supersonic jets ramming into a magnetized medium and explored different configurations of the magnetic field. The model takes into account the most relevant physical effects, namely thermal conduction and radiative losses. We compared the model results with observations, via the emission measure and the X-ray luminosity synthesized from the simulations. Results: Our model explains the formation of X-ray emitting stationary shocks in a natural way. The magnetic field collimates the plasma at the base of the jet and forms a magnetic nozzle there. After an initial transient, the nozzle leads to the formation of a shock diamond at its exit which is stationary over the time covered by the simulations ( 40-60 yr; comparable with timescales of the observations). The shock generates a point-like X-ray source located close to the base of the jet with luminosity comparable with that inferred from X-ray observations of protostellar jets. For the range of parameters explored, the evolution of the post-shock plasma is dominated by the radiative cooling, whereas the thermal conduction slightly affects the structure of the shock. A movie is available at http://www.aanda.org

X-ray free electron laser: opportunities for drug discovery.

PubMed

Cheng, Robert K Y; Abela, Rafael; Hennig, Michael

2017-11-08

Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Bioactive Formylated Flavonoids from Eugenia rigida: Isolation, Synthesis, and X-ray Crystallography.

PubMed

Zaki, Mohamed A; Nanayakkara, N P Dhammika; Hetta, Mona H; Jacob, Melissa R; Khan, Shabana I; Mohammed, Rabab; Ibrahim, Mohamed A; Samoylenko, Volodymyr; Coleman, Christina; Fronczek, Frank R; Ferreira, Daneel; Muhammad, Ilias

2016-09-23

Two new flavonoids, rac-6-formyl-5,7-dihydroxyflavanone (1) and 2',6'-dihydroxy-4'-methoxy-3'-methylchalcone (2), together with five known derivatives, rac-8-formyl-5,7-dihydroxyflavanone (3), 4',6'-dihydroxy-2'-methoxy-3'-methyldihydrochalcone (4), rac-7-hydroxy-5-methoxy-6-methylflavanone (5), 3'-formyl-2',4',6'-trihydroxy-5'-methyldihydrochalcone (6), and 3'-formyl-2',4',6'-trihydroxydihydrochalcone (7), were isolated from the leaves of Eugenia rigida. The individual (S)- and (R)-enantiomers of 1 and 3, together with the corresponding formylated flavones 8 (6-formyl-5,7-dihydroxyflavone) and 9 (8-formyl-5,7-dihydroxyflavone), as well as 2',4',6'-trihydroxychalcone (10), 3'-formyl-2',4',6'-trihydroxychalcone (11), and the corresponding 3'-formyl-2',4',6'-trihydroxydihydrochalcone (7) and 2',4',6'-trihydroxydihydrochalcone (12), were synthesized. The structures of the isolated and synthetic compounds were established via NMR, HRESIMS, and electronic circular dichroism data. In addition, the structures of 3, 5, and 8 were confirmed by single-crystal X-ray diffraction crystallography. The isolated and synthetic flavonoids were evaluated for their antimicrobial and cytotoxic activities against a panel of microorganisms and solid tumor cell lines.

High-throughput Crystallography for Structural Genomics

PubMed Central

Joachimiak, Andrzej

2009-01-01

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

Quantum crystallography: A perspective.

PubMed

Massa, Lou; Matta, Chérif F

2018-06-30

Extraction of the complete quantum mechanics from X-ray scattering data is the ultimate goal of quantum crystallography. This article delivers a perspective for that possibility. It is desirable to have a method for the conversion of X-ray diffraction data into an electron density that reflects the antisymmetry of an N-electron wave function. A formalism for this was developed early on for the determination of a constrained idempotent one-body density matrix. The formalism ensures pure-state N-representability in the single determinant sense. Applications to crystals show that quantum mechanical density matrices of large molecules can be extracted from X-ray scattering data by implementing a fragmentation method termed the kernel energy method (KEM). It is shown how KEM can be used within the context of quantum crystallography to derive quantum mechanical properties of biological molecules (with low data-to-parameters ratio). © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Crystallography: past and present

NASA Astrophysics Data System (ADS)

Hodeau, J.-L.; Guinebretiere, R.

2007-12-01

In the 19th century, crystallography referred to the study of crystal shapes. Such studies by Haüy and Bravais allowed the establishment of important hypotheses such as (i) “les molécules intégrantes qui sont censées être les plus petits solides que l’on puisse extraire d’un minéral” [1], (ii) the definition of the crystal lattice and (iii) “le cristal est clivable parallèlement à deux ou trois formes cristallines” [2]. This morphological crystallography defined a crystal like “a chemically homogeneous solid, wholly or partly bounded by natural planes that intersect at predetermined angles” [3]. It described the main symmetry elements and operations, nomenclatures of different crystal forms and also the theory of twinning. A breakthrough appeared in 1912 with the use of X-rays by M. von Laue and W.H. and W.L. Bragg. This experimental development allowed the determination of the atomic content of each unit cell constituting the crystal and defined a crystal as “any solid in which an atomic pattern is repeated periodically in three dimensions, that is, any solid that “diffracts” an incident X-ray beam” [3]. Mathematical tools like the Patterson methods, the direct methods, were developed. The way for solving crystalline structure was opened first for simple compounds and at that time crystallography was associated mainly with perfect crystals. In the fifties, crystallographers already had most apparatus and fundamental methods at their disposal; however, we had to wait for the development of computers to see the full use of these tools. Furthermore the development of new sources of neutrons, electrons and synchrotron X-rays allowed the studies of complex compounds like large macromolecules in biology. Nowadays, one of the new frontiers for crystallographers is to relate the crystal structure to its physical-chemical-biological properties, this means that an accurate structural determination is needed to focus on a selective part of the

Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods

PubMed Central

Mandal, Kalyaneswar; Pentelute, Brad L; Tereshko, Valentina; Thammavongsa, Vilasak; Schneewind, Olaf; Kossiakoff, Anthony A; Kent, Stephen B H

2009-01-01

We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers l-plectasin and d-plectasin were prepared by total chemical synthesis; interestingly, l-plectasin showed the expected antimicrobial activity, while d-plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X-ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group with one l-plectasin molecule and one d-plectasin molecule forming the unit cell. Dimer-like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%–15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation. PMID:19472324

Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis.

PubMed

East, Alexandra; Mechaly, Ariel E; Huysmans, Gerard H M; Bernarde, Cédric; Tello-Manigne, Diana; Nadeau, Nathalie; Pugsley, Anthony P; Buschiazzo, Alejandro; Alzari, Pedro M; Bond, Peter J; Francetic, Olivera

2016-01-05

The Klebsiella lipoprotein pullulanase (PulA) is exported to the periplasm, triacylated, and anchored via lipids in the inner membrane (IM) prior to its transport to the bacterial surface through a type II secretion system (T2SS). X-Ray crystallography and atomistic molecular dynamics (MD) simulations of PulA in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) model membrane provided an unprecedented molecular view of an N-terminal unstructured tether and the IM lipoprotein retention signal, and revealed novel interactions with the IM via N-terminal immunoglobulin-like domains in PulA. An efficiently secreted nonacylated variant (PulANA) showed similar peripheral membrane association during MD simulations, consistent with the binding of purified PulANA to liposomes. Remarkably, combined X-ray, MD, and functional studies identified a novel subdomain, Ins, inserted in the α-amylase domain, which is required for PulA secretion. Available data support a model in which PulA binding to the IM promotes interactions with the T2SS, possibly via the Ins subdomain. Copyright © 2016 Elsevier Ltd. All rights reserved.

X-Ray Crystallography as a Tool to Determine Three-Dimensional Structures of Commercial Enzymes Subjected to Treatment in Pressurized Fluids.

PubMed

Feiten, Mirian Cristina; Di Luccio, Marco; Santos, Karine F; de Oliveira, Débora; Oliveira, J Vladimir

2017-06-01

The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity. This paper presentes a short overview on how to streamline sample preparation for crystallographic studies of treated enzymes. We additionally revise recent developments on the effects of pressurized fluid treatment on activity and stability of commercial enzymes. Future directions and perspectives on the the role of crystallography as a tool to access the molecular mechanisms underlying enzymatic activity modulation upon treatment in pressurized fluids are also addressed.

Magnetic x-ray scattering studies of holmium using synchro- tron radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibbs, D.; Moncton, D.E.; D'Amico, K.L.

1985-07-08

We present the results of magnetic x-ray scattering experiments on the rare-earth metal holmium using synchrotron radiation. Direct high-resolution measurements of the nominally incommensurate magnetic satellite reflections reveal new lock-in behavior which we explain within a simple spin-discommensuration model. As a result of magnetoelastic coupling, the spin-discommensuration array produces additional x-ray diffraction satellites. Their observation further substantiates the model and demonstrates additional advantages of synchrotron radiation for magnetic-structure studies.

Complementary uses of small angle X-ray scattering and X-ray crystallography.

PubMed

Pillon, Monica C; Guarné, Alba

2017-11-01

Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques. Here we review how small-angle X-ray scattering can be combined with other structural biology techniques to study protein dynamics. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

XRayView: a teaching aid for X-ray crystallography.

PubMed

Phillips, G N

1995-10-01

A software package, XRayView, has been developed that uses interactive computer graphics to introduce basic concepts of x-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography. Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space. XRayView is designed with "user-friendliness" in mind, using pull-down menus to control the program. Many of the experiences of using real x-ray diffraction equipment to examine crystalline diffraction can be simulated. Exercises are available on-line to guide the users through many typical x-ray diffraction experiments.

Quantum Crystallography: Density Matrix-Density Functional Theory and the X-Ray Diffraction Experiment

NASA Astrophysics Data System (ADS)

Soirat, Arnaud J. A.

Density Matrix Theory is a Quantum Mechanical formalism in which the wavefunction is eliminated and its role taken over by reduced density matrices. The interest of this is that, it allows one, in principle, to calculate any electronic property of a physical system, without having to solve the Schrodinger equation, using only two entities much simpler than an N-body wavefunction: first and second -order reduced density matrices. In practice, though, this very promising possibility faces the tremendous theoretical problem of N-representability, which has been solved for the former, but, until now, voids any hope of theoretically determining the latter. However, it has been shown that single determinant reduced density matrices of any order may be recovered from coherent X-ray diffraction data, if one provides a proper Quantum Mechanical description of the Crystallography experiment. A deeper investigation of this method is the purpose of this work, where we, first, further study the calculation of X-ray reduced density matrices N-representable by a single Slater determinant. In this context, we independently derive necessary and sufficient conditions for the uniqueness of the method. We then show how to account for electron correlation in this model. For the first time, indeed, we derive highly accurate, yet practical, density matrices approximately N-representable by correlated-determinant wavefunctions. The interest of such a result lies in the Quantum Mechanical validity of these density matrices, their property of being entirely obtainable from X-ray coherent diffraction data, their very high accuracy conferred by this known property of the N-representing wavefunction, as well as their definition as explicit functionals of the density. All of these properties are finally used in both a theoretical and a numerical application: in the former, we show that these density matrices may be used in the context of Density Functional Theory to highly accurately determine

Where is crystallography going?

PubMed Central

Ashton, Alun W.; Sorensen, Thomas

2018-01-01

Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide. PMID:29533241

Micro-crystallography comes of age

PubMed Central

Smith, Janet L.; Fischetti, Robert F.; Yamamoto, Masaki

2012-01-01

The latest revolution in macromolecular crystallography was incited by the development of dedicated, user friendly, micro-crystallography beamlines. Brilliant X-ray beams of diameter 20 microns or less, now available at most synchrotron sources, enable structure determination from samples that previously were inaccessible. Relative to traditional crystallography, crystals with one or more small dimensions have diffraction patterns with vastly improved signal-to-noise when recorded with an appropriately matched beam size. Structures can be solved from isolated, well diffracting regions within inhomogeneous samples. This review summarizes the technological requirements and approaches to producing micro-beams and how they continue to change the practice of crystallography. PMID:23021872

Crystallography with online optical and X-ray absorption spectroscopies demonstrates an ordered mechanism in copper nitrite reductase.

PubMed

Hough, Michael A; Antonyuk, Svetlana V; Strange, Richard W; Eady, Robert R; Hasnain, S Samar

2008-04-25

Nitrite reductases are key enzymes that perform the first committed step in the denitrification process and reduce nitrite to nitric oxide. In copper nitrite reductases, an electron is delivered from the type 1 copper (T1Cu) centre to the type 2 copper (T2Cu) centre where catalysis occurs. Despite significant structural and mechanistic studies, it remains controversial whether the substrates, nitrite, electron and proton are utilised in an ordered or random manner. We have used crystallography, together with online X-ray absorption spectroscopy and optical spectroscopy, to show that X-rays rapidly and selectively photoreduce the T1Cu centre, but that the T2Cu centre does not photoreduce directly over a typical crystallographic data collection time. Furthermore, internal electron transfer between the T1Cu and T2Cu centres does not occur, and the T2Cu centre remains oxidised. These data unambiguously demonstrate an 'ordered' mechanism in which electron transfer is gated by binding of nitrite to the T2Cu. Furthermore, the use of online multiple spectroscopic techniques shows their value in assessing radiation-induced redox changes at different metal sites and demonstrates the importance of ensuring the correct status of redox centres in a crystal structure determination. Here, optical spectroscopy has shown a very high sensitivity for detecting the change in T1Cu redox state, while X-ray absorption spectroscopy has reported on the redox status of the T2Cu site, as this centre has no detectable optical absorption.

Architectural plasticity of AMPK revealed by electron microscopy and X-ray crystallography

PubMed Central

Ouyang, Yan; Zhu, Li; Li, Yifang; Guo, Miaomiao; Liu, Yang; Cheng, Jin; Zhao, Jing; Wu, Yi

2016-01-01

Mammalian AMP-activated protein kinase (AMPK) acts as an important sensor of cellular energy homeostasis related with AMP/ADP to ATP ratio. The overall architecture of AMPK has been determined in either homotrimer or monomer form by electron microscopy (EM) and X-ray crystallography successively. Accordingly proposed models have consistently revealed a key role of the α subunit linker in sensing adenosine nucleoside binding on the γ subunit and mediating allosteric regulation of kinase domain (KD) activity, whereas there are vital differences in orienting N-terminus of α subunit and locating carbohydrate-binding module (CBM) of β subunit. Given that Mg2+, an indispensable cofactor of AMPK was present in the EM sample preparation buffer however absent when forming crystals, here we carried out further reconstructions without Mg2+ to expectably inspect if this ion may contribute to this difference. However, no essential alteration has been found in this study compared to our early work. Further analyses indicate that the intra-molecular movement of the KD and CBM are most likely due to the flexible linkage of the disordered linkers with the rest portion as well as a contribution from the plasticity in the inter-molecular assembly mode, which might ulteriorly reveal an architectural complication of AMPK. PMID:27063142

Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR

PubMed Central

Macpherson, Alex; Smith-Penzel, Susanne; Basse, Nicolas; Lecomte, Fabien; Deboves, Hervé; Taylor, Richard D.; Norman, Tim; Porter, John; Waters, Lorna C.; Westwood, Marta; Cossins, Ben; Cain, Katharine; White, James; Griffin, Robert; Prosser, Christine; Kelm, Sebastian; Sullivan, Amy H.; Fox, David; Carr, Mark D.; Henry, Alistair; Taylor, Richard; Meier, Beat H.; Oschkinat, Hartmut; Lawson, Alastair D.

2018-01-01

Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)–Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 kHz after sedimentation, exploiting very fast spinning of the nondeuterated soluble 42 kDa receptor construct to obtain resolved proton-detected 2D and 3D NMR spectra. FcRn plays a crucial role in regulation of IgG and serum albumin catabolism. It is a clinically validated drug target for the treatment of autoimmune diseases caused by pathogenic antibodies via the inhibition of its interaction with IgG. We herein present the discovery of a small molecule that binds into a conserved cavity of the heterodimeric, extracellular domain composed of an α-chain and β2-microglobulin (β2m) (FcRnECD, 373 residues). X-ray crystallography was used alongside NMR at 100 kHz MAS with sedimented soluble protein to explore possibilities for refining the compound as an allosteric modulator. Proton-detected MAS NMR experiments on fully protonated [13C,15N]-labeled FcRnECD yielded ligand-induced chemical-shift perturbations (CSPs) for residues in the binding pocket and allosteric changes close to the interface of the two receptor heterodimers present in the asymmetric unit as well as potentially in the albumin interaction site. X-ray structures with and without ligand suggest the need for an optimized ligand to displace the α-chain with respect to β2m, both of which participate in the FcRnECD–IgG interaction site. Our investigation establishes a method to characterize structurally small molecule binding to nondeuterated large proteins by NMR, even in their glycosylated form, which may prove highly valuable for structure-based drug discovery campaigns. PMID:29782488

Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR.

PubMed

Stöppler, Daniel; Macpherson, Alex; Smith-Penzel, Susanne; Basse, Nicolas; Lecomte, Fabien; Deboves, Hervé; Taylor, Richard D; Norman, Tim; Porter, John; Waters, Lorna C; Westwood, Marta; Cossins, Ben; Cain, Katharine; White, James; Griffin, Robert; Prosser, Christine; Kelm, Sebastian; Sullivan, Amy H; Fox, David; Carr, Mark D; Henry, Alistair; Taylor, Richard; Meier, Beat H; Oschkinat, Hartmut; Lawson, Alastair D

2018-05-01

Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)-Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 kHz after sedimentation, exploiting very fast spinning of the nondeuterated soluble 42 kDa receptor construct to obtain resolved proton-detected 2D and 3D NMR spectra. FcRn plays a crucial role in regulation of IgG and serum albumin catabolism. It is a clinically validated drug target for the treatment of autoimmune diseases caused by pathogenic antibodies via the inhibition of its interaction with IgG. We herein present the discovery of a small molecule that binds into a conserved cavity of the heterodimeric, extracellular domain composed of an α-chain and β2-microglobulin (β2m) (FcRnECD, 373 residues). X-ray crystallography was used alongside NMR at 100 kHz MAS with sedimented soluble protein to explore possibilities for refining the compound as an allosteric modulator. Proton-detected MAS NMR experiments on fully protonated [13C,15N]-labeled FcRnECD yielded ligand-induced chemical-shift perturbations (CSPs) for residues in the binding pocket and allosteric changes close to the interface of the two receptor heterodimers present in the asymmetric unit as well as potentially in the albumin interaction site. X-ray structures with and without ligand suggest the need for an optimized ligand to displace the α-chain with respect to β2m, both of which participate in the FcRnECD-IgG interaction site. Our investigation establishes a method to characterize structurally small molecule binding to nondeuterated large proteins by NMR, even in their glycosylated form, which may prove highly valuable for structure-based drug discovery campaigns.

Magnetic properties of X-ray bright points. [in sun

NASA Technical Reports Server (NTRS)

Golub, L.; Krieger, A. S.; Harvey, J. W.; Vaiana, G. S.

1977-01-01

Using high-resolution Kitt Peak National Observatory magnetograms and sequences of simultaneous S-054 soft X-ray solar images, the properties of X-ray bright points (XBP) and ephemeral active regions (ER) are compared. All XBP appear on the magnetograms as bipolar features, except for very recently emerged or old and decayed XBP. The separation of the magnetic bipoles is found to increase with the age of the XBP, with an average emergence growth rate of 2.2 plus or minus 0.4 km per sec. The total magnetic flux in a typical XBP living about 8 hr is found to be about two times ten to the nineteenth power Mx. A proportionality is found between XBP lifetime and total magnetic flux, equivalent to about ten to the twentieth power Mx per day of lifetime.

XAFS and Protein Crystallography Beamline BL38B1 at SPring-8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanida, Hajime; Miura, Keiko; Takeshita, Kunikazu

2004-05-12

The SPring-8 bending magnet beamline BL38B1 is designed for R and D of optics, detectors, experiments for XAFS and protein X-ray crystallography (PX). This beamline has a multi-purpose hutch for two experimental stations of XAFS and PX, and removable optical benches used for R and D of detectors and instruments. The design and the performance of the beamline are presented.

A compact permanent-magnet system for measuring magnetic circular dichroism in resonant inelastic soft X-ray scattering.

PubMed

Miyawaki, Jun; Suga, Shigemasa; Fujiwara, Hidenori; Niwa, Hideharu; Kiuchi, Hisao; Harada, Yoshihisa

2017-03-01

A compact and portable magnet system for measuring magnetic dichroism in resonant inelastic soft X-ray scattering (SX-RIXS) has been developed at the beamline BL07LSU in SPring-8. A magnetic circuit composed of Nd-Fe-B permanent magnets, which realised ∼0.25 T at the center of an 11 mm gap, was rotatable around the axis perpendicular to the X-ray scattering plane. Using the system, a SX-RIXS spectrum was obtained under the application of the magnetic field at an angle parallel, nearly 45° or perpendicular to the incident X-rays. A dedicated sample stage was also designed to be as compact as possible, making it possible to perform SX-RIXS measurements at arbitrary incident angles by rotating the sample stage in the gap between the magnetic poles. This system enables facile studies of magnetic dichroism in SX-RIXS for various experimental geometries of the sample and the magnetic field. A brief demonstration of the application is presented.

Correlation between protein sequence similarity and x-ray diffraction quality in the protein data bank.

PubMed

Lu, Hui-Meng; Yin, Da-Chuan; Ye, Ya-Jing; Luo, Hui-Min; Geng, Li-Qiang; Li, Hai-Sheng; Guo, Wei-Hong; Shang, Peng

2009-01-01

As the most widely utilized technique to determine the 3-dimensional structure of protein molecules, X-ray crystallography can provide structure of the highest resolution among the developed techniques. The resolution obtained via X-ray crystallography is known to be influenced by many factors, such as the crystal quality, diffraction techniques, and X-ray sources, etc. In this paper, the authors found that the protein sequence could also be one of the factors. We extracted information of the resolution and the sequence of proteins from the Protein Data Bank (PDB), classified the proteins into different clusters according to the sequence similarity, and statistically analyzed the relationship between the sequence similarity and the best resolution obtained. The results showed that there was a pronounced correlation between the sequence similarity and the obtained resolution. These results indicate that protein structure itself is one variable that may affect resolution when X-ray crystallography is used.

Magnetically-coupled microcalorimeter arrays for x-ray astrophysics

NASA Astrophysics Data System (ADS)

Bandler, Simon

The "X-ray Surveyor" has been listed by NASA as one of the four major large mission concepts to be studied in the next Astrophysics Decadal Review in its preliminary list of large concepts. One of the key instruments on such a mission would be a very large format X-ray microcalorimeter array, with an array size of greater than 100 thousand pixels. Magnetically-coupled microcalorimeters (MCC) are one of the technologies with the greatest potential to meet the requirements of this mission, and this proposal is one to carry out research specifically to reach the goals of this vision. The "X-ray Surveyor" is a concept for a future mission that will make X-ray observations that are instrumental to understanding the quickly emerging population of galaxies and supermassive black holes at z ~10. The observations will trace the formation of galaxies and their assembly into large-scale structures starting from the earliest possible epochs. This mission would be observing baryons and large-scale physical processes outside of the very densest regions in the local Universe. This can be achieved with an X-ray observatory with similar angular resolution as Chandra but with significantly improved optic area and detector sensitivity. Chandra-scale angular resolution (1" or better) is essential in building more powerful, higher throughput observatories to avoid source confusion and remain photon-limited rather than background-limited. A prime consideration for the microcalorimeter camera on this type of mission is maintaining ~ 1 arcsec spatial resolution over the largest possible field of view, even if this means a slight trade-off against the spectral resolution. A uniform array of 1" pixels covering at least 5'x5' field of view is desired. To reduce the number of sensors read out, in geometries where extremely fine pitch (~50 microns) is desired, the most promising technologies are those in which a thermal sensor such an MCC can read out a sub-array of 20-25 individual 1'�

Asymmetry in serial femtosecond crystallography data.

PubMed

Sharma, Amit; Johansson, Linda; Dunevall, Elin; Wahlgren, Weixiao Y; Neutze, Richard; Katona, Gergely

2017-03-01

Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of the Blastochloris viridis photosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background.

Exploring the Hard and Soft X-ray Emission of Magnetic Cataclysmic Variables

NASA Astrophysics Data System (ADS)

de Martino, D.; Anzolin, G.; Bonnet-Bidaud, J.-M.; Falanga, M.; Matt, G.; Mouchet, M.; Mukai, K.; Masetti, N.

2009-05-01

A non-negligible fraction of galactic hard (>20 keV) X-ray sources were identified as CVs of the magnetic Intermediate Polar type in INTEGRAL, SWIFT and RXTE surveys, that suggests a still hidden but potentially important population of faint hard X-ray sources. Simbol-X has the unique potential to simultaneously characterize their variable and complex soft and hard X-ray emission thus allowing to understand their putative role in galactic populations of X-ray sources.

Crystal and Vibrational Structure of Energetic 3,5-dinitro 1,3,5-oxadiazinane (DOD) by Single Crystal X-ray Diffractometry and Raman Spectroscopy

DTIC Science & Technology

2018-03-19

calculations using a temperature of 298 K. 15. SUBJECT TERMS 3,5-dinitro-1,3,5-oxadiazinane (DOD), X-ray crystallography , Raman, energetic material...X-ray analysis. 2.2 Characterization X-ray Crystallography . DOD crystals were characterized with a SuperNova, Dualflex, EosS2 diffractometer using

The accurate assessment of small-angle X-ray scattering data

DOE PAGES

Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; ...

2015-01-23

Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targetsmore » for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.« less

Fragment-based screening by protein crystallography: successes and pitfalls.

PubMed

Chilingaryan, Zorik; Yin, Zhou; Oakley, Aaron J

2012-10-08

Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality.

Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls

PubMed Central

Chilingaryan, Zorik; Yin, Zhou; Oakley, Aaron J.

2012-01-01

Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality. PMID:23202926

Micro-crystallography comes of age.

PubMed

Smith, Janet L; Fischetti, Robert F; Yamamoto, Masaki

2012-10-01

The latest revolution in macromolecular crystallography was incited by the development of dedicated, user friendly, micro-crystallography beam lines. Brilliant X-ray beams of diameter 20 μm or less, now available at most synchrotron sources, enable structure determination from samples that previously were inaccessible. Relative to traditional crystallography, crystals with one or more small dimensions have diffraction patterns with vastly improved signal-to-noise when recorded with an appropriately matched beam size. Structures can be solved from isolated, well diffracting regions within inhomogeneous samples. This review summarizes the technological requirements and approaches to producing micro-beams and how they continue to change the practice of crystallography. Copyright © 2012 Elsevier Ltd. All rights reserved.

Time-resolved structural studies with serial crystallography: A new light on retinal proteins

PubMed Central

Panneels, Valérie; Wu, Wenting; Tsai, Ching-Ju; Nogly, Przemek; Rheinberger, Jan; Jaeger, Kathrin; Cicchetti, Gregor; Gati, Cornelius; Kick, Leonhard M.; Sala, Leonardo; Capitani, Guido; Milne, Chris; Padeste, Celestino; Pedrini, Bill; Li, Xiao-Dan; Standfuss, Jörg; Abela, Rafael; Schertler, Gebhard

2015-01-01

Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination. PMID:26798817

A Search for X-ray Emission from the First Magnetically Active T Dwarf

NASA Astrophysics Data System (ADS)

Williams, Peter

2015-09-01

Ultracool dwarfs (spectral types >M7) were long expected to be magnetically inactive, but concerted X-ray and radio observations (mostly by our group) have led to the discovery of magnetic activity and a characterization of its basic properties. We have recently discovered periodic radio bursts from the T6.5 dwarf 2MASS 1047+21, by far the coolest (900 K) substellar object detected in the radio, implying high levels of magnetic activity well into the brown dwarf regime and making it a uniquely compelling target in the challenging search for ultracool X-ray emission. We propose a 40 ks observation with ACIS-S and the VLA that will cover 6 full rotations, place the deepest constraints on X-ray luminosity to date, and may lead to the first detection of X-ray emission from a T dwarf.

Local X-ray magnetic circular dichroism study of Fe/Cu(111) using a tunneling smart tip

PubMed Central

DiLullo, Andrew; Shirato, Nozomi; Cummings, Marvin; Kersell, Heath; Chang, Hao; Rosenmann, Daniel; Miller, Dean; Freeland, John W.; Hla, Saw-Wai; Rose, Volker

2016-01-01

Localized spectroscopy with simultaneous topographic, elemental and magnetic information is presented. A synchrotron X-ray scanning tunneling microscope has been employed for the local study of the X-ray magnetic circular dichroism at the Fe L 2,3-edges of a thin iron film grown on Cu(111). Polarization-dependent X-ray absorption spectra have been obtained through a tunneling smart tip that serves as a photoelectron detector. In contrast to conventional spin-polarized scanning tunneling microscopy, X-ray excitations provide magnetic contrast even with a non-magnetic tip. Intensity variations in the photoexcited tip current point to chemical variations within a single magnetic Fe domain. PMID:26917146

Local X-ray magnetic circular dichroism study of Fe/Cu(111) using a tunneling smart tip

DOE PAGES

DiLullo, Andrew; Shirato, Nozomi; Cummings, Marvin; ...

2016-01-28

Localized spectroscopy with simultaneous topographic, elemental and magnetic information is presented. A synchrotron X-ray scanning tunneling microscope has been employed for the local study of the X-ray magnetic circular dichroism at the FeL 2,3-edges of a thin iron film grown on Cu(111). Polarization-dependent X-ray absorption spectra have been obtained through a tunneling smart tip that serves as a photoelectron detector. In contrast to conventional spin-polarized scanning tunneling microscopy, X-ray excitations provide magnetic contrast even with a non-magnetic tip. Intensity variations in the photoexcited tip current point to chemical variations within a single magnetic Fe domain.

Local X-ray magnetic circular dichroism study of Fe/Cu(111) using a tunneling smart tip.

PubMed

DiLullo, Andrew; Shirato, Nozomi; Cummings, Marvin; Kersell, Heath; Chang, Hao; Rosenmann, Daniel; Miller, Dean; Freeland, John W; Hla, Saw-Wai; Rose, Volker

2016-03-01

Localized spectroscopy with simultaneous topographic, elemental and magnetic information is presented. A synchrotron X-ray scanning tunneling microscope has been employed for the local study of the X-ray magnetic circular dichroism at the Fe L2,3-edges of a thin iron film grown on Cu(111). Polarization-dependent X-ray absorption spectra have been obtained through a tunneling smart tip that serves as a photoelectron detector. In contrast to conventional spin-polarized scanning tunneling microscopy, X-ray excitations provide magnetic contrast even with a non-magnetic tip. Intensity variations in the photoexcited tip current point to chemical variations within a single magnetic Fe domain.

Chemical Crystallography at the Advanced Light Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCormick, Laura; Giordano, Nico; Teat, Simon

Chemical crystallography at synchrotrons was pioneered at the Daresbury SRS station 9.8. The chemical crystallography beamlines at the Advanced Light Source seek to follow that example, with orders of magnitude more flux than a lab source, and various in situ experiments. This article thus attempts to answer why a chemist would require synchrotron X-rays, to describe the techniques available at the ALS chemical crystallography beamlines, and place the current facilities in a historical context.

Chemical Crystallography at the Advanced Light Source

DOE PAGES

McCormick, Laura; Giordano, Nico; Teat, Simon; ...

2017-12-18

Chemical crystallography at synchrotrons was pioneered at the Daresbury SRS station 9.8. The chemical crystallography beamlines at the Advanced Light Source seek to follow that example, with orders of magnitude more flux than a lab source, and various in situ experiments. This article thus attempts to answer why a chemist would require synchrotron X-rays, to describe the techniques available at the ALS chemical crystallography beamlines, and place the current facilities in a historical context.

A Novel X-ray Diffractometer for the Florida Split Coil 25 Tesla Magnet

NASA Astrophysics Data System (ADS)

Wang, Shengyu; Kovalev, Alexey; Suslov, Alexey; Siegrist, Theo

2014-03-01

At National High Magnetic Field Laboratory (NHMFL), we are developing a unique X-ray diffractometer for the 25 Tesla Florida Split Coil Magnet for scattering experiments under extremely high static magnetic fields. The X-ray source is a sealed tube (copper or molybdenum anode), connected to the magnet by an evacuated beam tunnel. The detectors are either an image plate or a silicon drift detector, with the data acquisition system based on LabVIEW. Our preliminary experimental results showed that the performance of the detector electronics and the X-ray generator is reliable in the fringe magnetic fields produced at the highest field of 25 T. Using this diffractometer, we will make measurements on standard samples, such as LaB6, Al2O3 and Si, to calibrate the diffraction system. Magnetic samples, such as single crystal HoMnO3 and stainless steel 301 alloys will be measured subsequently. The addition of X-ray diffraction to the unique split coil magnet will significantly expand the NHMFL experimental capabilities. Therefore, external users will be able to probe spin - lattice interactions at static magnetic fields up to 25T. This project is supported by NSF-DMR Award No.1257649. NHMFL is supported by NSF Cooperative Agreement No. DMR-1157490, the State of Florida, and the U.S. DoE.

X-ray Characterization of Oxide-based Magnetic Semiconductors

NASA Astrophysics Data System (ADS)

Idzerda, Yves

2008-05-01

Although the evidence for magnetic semiconductors (not simply semiconductors which are ferromagnetic) is compelling, there is much uncertainty in the mechanism for the polarization of the carriers, suggesting that it must be quite novel. Recent experimental evidence suggests that this mechanism is similar to the polaron percolation theory proposed by Kaminski and Das Sarma,ootnotetextKaminski and S. Das Sarma, Physical Review Letters 88, 247202 (2002). which was recently applied specifically to doped oxides by Coey et al.ootnotetextJ. M. D. Coey, M. Venkatesan, and C. B. Fitzgerald, Nature Materials 4, 173 (2005). where the ferromagnetism is driven by the percolation of polarons generated by defects or dopants. We have used X-ray absorption spectroscopy at the L-edges and K-edges for low concentrations transition metal (TM) doped magnetic oxides (including TiO2, La1-xSrxO3, HfO2, and In2O3). We have found that in most cases, the transition metal assumes a valence consistent with being at a substitutional, and not interstitial site. We have also measured the X-ray Magnetic Circular Dichroism spectra. Although these materials show strong bulk magnetization, we are unable to detect a robust dichroism feature associated with magnetic elements in the host semiconductor. In the cases where a dichroism signal was observed, it was very weak and could be ascribed to a distinct ferromagnetic phase (TM metal cluster, TM oxide particulate, etc.) separate from the host material. This fascinating absence of a dichroic signal and its significant substantiation of important features of the polaron percolation model may help to finally resolve the issue of ferromagnetism in magnetically doped oxides.

Rapid X-ray Photoreduction of Dimetal-Oxygen Cofactors in Ribonucleotide Reductase

PubMed Central

Sigfridsson, Kajsa G. V.; Chernev, Petko; Leidel, Nils; Popović-Bijelić, Ana; Gräslund, Astrid; Haumann, Michael

2013-01-01

Prototypic dinuclear metal cofactors with varying metallation constitute a class of O2-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O2 activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques. PMID:23400774

Rapid X-ray photoreduction of dimetal-oxygen cofactors in ribonucleotide reductase.

PubMed

Sigfridsson, Kajsa G V; Chernev, Petko; Leidel, Nils; Popovic-Bijelic, Ana; Gräslund, Astrid; Haumann, Michael

2013-04-05

Prototypic dinuclear metal cofactors with varying metallation constitute a class of O2-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O2 activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques.

Resonant magnetic X-ray scattering studies of heavy fermion superconductors

NASA Astrophysics Data System (ADS)

Gaulin, B. D.; Isaacs, E. D.; Lussier, J. G.; Reimers, J. N.; Gibbs, D.; Zschack, P.; Schröder, A.; Taillefer, L.; Garrett, J. D.

1994-04-01

The uranium-based heavy fermion superconductors which are known to display weak antiferromagnetism at low temperatures are well suited to study by the newly developed resonant magnetic X-ray scattering technique. We review recent synchrotron X-ray scattering studies of the magnetic behavior of UPd 2Al 3 and URu 2Si 2 and the interaction between magnetism and superconductivity in these materials. These measurements show resolution-limited magnetic Bragg peaks in UPd 2Al 3 in contrast to those in URu 2Si 2. The order parameter as measured at the (0 0 {1}/{2}) magnetic reciprocal lattice position in UPd 2Al 3 is different from that at (0, 0, {3}/{2}), the latter of which indicates a strong anomaly at TNI ∼ 11.8 K below the sharp onset of the antiferromagnetic phase at TN ∼ 14.5 K. Finally, the behavior of the (0 0 {1}/{2}) order parameter is smooth for T ≤ Tc = 2.00 ± 0.04 K.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography*

PubMed Central

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N.; Nishida, Clinton R.; de Montellano, Paul R. Ortiz

2015-01-01

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. PMID:25670859

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE PAGES

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; ...

2015-02-10

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

X-ray evaluation of SEM technique for determining the crystallography of echinoid skeletons.

PubMed

Dillaman, R M; Hart, H V

1981-01-01

Coronal plates of the sea urchin Strongylocentrotus purpuratus have a microstructure typified by smooth textured trabeculae. When plates were decorated with calcite crystals each rhombohedron had the same orientation regardless of its location on the plate. When the sample was oriented so that the three edges of the rhombohedron formed equal 120 degrees angles and the three crystal faces appeared to form equal angles with the plane of the photograph, the c-axis of the plate paralleled the electron beam and the three a-axes were 30 degrees counterclockwise from the edges. These a-axes were then related to a plate edge recorded in a low magnification micrograph. Directions of the a-axes of each plate were also measured using a back-reflection Laue x-ray diffraction camera. A comparison of a-axes measured by the two techniques showed an average difference of 3 degrees, indicating that decorated crystal grew in crystallographic continuity with the plate. Assuming this relationship remains constant, the decoration technique appears to be an accurate and efficient method for evaluating the crystallography of echinoid skeletal units. Analysis of a polar plot of a-axes for 11 plates indicated that the a-axes were not randomly oriented; however, definitive relationships must await more extensive investigations.

Graphene-based microfluidics for serial crystallography.

PubMed

Sui, Shuo; Wang, Yuxi; Kolewe, Kristopher W; Srajer, Vukica; Henning, Robert; Schiffman, Jessica D; Dimitrakopoulos, Christos; Perry, Sarah L

2016-08-02

Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.

Interfacial magnetism in complex oxide heterostructures probed by neutrons and x-rays.

PubMed

Liu, Yaohua; Ke, Xianglin

2015-09-23

Magnetic complex-oxide heterostructures are of keen interest because a wealth of phenomena at the interface of dissimilar materials can give rise to fundamentally new physics and potentially valuable functionalities. Altered magnetization, novel magnetic coupling and emergent interfacial magnetism at the epitaxial layered-oxide interfaces are under intensive investigation, which shapes our understanding on how to utilize those materials, particularly for spintronics. Neutron and x-ray based techniques have played a decisive role in characterizing interfacial magnetic structures and clarifying the underlying physics in this rapidly developing field. Here we review some recent experimental results, with an emphasis on those studied via polarized neutron reflectometery and polarized x-ray absorption spectroscopy. We conclude with some perspectives.

Bright X-ray arcs and the emergence of solar magnetic flux

NASA Technical Reports Server (NTRS)

Chapman, G. A.; Broussard, R. M.

1977-01-01

The Skylab S-056 and S-082A experiments and ground-based magnetograms have been used to study the role of bright X-ray arcs and the emergence of solar magnetic flux in the McMath region 12476. The S-056 X-ray images show a system of one or sometimes two bright arcs within a diffuse emitting region. The arcs seem to directly connect regions of opposite magnetic polarity in the photosphere. Magnetograms suggest the possible emergence of a magnetic flux. The width of the main arc is approximately 6 arcsec when most clearly defined, and the length is approximately 30-50 arcsec. Although the arc system is observed to vary in brightness over a period exceeding 24 hours, it remains fixed in orientation. The temperature of the main arc is approximately 3 x 10 to the 6th K. It is suggested that merging magnetic fields may provide the primary energy source, perhaps accompanied by resistive heating from a force-free current.

Onset of the Magnetic Explosion in Solar Polar Coronal X-Ray Jets

NASA Astrophysics Data System (ADS)

Moore, Ronald L.; Sterling, Alphonse C.; Panesar, Navdeep K.

2018-05-01

We follow up on the Sterling et al. discovery that nearly all polar coronal X-ray jets are made by an explosive eruption of a closed magnetic field carrying a miniature filament in its core. In the same X-ray and EUV movies used by Sterling et al., we examine the onset and growth of the driving magnetic explosion in 15 of the 20 jets that they studied. We find evidence that (1) in a large majority of polar X-ray jets, the runaway internal/tether-cutting reconnection under the erupting minifilament flux rope starts after both the minifilament’s rise and the spire-producing external/breakout reconnection have started; and (2) in a large minority, (a) before the eruption starts, there is a current sheet between the explosive closed field and the ambient open field, and (b) the eruption starts with breakout reconnection at that current sheet. The variety of event sequences in the eruptions supports the idea that the magnetic explosions that make polar X-ray jets work the same way as the much larger magnetic explosions that make a flare and coronal mass ejection (CME). That idea and recent observations indicating that magnetic flux cancellation is the fundamental process that builds the field in and around the pre-jet minifilament and triggers that field’s jet-driving explosion together suggest that flux cancellation inside the magnetic arcade that explodes in a flare/CME eruption is usually the fundamental process that builds the explosive field in the core of the arcade and triggers that field’s explosion.

X-rays in the Cryo-EM Era: Structural Biology’s Dynamic Future

PubMed Central

Shoemaker, Susannah C.; Ando, Nozomi

2018-01-01

Over the past several years, single-particle cryo-electron microscopy (cryo-EM) has emerged as a leading method for elucidating macromolecular structures at near-atomic resolution, rivaling even the established technique of X-ray crystallography. Cryo-EM is now able to probe proteins as small as hemoglobin (64 kDa), while avoiding the crystallization bottleneck entirely. The remarkable success of cryo-EM has called into question the continuing relevance of X-ray methods, particularly crystallography. To say that the future of structural biology is either cryo-EM or crystallography, however, would be misguided. Crystallography remains better suited to yield precise atomic coordinates of macromolecules under a few hundred kDa in size, while the ability to probe larger, potentially more disordered assemblies is a distinct advantage of cryo-EM. Likewise, crystallography is better equipped to provide high-resolution dynamic information as a function of time, temperature, pressure, and other perturbations, whereas cryo-EM offers increasing insight into conformational and energy landscapes, particularly as algorithms to deconvolute conformational heterogeneity become more advanced. Ultimately, the future of both techniques depends on how their individual strengths are utilized to tackle questions on the frontiers of structural biology. Structure determination is just one piece of a much larger puzzle: a central challenge of modern structural biology is to relate structural information to biological function. In this perspective, we share insight from several leaders in the field and examine the unique and complementary ways in which X-ray methods and cryo-EM can shape the future of structural biology. PMID:29227642

New carbocyclic nucleoside analogues with a bicyclo[2.2.1]heptane fragment as sugar moiety; synthesis, X-ray crystallography and anticancer activity.

PubMed

Tănase, Constantin I; Drăghici, Constantin; Căproiu, Miron Teodor; Shova, Sergiu; Mathe, Christophe; Cocu, Florea G; Enache, Cristian; Maganu, Maria

2014-01-01

An amine group was synthesized starting from an optically active bicyclo[2.2.1]heptane compound, which was then used to build the 5 atoms ring of a key 6-chloropurine intermediate. This was then reacted with ammonia and selected amines obtaining new adenine- and 6-substituted adenine conformationally constrained carbocyclic nucleoside analogues with a bicyclo[2.2.1]heptane skeleton in the sugar moiety. X-ray crystallography confirmed an exo-coupling of base to the ring and a L configuration of the nucleoside analogues. The compounds were tested for anticancer activity. Copyright © 2013 Elsevier Ltd. All rights reserved.

X-ray studies of highly magnetized neutron stars and their environs

NASA Astrophysics Data System (ADS)

Kumar, Harsha Sanjeev

Supernova explosions are among the most energetic events known in the universe, leaving supernova remnants (SNRs) as their relics. The cores of massive stars collapse to form neutron stars, among the most compact and strongest magnets in the cosmos. The thesis studies a sample of such magnetic "beauties" in X-rays, the magnetars and high-magnetic field pulsars (HBPs), with the motivation to understand their evolutionary links. We also address the connection between these sources by investigating their environs through their securely associated SNRs. Magnetars have ultra-high magnetic fields B ~ 1014 -- 1015 Gauss (G) and include the soft-gamma repeaters (SGRs) and anomalous X-ray pulsars (AXPs). The HBPs have magnetic fields B ~ 1013 -- 10 14 G, intermediate between the classical rotation-powered pulsars (B ~ 1012 G) and magnetars. We focussed on two HBPs: J1119-6127 and J1846-0258, with similar spin-properties and associated with the SNRs G292.2-0.5 and Kes 75, respectively. In our studies, magnetar-like behavior was discovered from the Crab-like pulsar J1846-0258, clearly establishing a connection between the HBPs and magnetars for the first time, while no such behavior has been observed from PSR J1119-6127 so far. J1119-6127's overall X-ray properties together with its compact pulsar wind nebula resemble more the classical rotation-powered pulsars. We studied two magnetars, one from each sub-class: SGR 0501+4516 and AXP 1E 1841-045. The spectral and statistical analysis of the bursts and the persistent X-ray emission properties observed from them were found consistent with the magnetar model predictions as well as those seen in other SGRs. Finally, we probed the environment of these stellar magnets by performing a detailed X-ray imaging and spatially resolved spectroscopic study of two SNRs: G292.2-0.5 and Kes 73 associated with J1119-6127 and 1E 1841-045, respectively. We found that both SNRs point to very massive progenitors ( ≳ 25 solar masses), further

Interfacial Magnetism in Complex Oxide Heterostructures Probed by Neutrons and X-rays

DOE PAGES

Liu, Yaohua; Ke, Xianglin

2015-09-02

Magnetic complex-oxide heterostructures are of keen interest because a wealth of phenomena at the interface of dissimilar materials can give rise to fundamentally new physics and potentially valuable functionalities. Altered magnetization, novel magnetic coupling and emergent interfacial magnetism at the epitaxial layered-oxide interfaces have all been intensively investigated, which shapes our understanding on how to utilize those materials, particularly for spintronics. Neutron and x-ray based techniques have played a decisive role in characterizing interfacial magnetic structures and clarifying the underlying physics in this rapidly developing field. Here we review some recent experimental results, with an emphasis on those studied viamore » polarized neutron reflectometery and polarized x-ray absorption spectroscopy. We conclude with some perspectives.« less

Accurate determination of segmented X-ray detector geometry

PubMed Central

Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius; White, Thomas A.; Chapman, Henry N.; Barty, Anton

2015-01-01

Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical for many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. We show that the refined detector geometry greatly improves the results of experiments. PMID:26561117

Accurate determination of segmented X-ray detector geometry

DOE PAGES

Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius; ...

2015-10-22

Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical formore » many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. Furthermore, we show that the refined detector geometry greatly improves the results of experiments.« less

Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography.

PubMed

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N; Nishida, Clinton R; de Montellano, Paul R Ortiz

2015-04-17

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional (1)H,(15)N HSQC chemical shift perturbation mapping of (15)N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Highly magnetic Co nanoparticles fabricated by X-ray radiolysis

NASA Astrophysics Data System (ADS)

Clifford, Dustin M.; Castano, Carlos E.; Rojas, Jessika V.

2018-03-01

Advanced routes for the synthesis of nanomaterials, such as ferromagnetic nanoparticles, are being explored that are easy to perform using cost-effective and non-toxic precursors. Radiolytic syntheses based on the use of X-rays as ionizing radiation are promising towards this effort. X-rays were used to produce highly magnetic cobalt nanoparticles (NPs), stable in air up to 200 °C, from the radiolysis of water. Crystal structure analysis by XRD indicates a mixture of Cofcc, 63%, and Cohcp, 37%, phases. Magnetic analysis by VSM gave a saturation magnetization (Ms) 136 emu/g at 1 T and coercivity (Hc) = 325 Oe when the reaction solution was purged with N2 while an air-purged treatment resulted in Co NPs having 102 emu/g with a coercivity (Hc) 270 Oe. Overall, the reduction of Co2+ occurred in an aqueous reaction environment without addition of chemical reductants resulting in Co NPs with size distribution from 20 to 140 nm. This clean approach at ambient temperature produced highly magnetic Co NPs that may be used for switching devices (i.e. reed switches) or as additives for alloys that require high Curie points.

Retrieving spin textures on curved magnetic thin films with full-field soft X-ray microscopies

DOE PAGES

Streubel, Robert; Kronast, Florian; Fischer, Peter; ...

2015-07-03

X-ray tomography is a well-established technique to characterize 3D structures in material sciences and biology; its magnetic analogue—magnetic X-ray tomography—is yet to be developed. We demonstrate the visualization and reconstruction of magnetic domain structures in a 3D curved magnetic thin films with tubular shape by means of full-field soft X-ray microscopies. In the 3D arrangement of the magnetization is retrieved from a set of 2D projections by analysing the evolution of the magnetic contrast with varying projection angle. By using reconstruction algorithms to analyse the angular evolution of 2D projections provides quantitative information about domain patterns and magnetic coupling phenomenamore » between windings of azimuthally and radially magnetized tubular objects. In conclusion, the present approach represents a first milestone towards visualizing magnetization textures of 3D curved thin films with virtually arbitrary shape.« less

Retrieving spin textures on curved magnetic thin films with full-field soft X-ray microscopies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Streubel, Robert; Kronast, Florian; Fischer, Peter

X-ray tomography is a well-established technique to characterize 3D structures in material sciences and biology; its magnetic analogue—magnetic X-ray tomography—is yet to be developed. We demonstrate the visualization and reconstruction of magnetic domain structures in a 3D curved magnetic thin films with tubular shape by means of full-field soft X-ray microscopies. In the 3D arrangement of the magnetization is retrieved from a set of 2D projections by analysing the evolution of the magnetic contrast with varying projection angle. By using reconstruction algorithms to analyse the angular evolution of 2D projections provides quantitative information about domain patterns and magnetic coupling phenomenamore » between windings of azimuthally and radially magnetized tubular objects. In conclusion, the present approach represents a first milestone towards visualizing magnetization textures of 3D curved thin films with virtually arbitrary shape.« less

AXSIS: Exploring the frontiers in attosecond X-ray science, imaging and spectroscopy.

PubMed

Kärtner, F X; Ahr, F; Calendron, A-L; Çankaya, H; Carbajo, S; Chang, G; Cirmi, G; Dörner, K; Dorda, U; Fallahi, A; Hartin, A; Hemmer, M; Hobbs, R; Hua, Y; Huang, W R; Letrun, R; Matlis, N; Mazalova, V; Mücke, O D; Nanni, E; Putnam, W; Ravi, K; Reichert, F; Sarrou, I; Wu, X; Yahaghi, A; Ye, H; Zapata, L; Zhang, D; Zhou, C; Miller, R J D; Berggren, K K; Graafsma, H; Meents, A; Assmann, R W; Chapman, H N; Fromme, P

2016-09-01

X-ray crystallography is one of the main methods to determine atomic-resolution 3D images of the whole spectrum of molecules ranging from small inorganic clusters to large protein complexes consisting of hundred-thousands of atoms that constitute the macromolecular machinery of life. Life is not static, and unravelling the structure and dynamics of the most important reactions in chemistry and biology is essential to uncover their mechanism. Many of these reactions, including photosynthesis which drives our biosphere, are light induced and occur on ultrafast timescales. These have been studied with high time resolution primarily by optical spectroscopy, enabled by ultrafast laser technology, but they reduce the vast complexity of the process to a few reaction coordinates. In the AXSIS project at CFEL in Hamburg, funded by the European Research Council, we develop the new method of attosecond serial X-ray crystallography and spectroscopy, to give a full description of ultrafast processes atomically resolved in real space and on the electronic energy landscape, from co-measurement of X-ray and optical spectra, and X-ray diffraction. This technique will revolutionize our understanding of structure and function at the atomic and molecular level and thereby unravel fundamental processes in chemistry and biology like energy conversion processes. For that purpose, we develop a compact, fully coherent, THz-driven atto-second X-ray source based on coherent inverse Compton scattering off a free-electron crystal, to outrun radiation damage effects due to the necessary high X-ray irradiance required to acquire diffraction signals. This highly synergistic project starts from a completely clean slate rather than conforming to the specifications of a large free-electron laser (FEL) user facility, to optimize the entire instrumentation towards fundamental measurements of the mechanism of light absorption and excitation energy transfer. A multidisciplinary team formed by laser

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

PubMed Central

Warren, Anna J.; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R.; Horrell, Sam; McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-01-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required. PMID:23793151

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging.

PubMed

Warren, Anna J; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R; Horrell, Sam; McAuley, Katherine E; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-07-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

Trends in Ultracool Dwarf Magnetism. I. X-Ray Suppression and Radio Enhancement

NASA Astrophysics Data System (ADS)

Williams, P. K. G.; Cook, B. A.; Berger, E.

2014-04-01

Although ultracool dwarfs (UCDs) are now known to generate and dissipate strong magnetic fields, a clear understanding of the underlying dynamo is still lacking. We have performed X-ray and radio observations of seven UCDs in a narrow range of spectral type (M6.5-M9.5) but spanning a wide range of projected rotational velocities (vsin i ≈ 3-40 km s-1). We have also analyzed unpublished archival Chandra observations of four additional objects. All of the newly observed targets are detected in the X-ray, while only one is detected in the radio, with the remainder having sensitive upper limits. We present a database of UCDs with both radio and X-ray measurements and consider the data in light of the so-called Güdel-Benz relation (GBR) between magnetic activity in these bands. Some UCDs have very bright radio emission and faint X-ray emission compared to what would be expected for rapid rotators, while others show the opposite behavior. We show that UCDs would still be radio-overluminous relative to the GBR even if their X-ray emission were at standard rapid-rotator "saturation" levels. Recent results from Zeeman-Doppler imaging and geodynamo simulations suggest that rapidly rotating UCDs may harbor a bistable dynamo that supports either a stronger, axisymmetric magnetic field or a weaker, non-axisymmetric field. We suggest that the data can be explained in a scenario in which strong-field objects obey the GBR while weak-field objects are radio-overluminous and X-ray-underluminous, possibly because of a population of gyrosynchrotron-emitting coronal electrons that is continuously replenished by low-energy reconnection events.

A comparison of coronal X-ray structures of active regions with magnetic fields computed from photospheric observations

NASA Technical Reports Server (NTRS)

Poletto, G.; Vaiana, G. S.; Zombeck, M. V.; Krieger, A. S.; Timothy, A. F.

1975-01-01

The appearances of several X-ray active regions observed on March 7, 1970 and June 15, 1973 are compared with the corresponding coronal magnetic-field topology. Coronal fields have been computed from measurements of the longitudinal component of the underlying magnetic fields, based on the current-free hypothesis. An overall correspondence between X-ray structures and calculated field lines is established, and the magnetic counterparts of different X-ray features are also examined. A correspondence between enhanced X-ray emission and the location of compact closed field lines is suggested. Representative magnetic-field values calculated under the assumption of current-free fields are given for heights up to 200 sec.

Accounting for partiality in serial crystallography using ray-tracing principles

PubMed Central

Kroon-Batenburg, Loes M. J.; Schreurs, Antoine M. M.; Ravelli, Raimond B. G.; Gros, Piet

2015-01-01

Serial crystallography generates ‘still’ diffraction data sets that are composed of single diffraction images obtained from a large number of crystals arbitrarily oriented in the X-ray beam. Estimation of the reflection partialities, which accounts for the expected observed fractions of diffraction intensities, has so far been problematic. In this paper, a method is derived for modelling the partialities by making use of the ray-tracing diffraction-integration method EVAL. The method estimates partialities based on crystal mosaicity, beam divergence, wavelength dispersion, crystal size and the interference function, accounting for crystallite size. It is shown that modelling of each reflection by a distribution of interference-function weighted rays yields a ‘still’ Lorentz factor. Still data are compared with a conventional rotation data set collected from a single lysozyme crystal. Overall, the presented still integration method improves the data quality markedly. The R factor of the still data compared with the rotation data decreases from 26% using a Monte Carlo approach to 12% after applying the Lorentz correction, to 5.3% when estimating partialities by EVAL and finally to 4.7% after post-refinement. The merging R int factor of the still data improves from 105 to 56% but remains high. This suggests that the accuracy of the model parameters could be further improved. However, with a multiplicity of around 40 and an R int of ∼50% the merged still data approximate the quality of the rotation data. The presented integration method suitably accounts for the partiality of the observed intensities in still diffraction data, which is a critical step to improve data quality in serial crystallography. PMID:26327370

Accounting for partiality in serial crystallography using ray-tracing principles.

PubMed

Kroon-Batenburg, Loes M J; Schreurs, Antoine M M; Ravelli, Raimond B G; Gros, Piet

2015-09-01

Serial crystallography generates `still' diffraction data sets that are composed of single diffraction images obtained from a large number of crystals arbitrarily oriented in the X-ray beam. Estimation of the reflection partialities, which accounts for the expected observed fractions of diffraction intensities, has so far been problematic. In this paper, a method is derived for modelling the partialities by making use of the ray-tracing diffraction-integration method EVAL. The method estimates partialities based on crystal mosaicity, beam divergence, wavelength dispersion, crystal size and the interference function, accounting for crystallite size. It is shown that modelling of each reflection by a distribution of interference-function weighted rays yields a `still' Lorentz factor. Still data are compared with a conventional rotation data set collected from a single lysozyme crystal. Overall, the presented still integration method improves the data quality markedly. The R factor of the still data compared with the rotation data decreases from 26% using a Monte Carlo approach to 12% after applying the Lorentz correction, to 5.3% when estimating partialities by EVAL and finally to 4.7% after post-refinement. The merging R(int) factor of the still data improves from 105 to 56% but remains high. This suggests that the accuracy of the model parameters could be further improved. However, with a multiplicity of around 40 and an R(int) of ∼50% the merged still data approximate the quality of the rotation data. The presented integration method suitably accounts for the partiality of the observed intensities in still diffraction data, which is a critical step to improve data quality in serial crystallography.

CCD sensors in synchrotron X-ray detectors

NASA Astrophysics Data System (ADS)

Strauss, M. G.; Naday, I.; Sherman, I. S.; Kraimer, M. R.; Westbrook, E. M.; Zaluzec, N. J.

1988-04-01

The intense photon flux from advanced synchrotron light sources, such as the 7-GeV synchrotron being designed at Argonne, require integrating-type detectors. Charge-coupled devices (CCDs) are well suited as synchrotron X-ray detectors. When irradiated indirectly via a phosphor followed by reducing optics, diffraction patterns of 100 cm 2 can be imaged on a 2 cm 2 CCD. With a conversion efficiency of ˜ 1 CCD electron/X-ray photon, a peak saturation capacity of > 10 6 X-rays can be obtained. A programmable CCD controller operating at a clock frequency of 20 MHz has been developed. The readout rate is 5 × 10 6 pixels/s and the shift rate in the parallel registers is 10 6 lines/s. The test detector was evaluated in two experiments. In protein crystallography diffraction patterns have been obtained from a lysozyme crystal using a conventional rotating anode X-ray generator. Based on these results we expect to obtain at a synchrotron diffraction images at a rate of ˜ 1 frame/s or a complete 3-dimensional data set from a single crystal in ˜ 2 min. In electron energy-loss spectroscopy (EELS), the CCD was used in a parallel detection mode which is similar to the mode array detectors are used in dispersive EXAFS. With a beam current corresponding to 3 × 10 9 electron/s on the detector, a series of 64 spectra were recorded on the CCD in a continuous sequence without interruption due to readout. The frame-to-frame pixel signal fluctuations had σ = 0.4% from which DQE = 0.4 was obtained, where the detector conversion efficiency was 2.6 CCD electrons/X-ray photon. These multiple frame series also showed the time-resolved modulation of the electron microscope optics by stray magnetic fields.

Nanosecond X-ray Photon Correlation Spectroscopy on Magnetic Skyrmions

DOE PAGES

Seaberg, M. H.; Holladay, B.; Lee, J. C. T.; ...

2017-08-09

We report an X-ray photon correlation spectroscopy method that exploits the recent development of the two-pulse mode at the Linac Coherent Light Source. By using coherent resonant X-ray magnetic scattering, we studied spontaneous fluctuations on nanosecond timescales in thin films of multilayered Fe/Gd that exhibit ordered stripe and skyrmion lattice phases. The correlation time of the fluctuations was found to differ between the skyrmion phase and near the stripe-skyrmion boundary. As a result, this technique will enable a significant new area of research on the study of equilibrium fluctuations in condensed matter.

Nanosecond X-ray Photon Correlation Spectroscopy on Magnetic Skyrmions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seaberg, M. H.; Holladay, B.; Lee, J. C. T.

We report an X-ray photon correlation spectroscopy method that exploits the recent development of the two-pulse mode at the Linac Coherent Light Source. By using coherent resonant X-ray magnetic scattering, we studied spontaneous fluctuations on nanosecond timescales in thin films of multilayered Fe/Gd that exhibit ordered stripe and skyrmion lattice phases. The correlation time of the fluctuations was found to differ between the skyrmion phase and near the stripe-skyrmion boundary. As a result, this technique will enable a significant new area of research on the study of equilibrium fluctuations in condensed matter.

Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

DOE PAGES

Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan; ...

2015-06-27

Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here in this study, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallizationmore » conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

PubMed Central

Uervirojnangkoorn, Monarin; Zeldin, Oliver B; Lyubimov, Artem Y; Hattne, Johan; Brewster, Aaron S; Sauter, Nicholas K; Brunger, Axel T; Weis, William I

2015-01-01

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited. DOI: http://dx.doi.org/10.7554/eLife.05421.001 PMID:25781634

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

DOE PAGES

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

2015-03-17

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. In conclusion, these developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

DOE PAGES

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

2015-03-17

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

Microfocus/Polycapillary-Optic Crystallographic X-Ray System

NASA Technical Reports Server (NTRS)

Joy, Marshall; Gubarev, Mikhail; Ciszak, Ewa

2005-01-01

A system that generates an intense, nearly collimated, nearly monochromatic, small-diameter x-ray beam has been developed for use in macromolecular crystallography. A conventional x-ray system for macromolecular crystallography includes a rotating-anode x-ray source, which is massive (.500 kg), large (approximately 2 by 2 by 1 m), and power-hungry (between 2 and 18 kW). In contrast, the present system generates a beam of the required brightness from a microfocus source, which is small and light enough to be mounted on a laboratory bench, and operates at a power level of only tens of watts. The figure schematically depicts the system as configured for observing x-ray diffraction from a macromolecular crystal. In addition to the microfocus x-ray source, the system includes a polycapillary optic . a monolithic block (typically a bundle of fused glass tubes) that contains thousands of straight or gently curved capillary channels, along which x-rays propagate with multiple reflections. This particular polycapillary optic is configured to act as a collimator; the x-ray beam that emerges from its output face consists of quasi-parallel subbeams with a small angular divergence and a diameter comparable to the size of a crystal to be studied. The gap between the microfocus x-ray source and the input face of the polycapillary optic is chosen consistently with the focal length of the polycapillary optic and the need to maximize the solid angle subtended by the optic in order to maximize the collimated x-ray flux. The spectrum from the source contains a significant component of Cu K (photon energy is 8.08 keV) radiation. The beam is monochromatized (for Cu K ) by a nickel filter 10 m thick. In a test, this system was operated at a power of 40 W (current of 897 A at an accelerating potential of 45 kV), with an anode x-ray spot size of 41+/-2 microns. Also tested, in order to provide a standard for comparison, was a commercial rotating-anode x-ray crystallographic system with a

Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis.

PubMed

Machado, Agnes Thiane Pereira; Fonseca, Emanuella Maria Barreto; Reis, Marcelo Augusto Dos; Saraiva, Antonio Marcos; Santos, Clelton Aparecido Dos; de Toledo, Marcelo Augusto Szymanski; Polikarpov, Igor; de Souza, Anete Pereira; Aparicio, Ricardo; Iulek, Jorge

2017-10-01

Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein. © 2017 Wiley Periodicals, Inc.

Trends in ultracool dwarf magnetism. I. X-ray suppression and radio enhancement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, P. K. G.; Berger, E.; Cook, B. A., E-mail: pwilliams@cfa.harvard.edu

2014-04-10

Although ultracool dwarfs (UCDs) are now known to generate and dissipate strong magnetic fields, a clear understanding of the underlying dynamo is still lacking. We have performed X-ray and radio observations of seven UCDs in a narrow range of spectral type (M6.5-M9.5) but spanning a wide range of projected rotational velocities (vsin i ≈ 3-40 km s{sup –1}). We have also analyzed unpublished archival Chandra observations of four additional objects. All of the newly observed targets are detected in the X-ray, while only one is detected in the radio, with the remainder having sensitive upper limits. We present a databasemore » of UCDs with both radio and X-ray measurements and consider the data in light of the so-called Güdel-Benz relation (GBR) between magnetic activity in these bands. Some UCDs have very bright radio emission and faint X-ray emission compared to what would be expected for rapid rotators, while others show the opposite behavior. We show that UCDs would still be radio-overluminous relative to the GBR even if their X-ray emission were at standard rapid-rotator 'saturation' levels. Recent results from Zeeman-Doppler imaging and geodynamo simulations suggest that rapidly rotating UCDs may harbor a bistable dynamo that supports either a stronger, axisymmetric magnetic field or a weaker, non-axisymmetric field. We suggest that the data can be explained in a scenario in which strong-field objects obey the GBR while weak-field objects are radio-overluminous and X-ray-underluminous, possibly because of a population of gyrosynchrotron-emitting coronal electrons that is continuously replenished by low-energy reconnection events.« less

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature.

PubMed

Ishigami, Izumi; Zatsepin, Nadia A; Hikita, Masahide; Conrad, Chelsie E; Nelson, Garrett; Coe, Jesse D; Basu, Shibom; Grant, Thomas D; Seaberg, Matthew H; Sierra, Raymond G; Hunter, Mark S; Fromme, Petra; Fromme, Raimund; Yeh, Syun-Ru; Rousseau, Denis L

2017-07-25

Cytochrome c oxidase (C c O), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine C c O (bC c O) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a 3 iron atom, with a bent Fe-C-O angle of ∼142°. In contrast, in the synchrotron structure, the Fe-CO bond is cleaved; CO relocates to a new site near Cu B , which, in turn, moves closer to the heme a 3 iron by ∼0.38 Å. Structural comparison reveals that ligand binding to the heme a 3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a 3 , thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.

Recent advances in racemic protein crystallography.

PubMed

Yan, Bingjia; Ye, Linzhi; Xu, Weiliang; Liu, Lei

2017-09-15

Solution of the three-dimensional structures of proteins is a critical step in deciphering the molecular mechanisms of their bioactivities. Among the many approaches for obtaining protein crystals, racemic protein crystallography has been developed as a unique method to solve the structures of an increasing number of proteins. Exploiting unnatural protein enantiomers in crystallization and resolution, racemic protein crystallography manifests two major advantages that are 1) to increase the success rate of protein crystallization, and 2) to obviate the phase problem in X-ray diffraction. The requirement of unnatural protein enantiomers in racemic protein crystallography necessitates chemical protein synthesis, which is hitherto accomplished through solid phase peptide synthesis and chemical ligation reactions. This review highlights the fundamental ideas of racemic protein crystallography and surveys the harvests in the field of racemic protein crystallography over the last five years from early 2012 to late 2016. Copyright © 2017. Published by Elsevier Ltd.

On the state of crystallography at the dawn of the electron microscopy revolution.

PubMed

Higgins, Matthew K; Lea, Susan M

2017-10-01

While protein crystallography has, for many years, been the most used method for structural analysis of macromolecular complexes, remarkable recent advances in high-resolution electron cryo-microscopy led to suggestions that 'the revolution will not be crystallised'. Here we highlight the current success rate, speed and ease of modern crystallographic structure determination and some recent triumphs of both 'classical' crystallography and the use of X-ray free electron lasers. We also outline fundamental differences between structure determination using X-ray crystallography and electron microscopy. We suggest that crystallography will continue to co-exist with electron microscopy as part of an integrated array of methods, allowing structural biologists to focus on fundamental biological questions rather than being constrained by the methods available. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Hard X-Ray Burst Detected From Caltech Plasma Jet Experiment Magnetic Reconnection Event

NASA Astrophysics Data System (ADS)

Marshall, Ryan S.; Bellan, Paul M.

2016-10-01

In the Caltech plasma jet experiment a 100 kA MHD driven jet becomes kink unstable leading to a Rayleigh-Taylor instability that quickly causes a magnetic reconnection event. Movies show that the Rayleigh-Taylor instability is simultaneous with voltage spikes across the electrodes that provide the current that drives the jet. Hard x-rays between 4 keV and 9 keV have now been observed using an x-ray scintillator detector mounted just outside of a kapton window on the vacuum chamber. Preliminary results indicate that the timing of the x-ray burst coincides with a voltage spike on the electrodes occurring in association with the Rayleigh-Taylor event. The x-ray signal accompanies the voltage spike and Rayleigh-Taylor event in approximately 50% of the shots. A possible explanation for why the x-ray signal is sometimes missing is that the magnetic reconnection event may be localized to a specific region of the plasma outside the line of sight of the scintillator. The x-ray signal has also been seen accompanying the voltage spike when no Rayleigh-Taylor is observed. This may be due to the interframe timing on the camera being longer than the very short duration of the Rayleigh-Taylor instability.

Minimalist coupled evolution model for stellar X-ray activity, rotation, mass loss, and magnetic field

NASA Astrophysics Data System (ADS)

Blackman, Eric G.; Owen, James E.

2016-05-01

Late-type main-sequence stars exhibit an X-ray to bolometric flux ratio that depends on {tilde{R}o}, the ratio of rotation period to convective turnover time, as {tilde{R}o}^{-ζ } with 2 ≤ ζ ≤ 3 for {tilde{R}o} > 0.13, but saturates with |ζ| < 0.2 for {tilde{R}o} < 0.13. Saturated stars are younger than unsaturated stars and show a broader spread of rotation rates and X-ray activity. The unsaturated stars have magnetic fields and rotation speeds that scale roughly with the square root of their age, though possibly flattening for stars older than the Sun. The connection between faster rotators, stronger fields, and higher activity has been established observationally, but a theory for the unified time-evolution of X-ray luminosity, rotation, magnetic field and mass loss that captures the above trends has been lacking. Here we derive a minimalist holistic framework for the time evolution of these quantities built from combining a Parker wind with new ingredients: (1) explicit sourcing of both the thermal energy launching the wind and the X-ray luminosity via dynamo produced magnetic fields; (2) explicit coupling of X-ray activity and mass-loss saturation to dynamo saturation (via magnetic helicity build-up and convection eddy shredding); (3) use of coronal equilibrium to determine how magnetic energy is divided into wind and X-ray contributions. For solar-type stars younger than the Sun, we infer conduction to be a subdominant power loss compared to X-rays and wind. For older stars, conduction is more important, possibly quenching the wind and reducing angular momentum loss. We focus on the time evolution for stars younger than the Sun, highlighting what is possible for further generalizations. Overall, the approach shows promise towards a unified explanation of all of the aforementioned observational trends.

Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination.

PubMed

Woods, Lucy A; Dolezal, Olan; Ren, Bin; Ryan, John H; Peat, Thomas S; Poulsen, Sally-Ann

2016-03-10

Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.

Electrostatic focal spot correction for x-ray tubes operating in strong magnetic fields.

PubMed

Lillaney, Prasheel; Shin, Mihye; Hinshaw, Waldo; Fahrig, Rebecca

2014-11-01

A close proximity hybrid x-ray/magnetic resonance (XMR) imaging system offers several critical advantages over current XMR system installations that have large separation distances (∼5 m) between the imaging fields of view. The two imaging systems can be placed in close proximity to each other if an x-ray tube can be designed to be immune to the magnetic fringe fields outside of the MR bore. One of the major obstacles to robust x-ray tube design is correcting for the effects of the MR fringe field on the x-ray tube focal spot. Any fringe field component orthogonal to the x-ray tube electric field leads to electron drift altering the path of the electron trajectories. The method proposed in this study to correct for the electron drift utilizes an external electric field in the direction of the drift. The electric field is created using two electrodes that are positioned adjacent to the cathode. These electrodes are biased with positive and negative potential differences relative to the cathode. The design of the focusing cup assembly is constrained primarily by the strength of the MR fringe field and high voltage standoff distances between the anode, cathode, and the bias electrodes. From these constraints, a focusing cup design suitable for the close proximity XMR system geometry is derived, and a finite element model of this focusing cup geometry is simulated to demonstrate efficacy. A Monte Carlo simulation is performed to determine any effects of the modified focusing cup design on the output x-ray energy spectrum. An orthogonal fringe field magnitude of 65 mT can be compensated for using bias voltages of +15 and -20 kV. These bias voltages are not sufficient to completely correct for larger orthogonal field magnitudes. Using active shielding coils in combination with the bias electrodes provides complete correction at an orthogonal field magnitude of 88.1 mT. Introducing small fields (<10 mT) parallel to the x-ray tube electric field in addition to the

Electrostatic focal spot correction for x-ray tubes operating in strong magnetic fields

PubMed Central

Lillaney, Prasheel; Shin, Mihye; Hinshaw, Waldo; Fahrig, Rebecca

2014-01-01

Purpose: A close proximity hybrid x-ray/magnetic resonance (XMR) imaging system offers several critical advantages over current XMR system installations that have large separation distances (∼5 m) between the imaging fields of view. The two imaging systems can be placed in close proximity to each other if an x-ray tube can be designed to be immune to the magnetic fringe fields outside of the MR bore. One of the major obstacles to robust x-ray tube design is correcting for the effects of the MR fringe field on the x-ray tube focal spot. Any fringe field component orthogonal to the x-ray tube electric field leads to electron drift altering the path of the electron trajectories. Methods: The method proposed in this study to correct for the electron drift utilizes an external electric field in the direction of the drift. The electric field is created using two electrodes that are positioned adjacent to the cathode. These electrodes are biased with positive and negative potential differences relative to the cathode. The design of the focusing cup assembly is constrained primarily by the strength of the MR fringe field and high voltage standoff distances between the anode, cathode, and the bias electrodes. From these constraints, a focusing cup design suitable for the close proximity XMR system geometry is derived, and a finite element model of this focusing cup geometry is simulated to demonstrate efficacy. A Monte Carlo simulation is performed to determine any effects of the modified focusing cup design on the output x-ray energy spectrum. Results: An orthogonal fringe field magnitude of 65 mT can be compensated for using bias voltages of +15 and −20 kV. These bias voltages are not sufficient to completely correct for larger orthogonal field magnitudes. Using active shielding coils in combination with the bias electrodes provides complete correction at an orthogonal field magnitude of 88.1 mT. Introducing small fields (<10 mT) parallel to the x-ray tube electric

The magnetic order of GdMn₂Ge₂ studied by neutron diffraction and x-ray resonant magnetic scattering.

PubMed

Granovsky, S A; Kreyssig, A; Doerr, M; Ritter, C; Dudzik, E; Feyerherm, R; Canfield, P C; Loewenhaupt, M

2010-06-09

The magnetic structure of GdMn₂Ge₂ (tetragonal I4/mmm) has been studied by hot neutron powder diffraction and x-ray resonant magnetic scattering techniques. These measurements, along with the results of bulk experiments, confirm the collinear ferrimagnetic structure with moment direction parallel to the c-axis below T(C) = 96 K and the collinear antiferromagnetic phase in the temperature region T(C) < T < T(N) = 365 K. In the antiferromagnetic phase, x-ray resonant magnetic scattering has been detected at Mn K and Gd L₂ absorption edges. The Gd contribution is a result of an induced Gd 5d electron polarization caused by the antiferromagnetic order of Mn-moments.

Magnetostatic focal spot correction for x-ray tubes operating in strong magnetic fields using iterative optimization

PubMed Central

Lillaney, Prasheel; Shin, Mihye; Conolly, Steven M.; Fahrig, Rebecca

2012-01-01

Purpose: Combining x-ray fluoroscopy and MR imaging systems for guidance of interventional procedures has become more commonplace. By designing an x-ray tube that is immune to the magnetic fields outside of the MR bore, the two systems can be placed in close proximity to each other. A major obstacle to robust x-ray tube design is correcting for the effects of the magnetic fields on the x-ray tube focal spot. A potential solution is to design active shielding that locally cancels the magnetic fields near the focal spot. Methods: An iterative optimization algorithm is implemented to design resistive active shielding coils that will be placed outside the x-ray tube insert. The optimization procedure attempts to minimize the power consumption of the shielding coils while satisfying magnetic field homogeneity constraints. The algorithm is composed of a linear programming step and a nonlinear programming step that are interleaved with each other. The coil results are verified using a finite element space charge simulation of the electron beam inside the x-ray tube. To alleviate heating concerns an optimized coil solution is derived that includes a neodymium permanent magnet. Any demagnetization of the permanent magnet is calculated prior to solving for the optimized coils. The temperature dynamics of the coil solutions are calculated using a lumped parameter model, which is used to estimate operation times of the coils before temperature failure. Results: For a magnetic field strength of 88 mT, the algorithm solves for coils that consume 588 A/cm2. This specific coil geometry can operate for 15 min continuously before reaching temperature failure. By including a neodymium magnet in the design the current density drops to 337 A/cm2, which increases the operation time to 59 min. Space charge simulations verify that the coil designs are effective, but for oblique x-ray tube geometries there is still distortion of the focal spot shape along with deflections of approximately

Metalloprotein Crystallography: More than a Structure.

PubMed

Bowman, Sarah E J; Bridwell-Rabb, Jennifer; Drennan, Catherine L

2016-04-19

Metal ions and metallocofactors play important roles in a broad range of biochemical reactions. Accordingly, it has been estimated that as much as 25-50% of the proteome uses transition metal ions to carry out a variety of essential functions. The metal ions incorporated within metalloproteins fulfill functional roles based on chemical properties, the diversity of which arises as transition metals can adopt different redox states and geometries, dictated by the identity of the metal and the protein environment. The coupling of a metal ion with an organic framework in metallocofactors, such as heme and cobalamin, further expands the chemical functionality of metals in biology. The three-dimensional visualization of metal ions and complex metallocofactors within a protein scaffold is often a starting point for enzymology, highlighting the importance of structural characterization of metalloproteins. Metalloprotein crystallography, however, presents a number of implicit challenges including correctly incorporating the relevant metal or metallocofactor, maintaining the proper environment for the protein to be purified and crystallized (including providing anaerobic, cold, or aphotic environments), and being mindful of the possibility of X-ray induced damage to the proteins or incorporated metal ions. Nevertheless, the incorporated metals or metallocofactors also present unique advantages in metalloprotein crystallography. The significant resonance that metals undergo with X-ray photons at wavelengths used for protein crystallography and the rich electronic properties of metals, which provide intense and spectroscopically unique signatures, allow a metalloprotein crystallographer to use anomalous dispersion to determine phases for structure solution and to use simultaneous or parallel spectroscopic techniques on single crystals. These properties, coupled with the improved brightness of beamlines, the ability to tune the wavelength of the X-ray beam, the availability of

Performance of a static-anode/flat-panel x-ray fluoroscopy system in a diagnostic strength magnetic field: A truly hybrid x-ray/MR imaging system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fahrig, R.; Wen, Z.; Ganguly, A.

2005-06-15

Minimally invasive procedures are increasing in variety and frequency, facilitated by advances in imaging technology. Our hybrid imaging system (GE Apollo{sup TM} flat panel, custom Brand x-ray static anode x-ray tube, GE Lunar high-frequency power supply and 0.5 T Signa SP{sup TM}) provides both x-ray and MR imaging capability to guide complex procedures without requiring motion of the patient between two distant gantries. The performance of the x-ray tube in this closely integrated system was evaluated by modeling and measuring both the response of the filament to an externally applied field and the behavior of the electron beam for fieldmore » strengths and geometries of interest. The performance of the detector was assessed by measuring the slanted-edge modulation transfer function (MTF) and when placed at zero field and at 0.5 T. Measured resonant frequencies of filaments can be approximated using a modified vibrating beam model, and were at frequencies well below the 25 kHz frequency of our generator for our filament geometry. The amplitude of vibration was not sufficient to cause shorting of the filament during operation within the magnetic field. A simple model of electrons in uniform electric and magnetic fields can be used to estimate the deflection of the electron beam on the anode for the fields of interest between 0.2 and 0.5 T. The MTF measured at the detector and the DQE showed no significant difference inside and outside of the magnetic field. With the proper modifications, an x-ray system can be fully integrated with a MR system, with minimal loss of image quality. Any x-ray tube can be assessed for compatibility when placed at a particular location within the field using the models. We have also concluded that a-Si electronics are robust against magnetic fields. Detailed knowledge of the x-ray system installation is required to provide estimates of system operation.« less

Performance of a static-anode/flat-panel x-ray fluoroscopy system in a diagnostic strength magnetic field: a truly hybrid x-ray/MR imaging system.

PubMed

Fahrig, R; Wen, Z; Ganguly, A; DeCrescenzo, G; Rowlands, J A; Stevens, G M; Saunders, R F; Pelc, N J

2005-06-01

Minimally invasive procedures are increasing in variety and frequency, facilitated by advances in imaging technology. Our hybrid imaging system (GE Apollo flat panel, custom Brand x-ray static anode x-ray tube, GE Lunar high-frequency power supply and 0.5 T Signa SP) provides both x-ray and MR imaging capability to guide complex procedures without requiring motion of the patient between two distant gantries. The performance of the x-ray tube in this closely integrated system was evaluated by modeling and measuring both the response of the filament to an externally applied field and the behavior of the electron beam for field strengths and geometries of interest. The performance of the detector was assessed by measuring the slanted-edge modulation transfer function (MTF) and when placed at zero field and at 0.5 T. Measured resonant frequencies of filaments can be approximated using a modified vibrating beam model, and were at frequencies well below the 25 kHz frequency of our generator for our filament geometry. The amplitude of vibration was not sufficient to cause shorting of the filament during operation within the magnetic field. A simple model of electrons in uniform electric and magnetic fields can be used to estimate the deflection of the electron beam on the anode for the fields of interest between 0.2 and 0.5 T. The MTF measured at the detector and the DQE showed no significant difference inside and outside of the magnetic field. With the proper modifications, an x-ray system can be fully integrated with a MR system, with minimal loss of image quality. Any x-ray tube can be assessed for compatibility when placed at a particular location within the field using the models. We have also concluded that a-Si electronics are robust against magnetic fields. Detailed knowledge of the x-ray system installation is required to provide estimates of system operation.

A full-field transmission x-ray microscope for time-resolved imaging of magnetic nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ewald, J.; Nisius, T.; Abbati, G.

Sub-nanosecond magnetization dynamics of small permalloy (Ni{sub 80}Fe{sub 20}) elements has been investigated with a new full-field transmission microscope at the soft X-ray beamline P04 of the high brilliance synchrotron radiation source PETRA III. The soft X-ray microscope generates a flat-top illumination field of 20 μm diameter using a grating condenser. A tilted nanostructured magnetic sample can be excited by a picosecond electric current pulse via a coplanar waveguide. The transmitted light of the sample plane is directly imaged by a micro zone plate with < 65 nm resolution onto a 2D gateable X-ray detector to select one particular bunch in themore » storage ring that probes the time evolution of the dynamic information successively via XMCD spectromicroscopy in a pump-probe scheme. In the experiments it was possible to generate a homogeneously magnetized state in patterned magnetic layers by a strong magnetic Oersted field pulse of 200 ps duration and directly observe the recovery to the initial flux-closure vortex patterns.« less

Analysis of RNA structure using small-angle X-ray scattering

PubMed Central

Cantara, William A.; Olson, Erik D.; Musier-Forsyth, Karin

2016-01-01

In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist. Recently, small-angle X-ray scattering (SAXS) has been increasingly employed to characterize the 3D structures of RNAs and RNA-protein complexes. SAXS is capable of providing low-resolution tertiary structure information under physiological conditions and with less intensive sample preparation and data analysis requirements than XRC, NMR and cryo-EM. In this article, we describe best practices involved in the process of RNA and RNA-protein sample preparation, SAXS data collection, data analysis, and structural model building. PMID:27777026

Johann Deisenhofer, Crystallography, and Proteins

Science.gov Websites

research using X-ray crystallography to elucidate for the first time the three-dimensional structure of a large membrane-bound protein molecule. This structure helped explain the process of photosynthesis, by a protein structure determination that relied on complementary features of two different beam lines

Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sutton, Kristin A.; Black, Paul J.; Mercer, Kermit R.

2013-12-01

Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage, to confirm a multi-track radiation-damage process and to develop a model of that process. Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV–visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5–0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. Themore » observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.« less

Direct detection of x-rays for protein crystallography employing a thick, large area CCD

DOEpatents

Atac, Muzaffer; McKay, Timothy

1999-01-01

An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography.

PubMed

Hamada, Kozo; Miyatake, Hideyuki; Terauchi, Akiko; Mikoshiba, Katsuhiko

2017-05-02

The inositol 1,4,5-trisphosphate (IP 3 ) receptor (IP 3 R) is an IP 3 -gated ion channel that releases calcium ions (Ca 2+ ) from the endoplasmic reticulum. The IP 3 -binding sites in the large cytosolic domain are distant from the Ca 2+ conducting pore, and the allosteric mechanism of how IP 3 opens the Ca 2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP 3 R in the absence and presence of IP 3 Analyses of two distinct space group crystals uncovered an IP 3 -dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP 3 R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP 3 -controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP 3 binding to the Ca 2+ channel.

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography

PubMed Central

Hamada, Kozo; Miyatake, Hideyuki; Terauchi, Akiko; Mikoshiba, Katsuhiko

2017-01-01

The inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) is an IP3-gated ion channel that releases calcium ions (Ca2+) from the endoplasmic reticulum. The IP3-binding sites in the large cytosolic domain are distant from the Ca2+ conducting pore, and the allosteric mechanism of how IP3 opens the Ca2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP3R in the absence and presence of IP3. Analyses of two distinct space group crystals uncovered an IP3-dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP3R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP3-controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP3 binding to the Ca2+ channel. PMID:28416699

Macromolecular crystallography beamline X25 at the NSLS

PubMed Central

Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E.

2014-01-01

Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community. PMID:24763654

How cryo‐electron microscopy and X‐ray crystallography complement each other

PubMed Central

Wang, Jia‐Wei

2016-01-01

Abstract With the ability to resolve structures of macromolecules at atomic resolution, X‐ray crystallography has been the most powerful tool in modern structural biology. At the same time, recent technical improvements have triggered a resolution revolution in the single particle cryo‐EM method. While the two methods are different in many respects, from sample preparation to structure determination, they both have the power to solve macromolecular structures at atomic resolution. It is important to understand the unique advantages and caveats of the two methods in solving structures and to appreciate the complementary nature of the two methods in structural biology. In this review we provide some examples, and discuss how X‐ray crystallography and cryo‐EM can be combined in deciphering structures of macromolecules for our full understanding of their biological mechanisms. PMID:27543495

Hinode observations and 3D magnetic structure of an X-ray bright point

NASA Astrophysics Data System (ADS)

Alexander, C. E.; Del Zanna, G.; Maclean, R. C.

2011-02-01

Aims: We present complete Hinode Solar Optical Telescope (SOT), X-Ray Telescope (XRT)and EUV Imaging Spectrometer (EIS) observations of an X-ray bright point (XBP) observed on the 10, 11 of October 2007 over its entire lifetime (~12 h). We aim to show how the measured plasma parameters of the XBP change over time and also what kind of similarities the X-ray emission has to a potential magnetic field model. Methods: Information from all three instruments on-board Hinode was used to study its entire evolution. XRT data was used to investigate the structure of the bright point and to measure the X-ray emission. The EIS instrument was used to measure various plasma parameters over the entire lifetime of the XBP. Lastly, the SOT was used to measure the magnetic field strength and provide a basis for potential field extrapolations of the photospheric fields to be made. These were performed and then compared to the observed coronal features. Results: The XBP measured ~15´´ in size and was found to be formed directly above an area of merging and cancelling magnetic flux on the photosphere. A good correlation between the rate of X-ray emission and decrease in total magnetic flux was found. The magnetic fragments of the XBP were found to vary on very short timescales (minutes), however the global quasi-bipolar structure remained throughout the lifetime of the XBP. The potential field extrapolations were a good visual fit to the observed coronal loops in most cases, meaning that the magnetic field was not too far from a potential state. Electron density measurements were obtained using a line ratio of Fe XII and the average density was found to be 4.95 × 109 cm-3 with the volumetric plasma filling factor calculated to have an average value of 0.04. Emission measure loci plots were then used to infer a steady temperature of log Te [ K] ~ 6.1. The calculated Fe XII Doppler shifts show velocity changes in and around the bright point of ±15 km s-1 which are observed to change

Conceptual design of novel IP-conveyor-belt Weissenberg-mode data-collection system with multi-readers for macromolecular crystallography. A comparison between Galaxy and Super Galaxy.

PubMed

Sakabe, N; Sakabe, K; Sasaki, K

2004-01-01

Galaxy is a Weissenberg-type high-speed high-resolution and highly accurate fully automatic data-collection system using two cylindrical IP-cassettes each with a radius of 400 mm and a width of 450 mm. It was originally developed for static three-dimensional analysis using X-ray diffraction and was installed on bending-magnet beamline BL6C at the Photon Factory. It was found, however, that Galaxy was also very useful for time-resolved protein crystallography on a time scale of minutes. This has prompted us to design a new IP-conveyor-belt Weissenberg-mode data-collection system called Super Galaxy for time-resolved crystallography with improved time and crystallographic resolution over that achievable with Galaxy. Super Galaxy was designed with a half-cylinder-shaped cassette with a radius of 420 mm and a width of 690 mm. Using 1.0 A incident X-rays, these dimensions correspond to a maximum resolutions of 0.71 A in the vertical direction and 1.58 A in the horizontal. Upper and lower screens can be used to set the frame size of the recorded image. This function is useful not only to reduce the frame exchange time but also to save disk space on the data server. The use of an IP-conveyor-belt and many IP-readers make Super Galaxy well suited for time-resolved, monochromatic X-ray crystallography at a very intense third-generation SR beamline. Here, Galaxy and a conceptual design for Super Galaxy are described, and their suitability for use as data-collection systems for macromolecular time-resolved monochromatic X-ray crystallography are compared.

Onset of the Magnetic Explosion in Solar Polar Coronal X-Ray Jets

NASA Astrophysics Data System (ADS)

Moore, Ronald L.; Sterling, Alphonse C.; Panesar, Navdeep

2017-08-01

We examine the onset of the driving magnetic explosion in 15 random polar coronal X-ray jets. Each eruption is observed in a coronal X-ray movie from Hinode and in a coronal EUV movie from Solar Dynamics Observatory. Contrary to the Sterling et al (2015, Nature, 523, 437) scenario for minifilament eruptions that drive polar coronal jets, these observations indicate: (1) in most polar coronal jets (a) the runaway internal tether-cutting reconnection under the erupting minifilament flux rope starts after the spire-producing breakout reconnection starts, not before it, and (b) aleady at eruption onset, there is a current sheet between the explosive closed magnetic field and ambient open field; and (2) the minifilament-eruption magnetic explosion often starts with the breakout reconnection of the outside of the magnetic arcade that carries the minifilament in its core. On the other hand, the diversity of the observed sequences of occurrence of events in the jet eruptions gives further credence to the Sterlling et al (2015, Nature, 523, 437) idea that the magnetic explosions that make a polar X-ray jet work the same way as the much larger magnetic explosions that make and flare and CME. We point out that this idea, and recent observations indicating that magnetic flux cancelation is the fundamental process that builds the field in and around pre-jet minifilaments and triggers the jet-driving magnetic explosion, together imply that usually flux cancelation inside the arcade that explodes in a flare/CME eruption is the fundamental process that builds the explosive field and triggers the explosion.This work was funded by the Heliophysics Division of NASA's Science Mission Directorate through its Living With a Star Targeted Research and Technology Program, its Heliophsyics Guest Investigators Program, and the Hinode Project.

Time-Resolved X-Ray Magnetic Circular Dichroism - A Selective Probe of Magnetization Dynamics on Nanosecond Timescales

NASA Astrophysics Data System (ADS)

Pizzini, Stefania; Vogel, Jan; Bonfim, Marlio; Fontaine, Alain

Many synchrotron radiation techniques have been developed in the last 15 years for studying the magnetic properties of thin-film materials. The most attractive properties of synchrotron radiation are its energy tunability and its time structure. The first property allows measurements in resonant conditions at an absorption edge of each of the magnetic elements constituting the probed sample, and the latter allows time-resolved measurements on subnanosecond timescales. In this review, we introduce some of the synchrotron-based techniques used for magnetic investigations. We then describe in detail X-ray magnetic circular dichroism (XMCD) and how time-resolved XMCD studies can be carried out in the pump-probe mode. Finally, we illustrate some applications to magnetization reversal dynamics in spin valves and tunnel junctions, using fast magnetic field pulses applied along the easy magnetization axis of the samples. Thanks to the element-selectivity of X-ray absorption spectroscopy, the magnetization dynamics of the soft (Permalloy) and the hard (cobalt) layers can be studied independently. In the case of spin valves, this allowed us to show that two magnetic layers that are strongly coupled in a static regime can become uncoupled on nanosecond timescales.Present address: Universidade Federal do Paraná, Centro Politécnico CP 19011, Curitiba - PR CEP 81531-990, Brazil

Radio emission from the X-ray pulsar Her X-1: a jet launched by a strong magnetic field neutron star?

NASA Astrophysics Data System (ADS)

van den Eijnden, J.; Degenaar, N.; Russell, T. D.; Miller-Jones, J. C. A.; Wijnands, R.; Miller, J. M.; King, A. L.; Rupen, M. P.

2018-01-01

Her X-1 is an accreting neutron star (NS) in an intermediate-mass X-ray binary. Like low-mass X-ray binaries (LMXBs), it accretes via Roche lobe overflow, but similar to many high-mass X-ray binaries containing a NS; Her X-1 has a strong magnetic field and slow spin. Here, we present the discovery of radio emission from Her X-1 with the Very Large Array. During the radio observation, the central X-ray source was partially obscured by a warped disc. We measure a radio flux density of 38.7 ± 4.8 μJy at 9 GHz but cannot constrain the spectral shape. We discuss possible origins of the radio emission, and conclude that coherent emission, a stellar wind, shocks and a propeller outflow are all unlikely explanations. A jet, as seen in LMXBs, is consistent with the observed radio properties. We consider the implications of the presence of a jet in Her X-1 on jet formation mechanisms and on the launching of jets by NSs with strong magnetic fields.

Perpendicular magnetic anisotropy in amorphous NdxCo1 -x thin films studied by x-ray magnetic circular dichroism

NASA Astrophysics Data System (ADS)

Cid, R.; Alameda, J. M.; Valvidares, S. M.; Cezar, J. C.; Bencok, P.; Brookes, N. B.; Díaz, J.

2017-06-01

The origin of perpendicular magnetic anisotropy (PMA) in amorphous NdxCo1 -x thin films is investigated using x-ray magnetic circular dichroism (XMCD) spectroscopy at the Co L2 ,3 and Nd M4 ,5 edges. The magnetic orbital and spin moments of the 3 d cobalt and 4 f neodymium electrons were measured as a function of the magnetic field orientation, neodymium concentration, and temperature. In all the studied samples, the magnetic anisotropy of the neodymium subnetwork is always oriented perpendicular to the plane, whereas the anisotropy of the orbital moment of cobalt is in the basal plane. The ratio Lz/Sz of the neodymium 4 f orbitals changes with the sample orientation angle, being higher and closer to the atomic expected value at normal orientation and smaller at grazing angles. This result is well explained by assuming that the 4 f orbital is distorted by the effect of an anisotropic crystal field when it is magnetized along its hard axis, clearly indicating that the 4 f states are not rotationally invariant. The magnetic anisotropy energy associated to the neodymium subnetwork should be proportional to this distortion, which we demonstrate is accessible by applying the XMCD sum rules for the spin and intensity at the Nd M4 ,5 edges. The analysis unveils a significant portion of neodymium atoms magnetically uncoupled to cobalt, i.e., paramagnetic, confirming the inhomogeneity of the films and the presence of a highly disordered neodymium rich phase already detected by extended x-ray-absorption fine structure (EXAFS) spectroscopy. The presence of these inhomogeneities is inherent to the evaporation preparation method when the chosen concentration in the alloy is far from its eutectic concentrations. An interesting consequence of the particular way in which cobalt and neodymium segregates in this system is the enhancement of the cobalt spin moment which reaches 1.95 μB in the sample with the largest segregation.

Closed bore XMR (CBXMR) systems for aortic valve replacement: active magnetic shielding of x-ray tubes.

PubMed

Bracken, John A; DeCrescenzo, Giovanni; Komljenovic, Philip; Lillaney, Prasheel V; Fahrig, Rebecca; Rowlands, J A

2009-05-01

Hybrid closed bore x-ray/MRI systems are being developed to improve the safety and efficacy of percutaneous aortic valve replacement procedures by harnessing the complementary strengths of the x-ray and MRI modalities in a single interventional suite without requiring patient transfer between two rooms. These systems are composed of an x-ray C-arm in close proximity (approximately 1 m) to an MRI scanner. The MRI magnetic fringe field can cause the electron beam in the x-ray tube to deflect. The deflection causes the x-ray field of view to shift position on the detector receptacle. This could result in unnecessary radiation exposure to the patient and the staff in the cardiac catheterization laboratory. Therefore, the electron beam deflection must be corrected. The authors developed an active magnetic shielding system that can correct for electron beam deflection to within an accuracy of 5% without truncating the field of view or increasing exposure to the patient. This system was able to automatically adjust to different field strengths as the external magnetic field acting on the x-ray tube was changed. Although a small torque was observed on the shielding coils of the active shielding system when they were placed in a magnetic field, this torque will not impact their performance if they are securely mounted on the x-ray tube and the C-arm. The heating of the coils of the shielding system for use in the clinic caused by electric current was found to be slow enough not to require a dedicated cooling system for one percutaneous aortic valve replacement procedure. However, a cooling system will be required if multiple procedures are performed in one session.

Low Altitude Solar Magnetic Reconnection, Type III Solar Radio Bursts, and X-ray Emissions.

PubMed

Cairns, I H; Lobzin, V V; Donea, A; Tingay, S J; McCauley, P I; Oberoi, D; Duffin, R T; Reiner, M J; Hurley-Walker, N; Kudryavtseva, N A; Melrose, D B; Harding, J C; Bernardi, G; Bowman, J D; Cappallo, R J; Corey, B E; Deshpande, A; Emrich, D; Goeke, R; Hazelton, B J; Johnston-Hollitt, M; Kaplan, D L; Kasper, J C; Kratzenberg, E; Lonsdale, C J; Lynch, M J; McWhirter, S R; Mitchell, D A; Morales, M F; Morgan, E; Ord, S M; Prabu, T; Roshi, A; Shankar, N Udaya; Srivani, K S; Subrahmanyan, R; Wayth, R B; Waterson, M; Webster, R L; Whitney, A R; Williams, A; Williams, C L

2018-01-26

Type III solar radio bursts are the Sun's most intense and frequent nonthermal radio emissions. They involve two critical problems in astrophysics, plasma physics, and space physics: how collective processes produce nonthermal radiation and how magnetic reconnection occurs and changes magnetic energy into kinetic energy. Here magnetic reconnection events are identified definitively in Solar Dynamics Observatory UV-EUV data, with strong upward and downward pairs of jets, current sheets, and cusp-like geometries on top of time-varying magnetic loops, and strong outflows along pairs of open magnetic field lines. Type III bursts imaged by the Murchison Widefield Array and detected by the Learmonth radiospectrograph and STEREO B spacecraft are demonstrated to be in very good temporal and spatial coincidence with specific reconnection events and with bursts of X-rays detected by the RHESSI spacecraft. The reconnection sites are low, near heights of 5-10 Mm. These images and event timings provide the long-desired direct evidence that semi-relativistic electrons energized in magnetic reconnection regions produce type III radio bursts. Not all the observed reconnection events produce X-ray events or coronal or interplanetary type III bursts; thus different special conditions exist for electrons leaving reconnection regions to produce observable radio, EUV, UV, and X-ray bursts.

Prospects for x-ray polarimetry measurements of magnetic fields in magnetized liner inertial fusion plasmas.

PubMed

Lynn, Alan G; Gilmore, Mark

2014-11-01

Magnetized Liner Inertial Fusion (MagLIF) experiments, where a metal liner is imploded to compress a magnetized seed plasma may generate peak magnetic fields ∼10(4) T (100 Megagauss) over small volumes (∼10(-10)m(3)) at high plasma densities (∼10(28)m(-3)) on 100 ns time scales. Such conditions are extremely challenging to diagnose. We discuss the possibility of, and issues involved in, using polarimetry techniques at x-ray wavelengths to measure magnetic fields under these extreme conditions.

Hard X-ray polarizer to enable simultaneous three-dimensional nanoscale imaging of magnetic structure and lattice strain

DOE PAGES

Logan, Jonathan; Harder, Ross; Li, Luxi; ...

2016-01-01

Recent progress in the development of dichroic Bragg coherent diffractive imaging, a new technique for simultaneous three-dimensional imaging of strain and magnetization at the nanoscale, is reported. This progress includes the installation of a diamond X-ray phase retarder at beamline 34-ID-C of the Advanced Photon Source. Here, the performance of the phase retarder for tuning X-ray polarization is demonstrated with temperature-dependent X-ray magnetic circular dichroism measurements on a gadolinium foil in transmission and on a Gd 5Si 2Ge 2crystal in diffraction geometry with a partially coherent, focused X-ray beam. Feasibility tests for dichroic Bragg coherent diffractive imaging are presented. Thesemore » tests include (1) using conventional Bragg coherent diffractive imaging to determine whether the phase retarder introduces aberrations using a nonmagnetic gold nanocrystal as a control sample, and (2) collecting coherent diffraction patterns of a magnetic Gd 5Si 2Ge 2nanocrystal with left- and right-circularly polarized X-rays. Future applications of dichroic Bragg coherent diffractive imaging for the correlation of strain and lattice defects with magnetic ordering and inhomogeneities are considered.« less

X-ray Spectroscopy and Magnetism in Mineralogy

NASA Astrophysics Data System (ADS)

Sainctavit, Philippe; Brice-Profeta, Sandrine; Gaudry, Emilie; Letard, Isabelle; Arrio, Marie-Anne

The objective of this paper is to present the kind of information that can be gained in the field of mineralogy from the use of x-ray magnetic spectroscopies. We review some of the questions that are unsettled and that could benefit from an interdisciplinary approach where magnetism, spectroscopy and mineralogy could be mixed. Most of the attention is focused on iron and some other 3d transition elements. The mineralogy of planetary cores and its relation with known meteorites are exemplified. The various oxide phases in the mantle and the nature of iron in these phases is also underlined. The presence of transition elements in insulating minerals and its relation with macroscopic properties such as the color of gemstones are reviewed. Finally an introduction to paleomagnetism is given with a special attention to nanomaghemites.

Deformable complex network for refining low-resolution X-ray structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chong; Wang, Qinghua; Ma, Jianpeng, E-mail: jpma@bcm.edu

2015-10-27

A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography. In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint withmore » the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.« less

An X-ray Pulsar with a Superstrong Magnetic Field in the Soft Gamma-Ray Repeater SGR1806-20

NASA Technical Reports Server (NTRS)

Kouveliotou, C.; Dieters, S.; Strohmayer, T.; vanParadijs, J.; Fishman, G. J.; Meegan, C. A.; Hurley, K.; Kommers, J.; Smith, I.; Frail, D.;

Anisotropic spin-density distribution and magnetic anisotropy of strained La1-xSrxMnO3 thin films: angle-dependent x-ray magnetic circular dichroism

NASA Astrophysics Data System (ADS)

Shibata, Goro; Kitamura, Miho; Minohara, Makoto; Yoshimatsu, Kohei; Kadono, Toshiharu; Ishigami, Keisuke; Harano, Takayuki; Takahashi, Yukio; Sakamoto, Shoya; Nonaka, Yosuke; Ikeda, Keisuke; Chi, Zhendong; Furuse, Mitsuho; Fuchino, Shuichiro; Okano, Makoto; Fujihira, Jun-ichi; Uchida, Akira; Watanabe, Kazunori; Fujihira, Hideyuki; Fujihira, Seiichi; Tanaka, Arata; Kumigashira, Hiroshi; Koide, Tsuneharu; Fujimori, Atsushi

2018-01-01

Magnetic anisotropies of ferromagnetic thin films are induced by epitaxial strain from the substrate via strain-induced anisotropy in the orbital magnetic moment and that in the spatial distribution of spin-polarized electrons. However, the preferential orbital occupation in ferromagnetic metallic La1-xSrxMnO3 (LSMO) thin films studied by x-ray linear dichroism (XLD) has always been found out-of-plane for both tensile and compressive epitaxial strain and hence irrespective of the magnetic anisotropy. In order to resolve this mystery, we directly probed the preferential orbital occupation of spin-polarized electrons in LSMO thin films under strain by angle-dependent x-ray magnetic circular dichroism (XMCD). Anisotropy of the spin-density distribution was found to be in-plane for the tensile strain and out-of-plane for the compressive strain, consistent with the observed magnetic anisotropy. The ubiquitous out-of-plane preferential orbital occupation seen by XLD is attributed to the occupation of both spin-up and spin-down out-of-plane orbitals in the surface magnetic dead layer.

Studies on the effect of the axial magnetic field on the x-ray bremsstrahlung in a 2.45 GHz permanent magnet microwave ion source.

PubMed

Kumar, Narender; Rodrigues, G; Lakshmy, P S; Baskaran, R; Mathur, Y; Ahuja, R; Kanjilal, D

2014-02-01

A compact microwave ion source has been designed and developed for operation at a frequency of 2.45 GHz. The axial magnetic field is based on two permanent magnet rings, operating in the "off-resonance" mode and is tunable by moving the permanent magnets. In order to understand the electron energy distribution function, x-ray bremsstrahlung has been measured in the axial direction. Simulation studies on the x-ray bremsstrahlung have been carried out to compare with the experimental results. The effect of the axial magnetic field with respect to the microwave launching position and the position of the extraction electrode on the x-ray bremsstrahlung have been studied.

Magnetic properties of strained multiferroic CoC r2O4 : A soft x-ray study

NASA Astrophysics Data System (ADS)

Windsor, Y. W.; Piamonteze, C.; Ramakrishnan, M.; Scaramucci, A.; Rettig, L.; Huever, J. A.; Bothschafter, E. M.; Bingham, N. S.; Alberca, A.; Avula, S. R. V.; Noheda, B.; Staub, U.

2017-06-01

Using resonant soft x-ray techniques we follow the magnetic behavior of a strained epitaxial film of CoC r2O4 , a type-II multiferroic. The film is [110] oriented, such that both the ferroelectric and ferromagnetic moments can coexist in-plane. X-ray magnetic circular dichroism (XMCD) is used in scattering and in transmission modes to probe the magnetization of Co and Cr separately. The transmission measurements utilized x-ray excited optical luminescence from the substrate. Resonant soft x-ray diffraction (RXD) was used to study the magnetic order of the low temperature phase. The XMCD signals of Co and Cr appear at the same ordering temperature TC≈90 K , and are always opposite in sign. The coercive field of the Co and of Cr moments is the same, and is approximately two orders of magnitude higher than in bulk. Through sum rules analysis an enlarged C o2 + orbital moment (mL) is found, which can explain this hardening. The RXD signal of the (q q 0) reflection appears below TS, the same ordering temperature as the conical magnetic structure in bulk, indicating that this phase remains multiferroic under strain. To describe the azimuthal dependence of this reflection, a slight modification is required to the spin model proposed by the conventional Lyons-Kaplan-Dwight-Menyuk theory for magnetic spinels.

Development of Position-Sensitive Magnetic Calorimeters for X-Ray Astronomy

NASA Technical Reports Server (NTRS)

Bandler, SImon; Stevenson, Thomas; Hsieh, Wen-Ting

2011-01-01

Metallic magnetic calorimeters (MMC) are one of the most promising devices to provide very high energy resolution needed for future astronomical x-ray spectroscopy. MMC detectors can be built to large detector arrays having thousands of pixels. Position-sensitive magnetic (PoSM) microcalorimeters consist of multiple absorbers thermally coupled to one magnetic micro calorimeter. Each absorber element has a different thermal coupling to the MMC, resulting in a distribution of different pulse shapes and enabling position discrimination between the absorber elements. PoSMs therefore achieve the large focal plane area with fewer number of readout channels without compromising spatial sampling. Excellent performance of PoSMs was achieved by optimizing the designs of key parameters such as the thermal conductance among the absorbers, magnetic sensor, and heat sink, as well as the absorber heat capacities. Micro fab ri - cation techniques were developed to construct four-absorber PoSMs, in which each absorber consists of a two-layer composite of bismuth and gold. The energy resolution (FWHM full width at half maximum) was measured to be better than 5 eV at 6 keV x-rays for all four absorbers. Position determination was demonstrated with pulse-shape discrimination, as well as with pulse rise time. X-ray microcalorimeters are usually designed to thermalize as quickly as possible to avoid degradation in energy resolution from position dependence to the pulse shapes. Each pixel consists of an absorber and a temperature sensor, both decoupled from the cold bath through a weak thermal link. Each pixel requires a separate readout channel; for instance, with a SQUID (superconducting quantum interference device). For future astronomy missions where thousands to millions of resolution elements are required, having an individual SQUID readout channel for each pixel becomes difficult. One route to attaining these goals is a position-sensitive detector in which a large continuous or

EVOLUTION OF INTERMEDIATE-MASS X-RAY BINARIES DRIVEN BY THE MAGNETIC BRAKING OF AP/BP STARS. I. ULTRACOMPACT X-RAY BINARIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Wen-Cong; Podsiadlowski, Philipp, E-mail: chenwc@pku.edu.cn

2016-10-20

It is generally believed that ultracompact X-ray binaries (UCXBs) evolved from binaries consisting of a neutron star accreting from a low-mass white dwarf (WD) or helium star where mass transfer is driven by gravitational radiation. However, the standard WD evolutionary channel cannot produce the relatively long-period (40–60 minutes) UCXBs with a high time-averaged mass-transfer rate. In this work, we explore an alternative evolutionary route toward UCXBs, where the companions evolve from intermediate-mass Ap/Bp stars with an anomalously strong magnetic field (100–10,000 G). Including the magnetic braking caused by the coupling between the magnetic field and an irradiation-driven wind induced bymore » the X-ray flux from the accreting component, we show that intermediate-mass X-ray binaries (IMXBs) can evolve into UCXBs. Using the MESA code, we have calculated evolutionary sequences for a large number of IMXBs. The simulated results indicate that, for a small wind-driving efficiency f = 10{sup −5}, the anomalous magnetic braking can drive IMXBs to an ultra-short period of 11 minutes. Comparing our simulated results with the observed parameters of 15 identified UCXBs, the anomalous magnetic braking evolutionary channel can account for the formation of seven and eight sources with f = 10{sup −3}, and 10{sup −5}, respectively. In particular, a relatively large value of f can fit three of the long-period, persistent sources with a high mass-transfer rate. Though the proportion of Ap/Bp stars in intermediate-mass stars is only 5%, the lifetime of the UCXB phase is ≳2 Gyr, producing a relatively high number of observable systems, making this an alternative evolutionary channel for the formation of UCXBs.« less

Topological X-Rays Revisited

ERIC Educational Resources Information Center

Lynch, Mark

2012-01-01

We continue our study of topological X-rays begun in Lynch ["Topological X-rays and MRI's," iJMEST 33(3) (2002), pp. 389-392]. We modify our definition of a topological magnetic resonance imaging and give an affirmative answer to the question posed there: Can we identify a closed set in a box by defining X-rays to probe the interior and without…

A Bright Future for Serial Femtosecond Crystallography with XFELs.

PubMed

Johansson, Linda C; Stauch, Benjamin; Ishchenko, Andrii; Cherezov, Vadim

2017-09-01

X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies. Here, we review the latest developments in instrumentation, sample delivery, data analysis, crystallization methods, and applications of SFX to important biological questions, and conclude with brief insights into the bright future of structural biology using XFELs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography.

PubMed

Banigan, James R; Mandal, Kalyaneswar; Sawaya, Michael R; Thammavongsa, Vilasak; Hendrickx, Antoni P A; Schneewind, Olaf; Yeates, Todd O; Kent, Stephen B H

2010-10-01

The 50-residue snake venom protein L-omwaprin and its enantiomer D-omwaprin were prepared by total chemical synthesis. Radial diffusion assays were performed against Bacillus megaterium and Bacillus anthracis; both L- and D-omwaprin showed antibacterial activity against B. megaterium. The native protein enantiomer, made of L-amino acids, failed to crystallize readily. However, when a racemic mixture containing equal amounts of L- and D-omwaprin was used, diffraction quality crystals were obtained. The racemic protein sample crystallized in the centrosymmetric space group P2(1)/c and its structure was determined at atomic resolution (1.33 A) by a combination of Patterson and direct methods based on the strong scattering from the sulfur atoms in the eight cysteine residues per protein. Racemic crystallography once again proved to be a valuable method for obtaining crystals of recalcitrant proteins and for determining high-resolution X-ray structures by direct methods.

Fe/Rh (100) multilayer magnetism probed by x-ray magnetic circular dichroism

NASA Astrophysics Data System (ADS)

Tomaz, M. A.; Ingram, D. C.; Harp, G. R.; Lederman, D.; Mayo, E.; O'brien, W. L.

1997-09-01

We report the layer-averaged magnetic moments of both Fe and Rh in sputtered Fe/Rh (100) multilayer thin films as measured by x-ray magnetic circular dichroism. We observe two distinct regimes in these films. The first is characterized by Rh moments of at least 1μB, Fe moments enhanced as much as 30% above bulk, and a bct crystal structure. The second regime is distinguished by sharp declines of both Fe and Rh moments accompanied by a transition to an fct crystal lattice. The demarcation between the two regions is identified as the layer thickness for which both bct and fct phases first coexist, which we term the critical thickness tcrit. We attribute the change in magnetic behavior to the structural transformation.

Characterization of CaMn2O4 By X-Ray Magnetic Linear Dichroism

NASA Astrophysics Data System (ADS)

Holroyd, Johnathon; Bhatkar, Harshawardhan; Arenholz, Elke; White, Ben; Neumeier, John; Idzerda, Yves

2008-05-01

Perovskite manganite such as LaxCa(1-x)MnO3 (LCMO) have recently drawn attention for their useful electronic and magnetic properties such as Colossal Magnetoresistance. It has been shown that under stress, LCMO thin films show changes in La and Ca concentrations near the interface. One potential impurity under La depleted conditions is antiferromagnetic CaMn2O4. In order to better understand the range of properties available within LCMO systems, it is important to be able to identify and characterize CaMn2O4 within LCMO thin films. X-ray absorption spectroscopy (XAS) and X-ray magnetic linear dichroism (XMLD) are well suited to this task due to their element specificity, sensitivity, and ability to characterize the measure the magnetic properties of antiferromagnetic systems. XAS and XMLD were measured on high quality single crystals of CaMn2O4. These spectra are distinguished from CaMnO3 and demonstrate antiferromagnetic structure.

Electronic and magnetic properties of manganite thin films with different compositions and its correlation with transport properties: An X-ray resonant magnetic scattering study

DOE PAGES

Singh, Surendra; Freeland, J. W.; Fitzsimmons, M. R.; ...

2014-12-08

Here, we present x-ray resonant magnetic dichroism and x-ray resonant magnetic scattering measurements of the temperature dependence of magnetism in Pr-doped La-Ca-Mn-O films grown on (110) NdGaO3 substrates. We observed thermal hysteresis of the ferromagnetism in one film that also showed large thermal hysteresis of ~18K in transport measurements. While in a second film of a different nominal chemistry, which showed very small thermal hysteresis ~3K in transport measurements, no thermal hysteresis of the ferromagnetism was observed. As a result, these macroscopic properties are correlated with evolution of surface magnetization across metal insulator transition for these films as observed bymore » soft x-ray resonant magnetic scattering measurements.« less

The Relation Between Magnetic Fields and X-ray Emission for Solar Microflares and Active Regions

NASA Astrophysics Data System (ADS)

Kirichenko, A. S.; Bogachev, S. A.

2017-09-01

We present the result of a comparison between magnetic field parameters and the intensity of X-ray emission for solar microflares with Geosynchronous Operational Environmental Satellites (GOES) classes from A0.02 to B5.1. For our study, we used the monochromatic MgXII Imaging Spectroheliometer (MISH), the Full-disk EUV Telescope (FET), and the Solar PHotometer in X-rays (SphinX) instruments onboard the Complex Orbital Observations Near-Earth of Activity of the Sun-Photon CORONAS- Photon spacecraft because of their high sensitivity in soft X-rays. The peak flare flux (PFF) for solar microflares was found to depend on the strength of the magnetic field and on the total unsigned magnetic flux as a power-law function. In the spectral range 2.8 - 36.6 Å, which shows very little increase related to microflares, the power-law index of the relation between the X-ray flux and magnetic flux for active regions is 1.48 ±0.86, which is close to the value obtained previously by Pevtsov et al. ( Astrophys. J. 598, 1387, 2003) for different types of solar and stellar objects. In the spectral range 1 - 8 Å, the power-law indices for PFF(B) and PFF(Φ) for microflares are 3.87 ±2.16 and 3 ±1.6, respectively. We also make suggestions on the heating mechanisms in active regions and microflares under the assumption of loops with constant pressure and heating using the Rosner-Tucker-Vaiana scaling laws.

Determination of X-ray flux using silicon pin diodes

PubMed Central

Owen, Robin L.; Holton, James M.; Schulze-Briese, Clemens; Garman, Elspeth F.

2009-01-01

Accurate measurement of photon flux from an X-ray source, a parameter required to calculate the dose absorbed by the sample, is not yet routinely available at macromolecular crystallography beamlines. The development of a model for determining the photon flux incident on pin diodes is described here, and has been tested on the macromolecular crystallography beamlines at both the Swiss Light Source, Villigen, Switzerland, and the Advanced Light Source, Berkeley, USA, at energies between 4 and 18 keV. These experiments have shown that a simple model based on energy deposition in silicon is sufficient for determining the flux incident on high-quality silicon pin diodes. The derivation and validation of this model is presented, and a web-based tool for the use of the macromolecular crystallography and wider synchrotron community is introduced. PMID:19240326

Difficult macromolecular structures determined using X-ray diffraction techniques.

PubMed

Hernández-Santoyo, Alejandra

2012-07-01

Macromolecular crystallography has been, for the last few decades, the main source of structural information of biological macromolecular systems and it is one of the most powerful techniques for the analysis of enzyme mechanisms and macromolecular interactions at the atomic level. In addition, it is also an extremely powerful tool for drug design. Recent technological and methodological developments in macromolecular X-ray crystallography have allowed solving structures that until recently were considered difficult or even impossible, such as structures at atomic or subatomic resolution or large macromolecular complexes and assemblies at low resolution. These developments have also helped to solve the 3D-structure of macromolecules from twin crystals. Recently, this technique complemented with cryo-electron microscopy and neutron crystallography has provided the structure of large macromolecular machines with great precision allowing understanding of the mechanisms of their function.

High-speed fixed-target serial virus crystallography

PubMed Central

Roedig, Philip; Ginn, Helen M.; Pakendorf, Tim; Sutton, Geoff; Harlos, Karl; Walter, Thomas S.; Meyer, Jan; Fischer, Pontus; Duman, Ramona; Vartiainen, Ismo; Reime, Bernd; Warmer, Martin; Brewster, Aaron S.; Young, Iris D.; Michels-Clark, Tara; Sauter, Nicholas K.; Kotecha, Abhay; Kelly, James; Rowlands, David J.; Sikorsky, Marcin; Nelson, Silke; Damiani, Daniel S.; Alonso-Mori, Roberto; Ren, Jingshan; Fry, Elizabeth E.; David, Christian; Stuart, David I.; Wagner, Armin; Meents, Alke

2017-01-01

We report a method for serial X-ray crystallography at X-ray free electron lasers (XFELs), which allows for full use of the current 120 Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micro-patterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery we were able to determine the crystal structures of a picornavirus, bovine enterovirus 2 (BEV2), and the cytoplasmic polyhedrosis virus type 18 polyhedrin. Total data collection times were less than 14 and 10 minutes, respectively. Our method requires only micrograms of sample and will therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for the most efficient use of the limited beamtime available at XFELs and should enable a substantial increase in sample throughput at these facilities. PMID:28628129

Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.

PubMed

Horrell, Sam; Antonyuk, Svetlana V; Eady, Robert R; Hasnain, S Samar; Hough, Michael A; Strange, Richard W

2016-07-01

Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07-1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a 'catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

Discovery and development of x-ray diffraction

NASA Astrophysics Data System (ADS)

Jeong, Yeuncheol; Yin, Ming; Datta, Timir

2013-03-01

In 1912 Max Laue at University of Munich reasoned x-rays to be short wavelength electromagnetic waves and figured interference would occur when scattered off crystals. Arnold Sommerfeld, W. Wien, Ewald and others, raised objections to Laue's idea, but soon Walter Friedrich succeeded in recording x-ray interference patterns off copper sulfate crystals. But the Laue-Ewald's 3-dimensional formula predicted excess spots. Fewer spots were observed. William Lawrence Bragg then 22 year old studying at Cambridge University heard the Munich results from father William Henry Brag, physics professor at Univ of Leeds. Lawrence figured the spots are 2-d interference of x-ray wavelets reflecting off successive atomic planes and derived a simple eponymous equation, the Bragg equation d*sin(theta) = n*lamda. 1913 onward the Braggs dominated the crystallography. Max Laue was awarded the physics Nobel in 1914 and the Braggs shared the same in 1915. Starting with Rontgen's first ever prize in 1901, the importance of x-ray techniques is evident from the four out of a total 16 physics Nobels between 1901-1917. We will outline the historical back ground and importance of x-ray diffraction giving rise to techniques that even in 2013, remain work horses in laboratories all over the globe.

C-shaped diastereomers containing cofacial thiophene-substituted quinoxaline rings: synthesis, photophysical properties, and X-ray crystallography.

PubMed

DeBlase, Catherine R; Finke, Ryan T; Porras, Jonathan A; Tanski, Joseph M; Nadeau, Jocelyn M

2014-05-16

Synthesis and characterization of two diastereomeric C-shaped molecules containing cofacial thiophene-substituted quinoxaline rings are described. A previously known bis-α-diketone was condensed with an excess of 4-bromo-1,2-diaminobenzene in the presence of zinc acetate to give a mixture of two C-shaped diastereomers with cofacial bromine-substituted quinoxaline rings. After chromatographic separation, thiophene rings were installed by a microwave-assisted Suzuki coupling reaction, resulting in highly emissive diastereomeric compounds that were studied by UV-vis, fluorescence, and NMR spectroscopy, as well as X-ray crystallography. The unique symmetry of each diastereomer was confirmed by NMR spectroscopy. NMR data indicated that the syn isomer has restricted rotation about the bond connecting the thiophene and quinoxaline rings, which was also observed in the solid state. The spectroscopic properties of the C-shaped diastereomers were compared to a model compound containing only a single thiophene-substituted quinoxaline ring. Ground state intramolecular π-π interactions in solution were detected by NMR and UV-vis spectroscopy. Red-shifted emission bands, band broadening, and large Stokes shifts were observed, which collectively suggest excited state π-π interactions that produce excimer-like emissions, as well as a remarkable positive emission solvatochromism, indicating charge-transfer character in the excited state.

Closed bore XMR (CBXMR) systems for aortic valve replacement: Active magnetic shielding of x-ray tubes

PubMed Central

Bracken, John A.; DeCrescenzo, Giovanni; Komljenovic, Philip; Lillaney, Prasheel V.; Fahrig, Rebecca; Rowlands, J. A.

2009-01-01

Hybrid closed bore x-ray∕MRI systems are being developed to improve the safety and efficacy of percutaneous aortic valve replacement procedures by harnessing the complementary strengths of the x-ray and MRI modalities in a single interventional suite without requiring patient transfer between two rooms. These systems are composed of an x-ray C-arm in close proximity (≈1 m) to an MRI scanner. The MRI magnetic fringe field can cause the electron beam in the x-ray tube to deflect. The deflection causes the x-ray field of view to shift position on the detector receptacle. This could result in unnecessary radiation exposure to the patient and the staff in the cardiac catheterization laboratory. Therefore, the electron beam deflection must be corrected. The authors developed an active magnetic shielding system that can correct for electron beam deflection to within an accuracy of 5% without truncating the field of view or increasing exposure to the patient. This system was able to automatically adjust to different field strengths as the external magnetic field acting on the x-ray tube was changed. Although a small torque was observed on the shielding coils of the active shielding system when they were placed in a magnetic field, this torque will not impact their performance if they are securely mounted on the x-ray tube and the C-arm. The heating of the coils of the shielding system for use in the clinic caused by electric current was found to be slow enough not to require a dedicated cooling system for one percutaneous aortic valve replacement procedure. However, a cooling system will be required if multiple procedures are performed in one session. PMID:19544789

Hydrogen atoms can be located accurately and precisely by x-ray crystallography.

PubMed

Woińska, Magdalena; Grabowsky, Simon; Dominiak, Paulina M; Woźniak, Krzysztof; Jayatilaka, Dylan

2016-05-01

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.

Hydrogen atoms can be located accurately and precisely by x-ray crystallography

PubMed Central

Woińska, Magdalena; Grabowsky, Simon; Dominiak, Paulina M.; Woźniak, Krzysztof; Jayatilaka, Dylan

2016-01-01

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A–H bond lengths with those from neutron measurements for A–H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors. PMID:27386545

Protein crystallography beamline BL2S1 at the Aichi synchrotron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watanabe, Nobuhisa; Nagae, Takayuki; Yamada, Yusuke

The protein crystallography beamline BL2S1, constructed at one of the 5 T superconducting bending-magnet ports of the Aichi synchrotron, is available to users associated with academic and industrial organizations. The beamline is mainly intended for use in X-ray diffraction measurements of single-crystals of macromolecules such as proteins and nucleic acids. Diffraction measurements for crystals of other materials are also possible, such as inorganic and organic compounds. BL2S1 covers the energy range 7–17 keV (1.8–0.7 Å) with an asymmetric-cut curved single-crystal monochromator [Ge(111) or Ge(220)], and a platinum-coated Si mirror is used for vertical focusing and as a higher-order cutoff filter.more » The beamline is equipped with a single-axis goniometer, a CCD detector, and an open-flow cryogenic sample cooler. Lastly, high-pressure protein crystallography with a diamond anvil cell can also be performed using this beamline.« less

Protein crystallography beamline BL2S1 at the Aichi synchrotron.

PubMed

Watanabe, Nobuhisa; Nagae, Takayuki; Yamada, Yusuke; Tomita, Ayana; Matsugaki, Naohiro; Tabuchi, Masao

2017-01-01

The protein crystallography beamline BL2S1, constructed at one of the 5 T superconducting bending-magnet ports of the Aichi synchrotron, is available to users associated with academic and industrial organizations. The beamline is mainly intended for use in X-ray diffraction measurements of single-crystals of macromolecules such as proteins and nucleic acids. Diffraction measurements for crystals of other materials are also possible, such as inorganic and organic compounds. BL2S1 covers the energy range 7-17 keV (1.8-0.7 Å) with an asymmetric-cut curved single-crystal monochromator [Ge(111) or Ge(220)], and a platinum-coated Si mirror is used for vertical focusing and as a higher-order cutoff filter. The beamline is equipped with a single-axis goniometer, a CCD detector, and an open-flow cryogenic sample cooler. High-pressure protein crystallography with a diamond anvil cell can also be performed using this beamline.

Soft gamma-ray repeaters and anomalous X-ray pulsars as highly magnetized white dwarfs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukhopadhyay, Banibrata; Rao, A.R., E-mail: bm@physics.iisc.ernet.in, E-mail: arrao@tifr.res.in

We explore the possibility that soft gamma-ray repeaters (SGRs) and anomalous X-ray pulsars (AXPs) are powered by highly magnetized white dwarfs (B-WDs). We take a sample of SGRs and AXPs and provide the possible parameter space in mass, radius, and surface magnetic field based on their observed properties (period and its derivative) and the assumption that these sources obey the mass-radius relation derived for the B-WDs. The radius and magnetic field of B-WDs are adequate to explain energies in SGRs/AXPs as the rotationally powered energy. In addition, B-WDs also adequately explain the perplexing radio transient GCRT J1745-3009 as a whitemore » dwarf pulsar. Note that the radius and magnetic fields of B-WDs are neither extreme (unlike of highly magnetized neutron stars) nor ordinary (unlike of magnetized white dwarfs, yet following the Chandrasekhar's mass-radius relation (C-WDs)). In order to explain SGRs/AXPs, while the highly magnetized neutron stars require an extra, observationally not well established yet, source of energy, the C-WDs predict large ultra-violet luminosity which is observationally constrained from a strict upper limit. Finally, we provide a set of basic differences between the magnetar and B-WD hypotheses for SGRs/AXPs.« less

The Race To X-ray Microbeam and Nanobeam Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ice, Gene E; Budai, John D; Pang, Judy

2011-01-01

X-ray microbeams are an emerging characterization tool with transformational implications for broad areas of science ranging from materials structure and dynamics, geophysics and environmental science to biophysics and protein crystallography. In this review, we discuss the race toward sub-10 nm- x-ray beams with the ability to penetrate tens to hundreds of microns into most materials and with the ability to determine local (crystal) structure. Examples of science enabled by current micro/nanobeam technologies are presented and we provide a perspective on future directions. Applications highlighted are chosen to illustrate the important features of various submicron beam strategies and to highlight themore » directions of current and future research. While it is clear that x-ray microprobes will impact science broadly, the practical limit for hard x-ray beam size, the limit to trace element sensitivity, and the ultimate limitations associated with near-atomic structure determinations are the subject of ongoing research.« less

Magnetic Dynamos and X-Ray Activity in Ultracool Dwarfs (UCDs): Surprises in the Radio Band

NASA Astrophysics Data System (ADS)

Williams, Peter K.; Cook, B. A.; Berger, E.

2014-01-01

Radio observations established early on that some brown dwarfs host kilogauss magnetic fields, despite their low temperatures and the absence of the shearing tachocline that is believed to be key to the solar dynamo. The observed radio emission is often surprisingly bright, exceeding the standard magnetic radio/X-ray (Güdel-Benz) relation by as much as five orders of magnitude. This effect is still not satisfactorily explained. In an attempt to improve matters, we have constructed and analyzed a comprehensive database of ultracool dwarfs with both radio and X-ray data, including new observations of seven targets with Chandra and the upgraded VLA. While all of the newly-observed objects were detected in the X-ray, only one was detected in the radio. These new targets are thus consistent with the standard relation, in striking contrast with some previous data. Some pairs of dwarfs with outwardly similar characteristics (spectral type, v sin i) have dramatically different emission properties, with radio/X-ray ratios that differ by two orders of magnitude. These results suggest that there is dramatic variance in ultracool magnetic activity. As we also discuss in a companion poster examining the relation between rotation and activity, variation in the topology of the magnetic field may explain the data. This work is supported in part by the NSF REU and DOD ASSURE programs under NSF grant no. 1262851 and by the Smithsonian Institution. We also acknowledge support from the NSF through Grant AST-1008361 and from NASA through Chandra Award Number G02-13007A issued by the Chandra X-ray Observatory Center, operated by the Smithsonian Astrophysical Observatory and NASA under contract NAS8-03060.

Cleavage crystallography of liquid metal embrittled aluminum alloys

NASA Technical Reports Server (NTRS)

Reynolds, A. P.; Stoner, G. E.

1991-01-01

The crystallography of liquid metal-induced transgranular cleavage in six aluminum alloys having a variety of microstructures has been determined via Laue X-ray back reflection. The cleavage crystallography was independent of alloy microstructure, and the cleavage plane was 100-plane oriented in all cases. It was further determined that the cleavage crystallography was not influenced by alloy texture. Examination of the fracture surface indicated that there was not a unique direction of crack propagation. In addition, the existence of 100-plane cleavage on alloy 2024 fracture surfaces was inferred by comparison of secondary cleavage crack intersection geometry on the 2024 surfaces with the geometry of secondary cleavage crack intersections on the test alloys.

Evidence that the X-Ray Plasma in Microflares is in a Sequence of Subresolution Magnetic Tubes

NASA Technical Reports Server (NTRS)

Moore, Ronald L.; Falconer, D. A.; Porter, Jason G.

1998-01-01

We analyze the cooling of the X-ray emitting thermal plasma in microflares observed in active regions by the Yohkoh Soft X-ray Telescope. A typical microflare appears to be a transient brightening of an entire small magnetic loop, often having a diameter near the limit of resolution (approximately 2 x 10(exp 8) cm) (Shimizu 1995, PASJ, 47, 251). The X-ray plasma in the loop cools by emission of XUV radiation and by heat conduction to the cooler plasma at the feet of the loop. The cooling rate is determined by the plasma temperature and density and the loop length. The plasma density is determined from the observed X-ray brightness of the loop in combination with the temperature, the loop diameter, and the filling factor. The filling factor is the volume fraction of the loop occupied by the subset of magnetic tubes that is filled by the X-ray plasma and that contains practically all of the X-ray plasma present in the microflare loop. Taking typical values from the hundreds of microflares measured by Shimizu (1995) (X-ray brightness through the thin aluminum filter approximately 4 x 10(exp 3) DN/s/pixel, lifetime approximately 5 min, temperature approximately 6 x 10(exp 6) K, loop length approximately 10(exp 9) cm, loop diameter approximately 3 x 10(exp 8) cm), we find that for filling factors greater than approximately 1% (1) the cooling time is much shorter than the duration of the microflare, and (2) conductive cooling strongly dominates over radiative cooling. Because the cooling time is so short and because the conductive heat flux goes mainly into increasing the plasma density via chromospheric evaporation, we are compelled to conclude that (1) heating to X-ray temperatures continues through nearly the entire life of a microflare, (2) the heating keeps changing to different field lines, so that any one magnetic tube in the sequence of heated tubes emits X-rays only briefly in the life of the microflare, and (3) at any instant during the microflare the tubes

Polarized x-ray emission from magnetized neutron stars: signature of strong-field vacuum polarization.

PubMed

Lai, Dong; Ho, Wynn C G

2003-08-15

In the atmospheric plasma of a strongly magnetized neutron star, vacuum polarization can induce a Mikheyev-Smirnov-Wolfenstein type resonance across which an x-ray photon may (depending on its energy) convert from one mode into the other, with significant changes in opacities and polarizations. We show that this vacuum resonance effect gives rise to a unique energy-dependent polarization signature in the surface emission from neutron stars. The detection of polarized x rays from neutron stars can provide a direct probe of strong-field quantum electrodynamics and constrain the neutron star magnetic field and geometry.

Polarized X-Ray Emission from Magnetized Neutron Stars: Signature of Strong-Field Vacuum Polarization

NASA Astrophysics Data System (ADS)

Lai, Dong; Ho, Wynn C.

2003-08-01

In the atmospheric plasma of a strongly magnetized neutron star, vacuum polarization can induce a Mikheyev-Smirnov-Wolfenstein type resonance across which an x-ray photon may (depending on its energy) convert from one mode into the other, with significant changes in opacities and polarizations. We show that this vacuum resonance effect gives rise to a unique energy-dependent polarization signature in the surface emission from neutron stars. The detection of polarized x rays from neutron stars can provide a direct probe of strong-field quantum electrodynamics and constrain the neutron star magnetic field and geometry.

Coherent convergent-beam time-resolved X-ray diffraction

PubMed Central

Spence, John C. H.; Zatsepin, Nadia A.; Li, Chufeng

2014-01-01

The use of coherent X-ray lasers for structural biology allows the use of nanometre diameter X-ray beams with large beam divergence. Their application to the structure analysis of protein nanocrystals and single particles raises new challenges and opportunities. We discuss the form of these coherent convergent-beam (CCB) hard X-ray diffraction patterns and their potential use for time-resolved crystallography, normally achieved by Laue (polychromatic) diffraction, for which the monochromatic laser radiation of a free-electron X-ray laser is unsuitable. We discuss the possibility of obtaining single-shot, angle-integrated rocking curves from CCB patterns, and the dependence of the resulting patterns on the focused beam coordinate when the beam diameter is larger or smaller than a nanocrystal, or smaller than one unit cell. We show how structure factor phase information is provided at overlapping interfering orders and how a common phase origin between different shots may be obtained. Their use in refinement of the phase-sensitive intensity between overlapping orders is suggested. PMID:24914153

Local structure and X-ray magnetic circular dichroism of Au in Au-Co nanoalloys

NASA Astrophysics Data System (ADS)

Maurizio, C.; Michieli, N.; Kalinic, B.; Mattarello, V.; Bello, V.; Wilhelm, F.; Ollefs, K.; Mattei, G.

2018-03-01

Coupling a plasmonic metal with a magnetic one in thin films and nanostructures is very interesting for the emerging field of magnetoplasmonics. In particular, coupling through alloying is a promising strategy to induce a magnetic moment on the plasmonic metal atoms, in a way that is intimately related to the local structure of the (metastable) alloy material. In this framework, Au:Co bimetallic films have been produced via magnetron co-sputtering deposition. X-ray absorption spectroscopy (XAS) at both Au- and Co-edges clearly indicates the formation of a full-metallic layer composed for the major part of a binary AuxCo1-x alloy, with x = 0.7-0.8. XAS and transmission electron microscopy analyses suggest the presence of a minor fraction of segregated metals. X-ray magnetic circular dichroism (XMCD) analysis at Au L2,3 edges detected a net magnetic moment of Au atoms (μ = 0.06 μB), significantly larger (≈3.5 times) that the one for Au-capped Co nanoclusters and comparable to the one for a Co-rich Au/Co multilayer, despite the 4 times larger concentration of Co with respect to the present case. This Au-Co magnetic coupling is favored by a high degree of mixing of the two metals in the alloy.

Stellar X-Ray Polarimetry

NASA Technical Reports Server (NTRS)

Swank, J.

2011-01-01

Most of the stellar end-state black holes, pulsars, and white dwarfs that are X-ray sources should have polarized X-ray fluxes. The degree will depend on the relative contributions of the unresolved structures. Fluxes from accretion disks and accretion disk corona may be polarized by scattering. Beams and jets may have contributions of polarized emission in strong magnetic fields. The Gravity and Extreme Magnetism Small Explorer (GEMS) will study the effects on polarization of strong gravity of black holes and strong magnetism of neutron stars. Some part of the flux from compact stars accreting from companion stars has been reflected from the companion, its wind, or accretion streams. Polarization of this component is a potential tool for studying the structure of the gas in these binary systems. Polarization due to scattering can also be present in X-ray emission from white dwarf binaries and binary normal stars such as RS CVn stars and colliding wind sources like Eta Car. Normal late type stars may have polarized flux from coronal flares. But X-ray polarization sensitivity is not at the level needed for single early type stars.

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

PubMed Central

Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J.; Brewster, Aaron S.; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G.; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R.; Miahnahri, Alan; White, William E.; Schafer, Donald W.; Seibert, M. Marvin; Koglin, Jason E.; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J.; Glatzel, Pieter; Zwart, Petrus H.; Grosse-Kunstleve, Ralf W.; Bogan, Michael J.; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K.; Adams, Paul D.; Sauter, Nicholas K.

2014-01-01

X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and free from radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract statistically significant high-resolution signals from fewer diffraction measurements. PMID:24633409

An Excel Spreadsheet for a One-Dimensional Fourier Map in X-ray Crystallography

ERIC Educational Resources Information Center

Clegg, William

2004-01-01

The teaching of crystal structure determination with single-crystal X-ray diffraction at undergraduate level faces numerous challenges. Single-crystal X-ray diffraction is used in a vast range of chemical research projects and forms the basis for a high proportion of structural results that are presented to high-school, undergraduate, and graduate…

Serial femtosecond X-ray diffraction of enveloped virus microcrystals

DOE PAGES

Lawrence, Robert M.; Conrad, Chelsie E.; Zatsepin, Nadia A.; ...

2015-08-20

Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ~700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ~40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is a pertinent step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

Protein Crystallography in Vaccine Research and Development.

PubMed

Malito, Enrico; Carfi, Andrea; Bottomley, Matthew J

2015-06-09

The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines.

Protein Crystallography in Vaccine Research and Development

PubMed Central

Malito, Enrico; Carfi, Andrea; Bottomley, Matthew J.

2015-01-01

The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines. PMID:26068237

Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography

PubMed Central

Zhu, Xiaohui; Hitchcock, Adam P.; Bazylinski, Dennis A.; Denes, Peter; Joseph, John; Lins, Ulysses; Marchesini, Stefano; Shiu, Hung-Wei; Tyliszczak, Tolek; Shapiro, David A.

2016-01-01

Characterizing the chemistry and magnetism of magnetotactic bacteria (MTB) is an important aspect of understanding the biomineralization mechanism and function of the chains of magnetosomes (Fe3O4 nanoparticles) found in such species. Images and X-ray absorption spectra (XAS) of magnetosomes extracted from, and magnetosomes in, whole Magnetovibrio blakemorei strain MV-1 cells have been recorded using soft X-ray ptychography at the Fe 2p edge. A spatial resolution of 7 nm is demonstrated. Precursor-like and immature magnetosome phases in a whole MV-1 cell were visualized, and their Fe 2p spectra were measured. Based on these results, a model for the pathway of magnetosome biomineralization for MV-1 is proposed. Fe 2p X-ray magnetic circular dichroism (XMCD) spectra have been derived from ptychography image sequences recorded using left and right circular polarization. The shape of the XAS and XMCD signals in the ptychographic absorption spectra of both sample types is identical to the shape and signals measured with conventional bright-field scanning transmission X-ray microscope. A weaker and inverted XMCD signal was observed in the ptychographic phase spectra of the extracted magnetosomes. The XMCD ptychographic phase spectrum of the intracellular magnetosomes differed from the ptychographic phase spectrum of the extracted magnetosomes. These results demonstrate that spectro-ptychography offers a superior means of characterizing the chemical and magnetic properties of MTB at the individual magnetosome level. PMID:27930297

Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography.

PubMed

Zhu, Xiaohui; Hitchcock, Adam P; Bazylinski, Dennis A; Denes, Peter; Joseph, John; Lins, Ulysses; Marchesini, Stefano; Shiu, Hung-Wei; Tyliszczak, Tolek; Shapiro, David A

2016-12-20

Characterizing the chemistry and magnetism of magnetotactic bacteria (MTB) is an important aspect of understanding the biomineralization mechanism and function of the chains of magnetosomes (Fe 3 O 4 nanoparticles) found in such species. Images and X-ray absorption spectra (XAS) of magnetosomes extracted from, and magnetosomes in, whole Magnetovibrio blakemorei strain MV-1 cells have been recorded using soft X-ray ptychography at the Fe 2p edge. A spatial resolution of 7 nm is demonstrated. Precursor-like and immature magnetosome phases in a whole MV-1 cell were visualized, and their Fe 2p spectra were measured. Based on these results, a model for the pathway of magnetosome biomineralization for MV-1 is proposed. Fe 2p X-ray magnetic circular dichroism (XMCD) spectra have been derived from ptychography image sequences recorded using left and right circular polarization. The shape of the XAS and XMCD signals in the ptychographic absorption spectra of both sample types is identical to the shape and signals measured with conventional bright-field scanning transmission X-ray microscope. A weaker and inverted XMCD signal was observed in the ptychographic phase spectra of the extracted magnetosomes. The XMCD ptychographic phase spectrum of the intracellular magnetosomes differed from the ptychographic phase spectrum of the extracted magnetosomes. These results demonstrate that spectro-ptychography offers a superior means of characterizing the chemical and magnetic properties of MTB at the individual magnetosome level.

Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography

DOE PAGES

Zhu, Xiaohui; Hitchcock, Adam P.; Bazylinski, Dennis A.; ...

2016-12-07

Characterizing the chemistry and magnetism of magnetotactic bacteria (MTB) is an important aspect of understanding the biomineralization mechanism and function of the chains of magnetosomes (Fe 3O 4 nanoparticles) found in such species. Images and X-ray absorption spectra (XAS) of magnetosomes extracted from, and magnetosomes in, whole Magnetovibrio blakemorei strain MV-1 cells have been recorded using soft X-ray ptychography at the Fe 2p edge. A spatial resolution of 7 nm is demonstrated. Precursor-like and immature magnetosome phases in a whole MV-1 cell were visualized, and their Fe 2p spectra were measured. Based on these results, a model for the pathwaymore » of magnetosome biomineralization for MV-1 is proposed. Fe 2p X-ray magnetic circular dichroism (XMCD) spectra have been derived from ptychography image sequences recorded using left and right circular polarization. The shape of the XAS and XMCD signals in the ptychographic absorption spectra of both sample types is identical to the shape and signals measured with conventional bright-field scanning transmission X-ray microscope. A weaker and inverted XMCD signal was observed in the ptychographic phase spectra of the extracted magnetosomes. The XMCD ptychographic phase spectrum of the intracellular magnetosomes differed from the ptychographic phase spectrum of the extracted magnetosomes. Lastly, these results demonstrate that spectro-ptychography offers a superior means of characterizing the chemical and magnetic properties of MTB at the individual magnetosome level.« less

O-Alkylated heavy atom carbohydrate probes for protein X-ray crystallography: Studies towards the synthesis of methyl 2-O-methyl-L-selenofucopyranoside.

PubMed

Sommer, Roman; Hauck, Dirk; Varrot, Annabelle; Imberty, Anne; Künzler, Markus; Titz, Alexander

2016-01-01

Selenoglycosides are used as reactive glycosyl donors in the syntheses of oligosaccharides. In addition, such heavy atom analogs of natural glycosides are useful tools for structure determination of their lectin receptors using X-ray crystallography. Some lectins, e.g., members of the tectonin family, only bind to carbohydrate epitopes with O-alkylated ring hydroxy groups. In this context, we report the first synthesis of an O -methylated selenoglycoside, specifically methyl 2- O -methyl-L-selenofucopyranoside, a ligand of the lectin tectonin-2 from the mushroom Laccaria bicolor . The synthetic route required a strategic revision and further optimization due to the intrinsic lability of alkyl selenoglycosides, in particular for the labile fucose. Here, we describe a successful synthetic access to methyl 2- O -methyl-L-selenofucopyranoside in 9 linear steps and 26% overall yield starting from allyl L-fucopyranoside.

An Exercise in X-Ray Diffraction Using the Polymorphic Transition of Nickel Chromite.

ERIC Educational Resources Information Center

Chipman, David W.

1980-01-01

Describes a laboratory experiment appropriate for a course in either x-ray crystallography or mineralogy. The experiment permits the direct observation of a polymorphic transition in nickel chromite without the use of a special heating stage or heating camera. (Author/GS)

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.

PubMed

Fuller, Franklin D; Gul, Sheraz; Chatterjee, Ruchira; Burgie, E Sethe; Young, Iris D; Lebrette, Hugo; Srinivas, Vivek; Brewster, Aaron S; Michels-Clark, Tara; Clinger, Jonathan A; Andi, Babak; Ibrahim, Mohamed; Pastor, Ernest; de Lichtenberg, Casper; Hussein, Rana; Pollock, Christopher J; Zhang, Miao; Stan, Claudiu A; Kroll, Thomas; Fransson, Thomas; Weninger, Clemens; Kubin, Markus; Aller, Pierre; Lassalle, Louise; Bräuer, Philipp; Miller, Mitchell D; Amin, Muhamed; Koroidov, Sergey; Roessler, Christian G; Allaire, Marc; Sierra, Raymond G; Docker, Peter T; Glownia, James M; Nelson, Silke; Koglin, Jason E; Zhu, Diling; Chollet, Matthieu; Song, Sanghoon; Lemke, Henrik; Liang, Mengning; Sokaras, Dimosthenis; Alonso-Mori, Roberto; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Boal, Amie K; Bollinger, J Martin; Krebs, Carsten; Högbom, Martin; Phillips, George N; Vierstra, Richard D; Sauter, Nicholas K; Orville, Allen M; Kern, Jan; Yachandra, Vittal K; Yano, Junko

2017-04-01

X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fuller, Franklin D.; Gul, Sheraz; Chatterjee, Ruchira

X-ray crystallography at X-ray free-electron laser (XFEL) sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy (XES), both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing new insights into the interplay between the protein structure/dynamics and chemistry at an active site. However, implementing such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly impacts the data quality. We present here a new, robust way of delivering controlled sample amountsmore » on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.« less

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

DOE PAGES

Fuller, Franklin D.; Gul, Sheraz; Chatterjee, Ruchira; ...

2017-02-27

X-ray crystallography at X-ray free-electron laser (XFEL) sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy (XES), both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing new insights into the interplay between the protein structure/dynamics and chemistry at an active site. However, implementing such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly impacts the data quality. We present here a new, robust way of delivering controlled sample amountsmore » on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.« less

Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing.

PubMed

Finfrock, Y Zou; Stern, Edward A; Alkire, R W; Kas, Joshua J; Evans-Lutterodt, Kenneth; Stein, Aaron; Duke, Norma; Lazarski, Krzysztof; Joachimiak, Andrzej

2013-08-01

Reported here are measurements of the penetration depth and spatial distribution of photoelectron (PE) damage excited by 18.6 keV X-ray photons in a lysozyme crystal with a vertical submicrometre line-focus beam of 0.7 µm full-width half-maximum (FWHM). The experimental results determined that the penetration depth of PEs is 5 ± 0.5 µm with a monotonically decreasing spatial distribution shape, resulting in mitigation of diffraction signal damage. This does not agree with previous theoretical predication that the mitigation of damage requires a peak of damage outside the focus. A new improved calculation provides some qualitative agreement with the experimental results, but significant errors still remain. The mitigation of radiation damage by line focusing was measured experimentally by comparing the damage in the X-ray-irradiated regions of the submicrometre focus with the large-beam case under conditions of equal exposure and equal volumes of the protein crystal, and a mitigation factor of 4.4 ± 0.4 was determined. The mitigation of radiation damage is caused by spatial separation of the dominant PE radiation-damage component from the crystal region of the line-focus beam that contributes the diffraction signal. The diffraction signal is generated by coherent scattering of incident X-rays (which introduces no damage), while the overwhelming proportion of damage is caused by PE emission as X-ray photons are absorbed.

Fast fluorescence techniques for crystallography beamlines

PubMed Central

Stepanov, Sergey; Hilgart, Mark; Yoder, Derek W.; Makarov, Oleg; Becker, Michael; Sanishvili, Ruslan; Ogata, Craig M.; Venugopalan, Nagarajan; Aragão, David; Caffrey, Martin; Smith, Janet L.; Fischetti, Robert F.

2011-01-01

This paper reports on several developments of X-ray fluorescence techniques for macromolecular crystallography recently implemented at the National Institute of General Medical Sciences and National Cancer Institute beamlines at the Advanced Photon Source. These include (i) three-band on-the-fly energy scanning around absorption edges with adaptive positioning of the fine-step band calculated from a coarse pass; (ii) on-the-fly X-ray fluorescence rastering over rectangular domains for locating small and invisible crystals with a shuttle-scanning option for increased speed; (iii) fluorescence rastering over user-specified multi-segmented polygons; and (iv) automatic signal optimization for reduced radiation damage of samples. PMID:21808424

A 1-D Study of the Ignition Space for Magnetic Indirect (X-ray) Drive Targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cobble, James Allen; Sinars, Daniel Brian

The ICF program today is investigating three approaches to achieving multi-MJ fusion yields and ignition: (1) laser indirect (x-ray) drive on the National Ignition Facility (NIF), (2) laser direct drive (primarily on the Omega laser facility at the University of Rochester), and (3) magnetic direct drive on the Z pulsed power facility. In this white paper we briefly consider a fourth approach, magnetic indirect drive, in which pulsedpower- driven x-ray sources are used in place of laser driven sources. We first look at some of the x-ray sources studied on Z prior to 2007 before the pulsed power ICF programmore » shifted to magnetic direct drive. We then show results from a series of 1D Helios calculations of double-shell capsules that suggest that these sources, scaled to higher temperatures, could be a promising path to achieving multi-MJ fusion yields and ignition. We advocate here that more detailed design calculations with widely accepted 2D/3D ICF codes should be conducted for a better assessment of the prospects.« less

Single-crystal Raman spectroscopy and X-ray crystallography at beamline X26-C of the NSLS

PubMed Central

Stoner-Ma, Deborah; Skinner, John M.; Schneider, Dieter K.; Cowan, Matt; Sweet, Robert M.; Orville, Allen M.

2011-01-01

Three-dimensional structures derived from X-ray diffraction of protein crystals provide a wealth of information. Features and interactions important for the function of macromolecules can be deduced and catalytic mechanisms postulated. Still, many questions can remain, for example regarding metal oxidation states and the interpretation of ‘mystery density’, i.e. ambiguous or unknown features within the electron density maps, especially at ∼2 Å resolutions typical of most macromolecular structures. Beamline X26-C at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory (BNL), provides researchers with the opportunity to not only determine the atomic structure of their samples but also to explore the electronic and vibrational characteristics of the sample before, during and after X-ray diffraction data collection. When samples are maintained under cryo-conditions, an opportunity to promote and follow photochemical reactions in situ as a function of X-ray exposure is also provided. Plans are in place to further expand the capabilities at beamline X26-C and to develop beamlines at NSLS-II, currently under construction at BNL, which will provide users access to a wide array of complementary spectroscopic methods in addition to high-quality X-ray diffraction data. PMID:21169688

New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences.

PubMed

Helliwell, John R

2017-08-31

Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with

History of Chandra X-Ray Observatory

NASA Image and Video Library

2000-12-18

This Chandra image of Jupiter shows concentrations of aurora x-rays near the north and south poles due to a single `hot spot' that pulsates with a period of 45 minutes, similar to high-latitude radio pulsation previously detected by NASA's Galileo and Cassini spacecraft. Previous x-ray detections of Jupiter have been made with other x-ray telescopes, but did not reveal that the sources of the x-rays, energetic oxygen and sulfur ions, would be located so near the poles. Previous theories held that ions were mostly coming from Jupiter's moon, lo. Chandra's ability to pinpoint the source of the x-rays discards this theory since ions coming from near lo's orbit carnot reach the observed high latitudes. One possibility is that particles flowing out from the Sun are captured in the outer regions of Jupiter's magnetic field, then accelerated and directed toward its magnetic pole. Once captured, the ions would bounce back and forth in the magnetic field from Jupiter's north pole to the south pole in an oscillating motion that could explain the pulsation.

Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography.

PubMed

Amano, Yasushi; Yamaguchi, Tomohiko; Tanabe, Eiki

2014-04-15

Soluble epoxide hydrolase (sEH) is a component of the arachidonic acid cascade and is a candidate target for therapies for hypertension or inflammation. Although many sEH inhibitors are available, their scaffolds are not structurally diverse, and knowledge of their specific interactions with sEH is limited. To obtain detailed structural information about protein-ligand interactions, we conducted fragment screening of sEH, analyzed the fragments using high-throughput X-ray crystallography, and determined 126 fragment-bound structures at high resolution. Aminothiazole and benzimidazole derivatives were identified as novel scaffolds that bind to the catalytic triad of sEH with good ligand efficiency. We further identified fragment hits that bound to subpockets of sEH called the short and long branches. The water molecule conserved in the structure plays an important role in binding to the long branch, whereas Asp496 and the main chain of Phe497 form hydrogen bonds with fragment hits in the short branch. Fragment hits and their crystal structures provide structural insights into ligand binding to sEH that will facilitate the discovery of novel and potent inhibitors of sEH. Copyright © 2014 Elsevier Ltd. All rights reserved.

High-throughput methods for electron crystallography.

PubMed

Stokes, David L; Ubarretxena-Belandia, Iban; Gonen, Tamir; Engel, Andreas

2013-01-01

Membrane proteins play a tremendously important role in cell physiology and serve as a target for an increasing number of drugs. Structural information is key to understanding their function and for developing new strategies for combating disease. However, the complex physical chemistry associated with membrane proteins has made them more difficult to study than their soluble cousins. Electron crystallography has historically been a successful method for solving membrane protein structures and has the advantage of providing a native lipid environment for these proteins. Specifically, when membrane proteins form two-dimensional arrays within a lipid bilayer, electron microscopy can be used to collect images and diffraction and the corresponding data can be combined to produce a three-dimensional reconstruction, which under favorable conditions can extend to atomic resolution. Like X-ray crystallography, the quality of the structures are very much dependent on the order and size of the crystals. However, unlike X-ray crystallography, high-throughput methods for screening crystallization trials for electron crystallography are not in general use. In this chapter, we describe two alternative methods for high-throughput screening of membrane protein crystallization within the lipid bilayer. The first method relies on the conventional use of dialysis for removing detergent and thus reconstituting the bilayer; an array of dialysis wells in the standard 96-well format allows the use of a liquid-handling robot and greatly increases throughput. The second method relies on titration of cyclodextrin as a chelating agent for detergent; a specialized pipetting robot has been designed not only to add cyclodextrin in a systematic way, but to use light scattering to monitor the reconstitution process. In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described.

Focusing X-ray free-electron laser pulses using Kirkpatrick-Baez mirrors at the NCI hutch of the PAL-XFEL.

PubMed

Kim, Jangwoo; Kim, Hyo Yun; Park, Jaehyun; Kim, Sangsoo; Kim, Sunam; Rah, Seungyu; Lim, Jun; Nam, Ki Hyun

2018-01-01

The Pohang Accelerator Laboratory X-ray Free-Electron Laser (PAL-XFEL) is a recently commissioned X-ray free-electron laser (XFEL) facility that provides intense ultrashort X-ray pulses based on the self-amplified spontaneous emission process. The nano-crystallography and coherent imaging (NCI) hutch with forward-scattering geometry is located at the hard X-ray beamline of the PAL-XFEL and provides opportunities to perform serial femtosecond crystallography and coherent X-ray diffraction imaging. To produce intense high-density XFEL pulses at the interaction positions between the X-rays and various samples, a microfocusing Kirkpatrick-Baez (KB) mirror system that includes an ultra-precision manipulator has been developed. In this paper, the design of a KB mirror system that focuses the hard XFEL beam onto a fixed sample point of the NCI hutch, which is positioned along the hard XFEL beamline, is described. The focusing system produces a two-dimensional focusing beam at approximately 2 µm scale across the 2-11 keV photon energy range. XFEL pulses of 9.7 keV energy were successfully focused onto an area of size 1.94 µm × 2.08 µm FWHM.

Using Two-Dimensional Colloidal Crystals to Understand Crystallography

ERIC Educational Resources Information Center

Bosse, Stephanie A.; Loening, Nikolaus M.

2008-01-01

X-ray crystallography is an essential technique for modern chemistry and biochemistry, but it is infrequently encountered by undergraduate students owing to lack of access to equipment, the time-scale for generating diffraction-quality molecular crystals, and the level of mathematics involved in analyzing the resulting diffraction patterns.…

Fingerprints of orbital physics in magnetic resonant inelastic X-ray scattering

NASA Astrophysics Data System (ADS)

Marra, Pasquale

2012-09-01

Orbital degrees of freedom play a major role in the physics of many strongly correlated transition metal compounds. However, they are still very difficult to access experimentally, in particular by neutron scattering. We propose here how to reveal orbital occupancies of the system ground state by magnetic resonant inelastic x-ray scattering (RIXS). This is possible because, unlike in neutron scattering, the intensity of the magnetic excitations in RIXS depends essentially on the symmetry of the orbitals where the spins are in.

X-Ray Polarization from High Mass X-Ray Binaries

NASA Technical Reports Server (NTRS)

Kallman, T.; Dorodnitsyn, A.; Blondin, J.

2015-01-01

X-ray astronomy allows study of objects which may be associated with compact objects, i.e. neutron stars or black holes, and also may contain strong magnetic fields. Such objects are categorically non-spherical, and likely non-circular when projected on the sky. Polarization allows study of such geometric effects, and X-ray polarimetry is likely to become feasible for a significant number of sources in the future. A class of potential targets for future X-ray polarization observations is the high mass X-ray binaries (HMXBs), which consist of a compact object in orbit with an early type star. In this paper we show that X-ray polarization from HMXBs has a distinct signature which depends on the source inclination and orbital phase. The presence of the X-ray source displaced from the star creates linear polarization even if the primary wind is spherically symmetric whenever the system is viewed away from conjunction. Direct X-rays dilute this polarization whenever the X-ray source is not eclipsed; at mid-eclipse the net polarization is expected to be small or zero if the wind is circularly symmetric around the line of centers. Resonance line scattering increases the scattering fraction, often by large factors, over the energy band spanned by resonance lines. Real winds are not expected to be spherically symmetric, or circularly symmetric around the line of centers, owing to the combined effects of the compact object gravity and ionization on the wind hydrodynamics. A sample calculation shows that this creates polarization fractions ranging up to tens of percent at mid-eclipse.

Can glenoid wear be accurately assessed using x-ray imaging? Evaluating agreement of x-ray and magnetic resonance imaging (MRI) Walch classification.

PubMed

Kopka, Michaela; Fourman, Mitchell; Soni, Ashish; Cordle, Andrew C; Lin, Albert

2017-09-01

The Walch classification is the most recognized means of assessing glenoid wear in preoperative planning for shoulder arthroplasty. This classification relies on advanced imaging, which is more expensive and less practical than plain radiographs. The purpose of this study was to determine whether the Walch classification could be accurately applied to x-ray images compared with magnetic resonance imaging (MRI) as the gold standard. We hypothesized that x-ray images cannot adequately replace advanced imaging in the evaluation of glenoid wear. Preoperative axillary x-ray images and MRI scans of 50 patients assessed for shoulder arthroplasty were independently reviewed by 5 raters. Glenoid wear was individually classified according to the Walch classification using each imaging modality. The raters then collectively reviewed the MRI scans and assigned a consensus classification to serve as the gold standard. The κ coefficient was used to determine interobserver agreement for x-ray images and independent MRI reads, as well as the agreement between x-ray images and consensus MRI. The inter-rater agreement for x-ray images and MRIs was "moderate" (κ = 0.42 and κ = 0.47, respectively) for the 5-category Walch classification (A1, A2, B1, B2, C) and "moderate" (κ = 0.54 and κ = 0.59, respectively) for the 3-category Walch classification (A, B, C). The agreement between x-ray images and consensus MRI was much lower: "fair-to-moderate" (κ = 0.21-0.51) for the 5-category and "moderate" (κ = 0.36-0.60) for the 3-category Walch classification. The inter-rater agreement between x-ray images and consensus MRI is "fair-to-moderate." This is lower than the previously reported reliability of the Walch classification using computed tomography scans. Accordingly, x-ray images are inferior to advanced imaging when assessing glenoid wear. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights

Direct surface magnetometry with photoemission magnetic x-ray dichroism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tobin, J.G.; Goodman, K.W.; Schumann, F.O.

1997-04-01

Element specific surface magnetometry remains a central goal of synchrotron radiation based studies of nanomagnetic structures. One appealing possibility is the combination of x-ray absorption dichroism measurements and the theoretical framework provided by the {open_quotes}sum rules.{close_quotes} Unfortunately, sum rule analysis are hampered by several limitations including delocalization of the final state, multi-electronic phenomena and the presence of surface dipoles. An alternative experiment, Magnetic X-Ray Dichroism in Photoelectron Spectroscopy, holds out promise based upon its elemental specificity, surface sensitivity and high resolution. Computational simulations by Tamura et al. demonstrated the relationship between exchange and spin orbit splittings and experimental data ofmore » linear and circular dichroisms. Now the authors have developed an analytical framework which allows for the direct extraction of core level exchange splittings from circular and linear dichroic photoemission data. By extending a model initially proposed by Venus, it is possible to show a linear relation between normalized dichroism peaks in the experimental data and the underlying exchange splitting. Since it is reasonable to expect that exchange splittings and magnetic moments track together, this measurement thus becomes a powerful new tool for direct surface magnetometry, without recourse to time consuming and difficult spectral simulations. The theoretical derivation will be supported by high resolution linear and circular dichroism data collected at the Spectromicroscopy Facility of the Advanced Light Source.« less

SIBYLS - A SAXS and protein crystallography beamline at the ALS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trame, Christine; MacDowell, Alastair A.; Celestre, Richard S.

2003-08-22

The new Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the Advanced Light Source will be dedicated to Macromolecular Crystallography (PX) and Small Angle X-ray Scattering (SAXS). SAXS will provide structural information of macromolecules in solutions and will complement high resolution PX studies on the same systems but in a crystalline state. The x-ray source is one of the 5 Tesla superbend dipoles recently installed at the ALS that allows for a hard x-ray program to be developed on the relatively low energy Advanced Light Source (ALS) ring (1.9 GeV). The beamline is equipped with fast interchangeable monochromator elements,more » consisting of either a pair of single Si(111) crystals for crystallography, or a pair of multilayers for the SAXS mode data collection (E/{Delta}E {approx} 1/110). Flux rates with Si(111) crystals for PX are measured as 2 x 10{sup 11} hv/sec/400 mA through a 100 {micro}m pinhole at 12.4 KeV. For SAXS the flux is up to 3 x 10{sup 13} photons/sec at 10 KeV with all apertures open when using the multilayer monochromator elements. The performance characteristics of this unique beamline will be described.« less

SIBYLS - a SAXS and Protein Crystallography Beamline at the ALS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trame, C.; MacDowell, A.A.; Celestre, R.S.

2004-05-12

The new Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the Advanced Light Source will be dedicated to Macromolecular Crystallography (PX) and Small Angle X-ray Scattering (SAXS). SAXS will provide structural information of macromolecules in solutions and will complement high resolution PX studies on the same systems but in a crystalline state. The x-ray source is one of the 5 Tesla superbend dipoles recently installed at the ALS that allows for a hard x-ray program to be developed on the relatively low energy Advanced Light Source (ALS) ring (1.9 GeV). The beamline is equipped with fast interchangeable monochromator elements,more » consisting of either a pair of single Si(111) crystals for crystallography, or a pair of multilayers for the SAXS mode data collection (E/{delta}E{approx}1/110). Flux rates with Si(111) crystals for PX are measured as 2x1011 hv/sec through a 100{mu}m pinhole at 12.4KeV. For SAXS the flux is up to 3x1013photons/sec at 10KeV with all apertures open when using the multilayer monochromator elements. The performance characteristics of this unique beamline will be described.« less

X-ray scattering study of pyrochlore iridates: Crystal structure, electronic, and magnetic excitations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clancy, J. P.; Gretarsson, H.; Lee, E. K. H.

2016-07-06

We have investigated the structural, electronic, and magnetic properties of the pyrochlore iridates Eu 2Ir 2O 7 and Pr 2Ir 2O 7 using a combination of resonant elastic x-ray scattering, x-ray powder diffraction, and resonant inelastic x-ray scattering (RIXS). The structural parameters of Eu 2Ir 2O 7 have been examined as a function of temperature and applied pressure, with a particular emphasis on regions of the phase diagram where electronic and magnetic phase transitions have been reported. We find no evidence of crystal symmetry change over the range of temperatures (~6 to 300 K) and pressures (~0.1 to 17 GPa)more » studied. We have also investigated the electronic and magnetic excitations in single-crystal samples of Eu 2Ir 2O 7 and Pr 2Ir 2O 7 using high-resolution Ir L- 3-edge RIXS. In spite of very different ground state properties, we find that these materials exhibit qualitatively similar excitation spectra, with crystal field excitations at ~3-5 eV, spin-orbit excitations at ~ 0.5-1 eV, and broad low-lying excitations below ~0.15 eV. In single-crystal samples of "Eu-rich" Eu 2Ir 2O 7 (found to possess an actual stoichiometry of Eu 2.18Ir 1.82O 7.06) we observe highly damped magnetic excitations at ~45 meV, which display significant momentum dependence. Here, we compare these results with recent dynamical structure factor calculations« less

Emerging opportunities in structural biology with X-ray free-electron lasers

PubMed Central

Schlichting, Ilme; Miao, Jianwei

2012-01-01

X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be “outrun” by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of “diffraction-before-destruction” has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical “phase problem” by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs. PMID:22922042

Magnetic and chemical nonuniformity in Ga{sub 1-x}Mn{sub x}As as probed with neutron & x-ray reflectivfity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirby, B. J.; Borchers, J. A.; Rhyne, J. J.

We have used complementary neutron and x-ray reflectivity techniques to examine the depth profiles of a series of as-grown and annealed Ga{sub 1-x}Mn{sub x}As thin films. A magnetization gradient is observed for two as-grown films and originates from a nonuniformity of Mn at interstitial sites, and not from local variations in Mn at Ga sites. Furthermore, we see that the depth-dependent magnetization can vary drastically among as-grown Ga{sub 1-x}Mn{sub x}As films despite being deposited under seemingly similar conditions. These results imply that the depth profile of interstitial Mn is dependent not only on annealing, but is also extremely sensitive tomore » initial growth conditions. We observe that annealing improves the magnetization by producing a surface layer that is rich in Mn and O, indicating that the interstitial Mn migrates to the surface. Finally, we expand upon our previous neutron reflectivity study of Ga{sub 1-x}Mn{sub x}As, by showing how the depth profile of the chemical composition at the surface and through the film thickness is directly responsible for the complex magnetization profiles observed in both as-grown and annealed films.« less

Unveiling the magnetic structure of VHE SNRs/PWNe with XIPE, the x-ray imaging-polarimetry explorer

NASA Astrophysics Data System (ADS)

de Ona Wilhelmi, E.; Vink, J.; Bykov, A.; Zanin, R.; Bucciantini, N.; Amato, E.; Bandiera, R.; Olmi, B.; Uvarov, Yu.; XIPE Science Working Group

2017-01-01

The dynamics, energetics and evolution of pulsar wind nebulae (PWNe) and supernova remnants (SNRs), are strongly affected by their magnetic field strength and distribution. They are usually strong, extended, sources of non-thermal X-ray radiation, producing intrinsically polarised radiation. The energetic wind around pulsars produces a highly-magnetised, structured flow, often displaying a jet and a torus and different features (i.e. wisps, knots). This magnetic-dominant wind evolves as it moves away from the pulsar magnetosphere to the surrounding large-scale nebula, becoming kinetic-dominant. Basic aspects such how this conversion is produced, or how the jets and torus are formed, as well as the level of turbulence in the nebula are still unknown. Likewise, the processes ruling the acceleration of particles in shell-like SNRs up to 1015 eV, including the amplification of the magnetic field, are not clear yet. Imaging polarimetry in this regard is crucial to localise the regions of shock acceleration and to measure the strength and the orientation of the magnetic field at these emission sites. X-ray polarimetry with the X-ray Imaging Polarimetry Explorer (XIPE) will allow the understanding of the magnetic field structure and intensity on different regions in SNRs and PWNe, helping to unveil long-standing questions such as i.e. acceleration of cosmic rays in SNRs or magnetic-to-kinetic energy transfer. SNRs and PWNe also represent the largest population of Galactic very-high energy gamma-ray sources, therefore the study of their magnetic distribution with XIPE will provide fundamental ingredients on the investigation of those sources at very high energies. We will discuss the physics case related to SNRs and PWNe and the expectations of the XIPE observations of some of the most prominent SNRs and PWNe.

Magnetic properties of Gd T2Zn20 (T =Fe , Co) investigated by x-ray diffraction and spectroscopy

NASA Astrophysics Data System (ADS)

Mardegan, J. R. L.; Francoual, S.; Fabbris, G.; Veiga, L. S. I.; Strempfer, J.; Haskel, D.; Ribeiro, R. A.; Avila, M. A.; Giles, C.

2016-01-01

We investigate the magnetic and electronic properties of the Gd T2Zn20 (T =Fe and Co) compounds using x-ray resonant magnetic scattering (XRMS), x-ray absorption near-edge structure (XANES), and x-ray magnetic circular dichroism (XMCD). The XRMS measurements reveal that GdCo2Zn20 has a commensurate antiferromagnetic spin structure with a magnetic propagation vector τ ⃗=(1/2 ,1/2 ,1/2 ) below the Néel temperature (TN˜ 5.7 K). Only the Gd ions carry a magnetic moment forming an antiferromagnetic structure with magnetic representation Γ6. For the ferromagnetic GdFe2Zn20 compound, an extensive investigation was performed at low temperature and under magnetic field using XANES and XMCD. A strong XMCD signal of about 12.5 % and 9.7 % is observed below the Curie temperature (TC˜85 K ) at the Gd L2 and L3 edges, respectively. In addition, a small magnetic signal of about 0.06 % of the jump is recorded at the Zn K edge, suggesting that the Zn 4 p states are spin polarized by the Gd 5 d extended orbitals.

Magnetic properties of GdT 2Zn 20 (T = Fe, Co) investigated by x-ray diffraction and spectroscopy

DOE PAGES

J. R. L. Mardegan; Fabbris, G.; Francoual, S.; ...

2016-01-26

In this study, we investigate the magnetic and electronic properties of the GdT 2Zn 20 (T=Fe and Co) compounds using x-ray resonant magnetic scattering (XRMS), x-ray absorption near-edge structure (XANES), and x-ray magnetic circular dichroism (XMCD). The XRMS measurements reveal that GdCo 2Zn 20 has a commensurate antiferromagnetic spin structure with a magnetic propagation vector →/ τ = (12,12,12) below the Néel temperature (T N ~ 5.7 K). Only the Gd ions carry a magnetic moment forming an antiferromagnetic structure with magnetic representation Γ 6. For the ferromagnetic GdFe 2Zn 20 compound, an extensive investigation was performed at low temperaturemore » and under magnetic field using XANES and XMCD. A strong XMCD signal of about 12.5% and 9.7% is observed below the Curie temperature (T C ~ 85K) at the Gd L 2 and L 3 edges, respectively. In addition, a small magnetic signal of about 0.06% of the jump is recorded at the Zn K edge, suggesting that the Zn 4p states are spin polarized by the Gd 5d extended orbitals.« less

Superconducting Effects in Optimization of Magnetic Penetration Thermometers for X-ray Microcalorimeters

NASA Technical Reports Server (NTRS)

Stevenson, Thomas R.; Balvin, M. A.; Denis, K. L.; Hsieh, W.-T.; Sadleir, J. E.; Bandler, Simon E.; Busch, Sarah E.; Merrell, W.; Kelly, Daniel P.; Nagler, Peter C.;

Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules.

PubMed

Oksanen, Esko; Chen, Julian C-H; Fisher, Suzanne Zoë

2017-04-07

Abstract : The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.

Neutron crystallography for the study of hydrogen bonds in macromolecules

DOE PAGES

Oksanen, Esko; Chen, Julian C.; Fisher, Zoe

2017-04-07

The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, themore » protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. Finally, this article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.« less

Neutron crystallography for the study of hydrogen bonds in macromolecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oksanen, Esko; Chen, Julian C.; Fisher, Zoe

The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, themore » protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. Finally, this article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.« less

Characterization of short-pulse laser-produced x-rays for diagnosing magnetically driven cylindrical isentropic compression

NASA Astrophysics Data System (ADS)

Sawada, Hiroshi; Daykin, Tyler; Bauer, Bruno; Beg, Farhat

2017-10-01

We have developed an experimental platform to study material properties of magnetically compressed cylinder using a 1 MA pulsed power generator Zebra and a 50 TW subpicosecond short-pulse laser Leopard at the UNR's Nevada Terawatt Facility. According to a MHD simulation, strong magnetic fields generated by 100 ns rise time Zebra current can quasi-isentropically compress a material to the strongly coupled plasma regime. Taking advantage of the cylindrical geometry, a metal rod can be brought to higher pressures than that in the planar geometry. To diagnose the compressed rod with high precision x-ray measurements, an initial laser-only experiment was carried out to characterize laser-produced x-rays. Interaction of a high-intensity, short-pulse laser with solids produces broadband and monochromatic x-rays with photon energies high enough to probe dense metal rods. Bremsstrahlung was measured with Imaging plate-based filter stack spectrometers and monochromatic 8.0 keV Cu K-alpha was recorded with an absolutely calibrated Bragg crystal spectrometer. The broadband x-ray source was applied to radiography of thick metal objects and different filter materials were tested. The experimental results and a design of a coupled experiment will be presented.

SMC X-3: the closest ultraluminous X-ray source powered by a neutron star with non-dipole magnetic field

NASA Astrophysics Data System (ADS)

Tsygankov, S. S.; Doroshenko, V.; Lutovinov, A. A.; Mushtukov, A. A.; Poutanen, J.

2017-09-01

Aims: The magnetic field of accreting neutron stars determines their overall behavior including the maximum possible luminosity. Some models require an above-average magnetic field strength (≳1013 G) in order to explain super-Eddington mass accretion rate in the recently discovered class of pulsating ultraluminous X-ray sources (ULX). The peak luminosity of SMC X-3 during its major outburst in 2016-2017 reached 2.5 × 1039 erg s-1 comparable to that in ULXs thus making this source the nearest ULX-pulsar. Determination of the magnetic field of SMC X-3 is the main goal of this paper. Methods: SMC X-3 belongs to the class of transient X-ray pulsars with Be optical companions, and exhibited a giant outburst in July 2016-March 2017. The source has been observed over the entire outburst with the Swift/XRT and Fermi/GBM telescopes, as well as the NuSTAR observatory. Collected data allowed us to estimate the magnetic field strength of the neutron star in SMC X-3 using several independent methods. Results: Spin evolution of the source during and between the outbursts, and the luminosity of the transition to the so-called propeller regime in the range of (0.3-7) × 1035 erg s-1 imply a relatively weak dipole field of (1-5) × 1012 G. On the other hand, there is also evidence for a much stronger field in the immediate vicinity of the neutron star surface. In particular, transition from super- to sub-critical accretion regime associated with the cease of the accretion column and very high peak luminosity favor a field that is an order of magnitude stronger. This discrepancy makes SMC X-3 a good candidate for possessing significant non-dipolar components of the field, and an intermediate source between classical X-ray pulsars and accreting magnetars which may constitute an appreciable fraction of ULX population.

Towards phasing using high X-ray intensity

DOE PAGES

Galli, Lorenzo; Son, Sang -Kil; Barends, Thomas R. M.; ...

2015-09-30

X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential `bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. In conclusion, a pattern sorting schememore » is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.« less

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR

Solar coronal magnetic field topology inferred from high resolution optical and x-ray movies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tarbell, T.; Frank, Z.; Hurlburt, N.

1993-01-01

The authors are using high resolution digital movies of solar active regions in optical and X-ray wavelengths to study solar flares and other transients. The optical movies were collected at the Swedish Solar Observatory on La Palma using the Lockheed tunable filtergraph system, in May-July, 1992. They include longitudinal and transverse magnetograms, H-alpha Doppler and intensity images at many wavelengths, Ca K, Na D, and white light images. Simultaneous X-ray images from Yohkoh are available much of the time. Several ways to establish the connectivity of some coronal magnetic field lines are being explored. Some of the clues available are:more » magnetic footpoint polarities and transverse field direction; H-alpha fibrils and loops seen in several wavelengths; proper motion and Dopper shifts of blobs moving along field lines; footprint brightening in micro-flares; spreading of flare ribbons during gradual phases of flares; X-ray morphology and correlations with H-alpha; and draining of flare loops. Examples of each of these will be shown on video.« less

X-ray diffraction study of the caged magnetic compound DyFe 2 Zn 20 at low temperatures

NASA Astrophysics Data System (ADS)

Ohashi, M.; Ohashi, K.; Sawabu, M.; Miyagawa, M.; Maeta, K.; Isikawa, Y.

2018-05-01

We have carried out high-angle X-ray powder diffraction measurements of the caged magnetic compound DyFe2Zn20 at low temperature between 14 and 300 K. Even though a strong magnetic anisotropy exists in the magnetization and magnetic susceptibility due to strong exchange interaction between Fe and Dy, almost all X-ray powder diffraction peaks correspond to Bragg reflections of the cubic structural models not only at room temperature paramagnetic state but also at low temperature magnetic ordering state. The Debye temperature is obtained to be 227 K from the results of the volumetric thermal expansion coefficient, which is approximately coincident with that of CeRu2Zn20 (245 K) and that of pure Zn metal (235 K).

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ishigami, Izumi; Zatsepin, Nadia A.; Hikita, Masahide

Here, cytochrome c oxidase (C cO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine C cO (bC cO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-raymore » crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe–C–O angle of ~142°. In contrast, in the synchrotron structure, the Fe–CO bond is cleaved; CO relocates to a new site near Cu B, which, in turn, moves closer to the heme a 3 iron by ~0.38 Å. Structural comparison reveals that ligand binding to the heme a 3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a 3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.« less

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

DOE PAGES

Ishigami, Izumi; Zatsepin, Nadia A.; Hikita, Masahide; ...

2017-07-11

Here, cytochrome c oxidase (C cO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine C cO (bC cO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-raymore » crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe–C–O angle of ~142°. In contrast, in the synchrotron structure, the Fe–CO bond is cleaved; CO relocates to a new site near Cu B, which, in turn, moves closer to the heme a 3 iron by ~0.38 Å. Structural comparison reveals that ligand binding to the heme a 3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a 3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.« less

Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges

PubMed Central

Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

2015-01-01

Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca2+-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca2+-binding sites of Ca2+-ATPase and that of the iron atom in the heme in catalase. PMID:25730881

Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

PubMed

Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

2015-03-17

Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

Analysis of solar X-ray data

NASA Technical Reports Server (NTRS)

Teske, R. G.

1972-01-01

Type III solar bursts occurring in the absence of solar flares were observed to be accompanied by weak X-radiation. The energy scale of an OSO-3 soft X-ray ion chamber was assessed using realistic theoretical X-ray spectra. Relationships between soft solar X-rays and solar activity were investigated. These included optical studies, the role of the Type III acceleration mechanism in establishing the soft X-ray source volume, H alpha flare intensity variations, and gross magnetic field structure.

Further comments on the effects of vacuum birefringence on the polarization of X-rays emitted from magnetic neutron stars

NASA Technical Reports Server (NTRS)

Chanan, G. A.; Novick, R.; Silver, E. H.

1979-01-01

The birefringence of the vacuum in the presence of strong (of the order of 1 teragauss) magnetic fields will in general affect the polarization of X-rays propagating through these fields. Two of the four Stokes parameters will vary so rapidly with wavelength as to be 'washed out' and unobservable, but the remaining two parameters will be unaffected. These results show that one conclusion of an earlier work is incorrect: Polarized X-ray emission from the surface of a magnetic neutron star will not in general be completely depolarized by the effects of vacuum birefringence. In particular, this birefringence has no effect on the linear polarization of cyclotron emission from the poles of magnetic neutron stars, and a similar result holds for synchrotron emission. More general cases of the propagation of polarized X-rays in magnetic fields are also discussed.

X-ray generator

DOEpatents

Dawson, John M.

1976-01-01

Apparatus and method for producing coherent secondary x-rays that are controlled as to direction by illuminating a mixture of high z and low z gases with an intense burst of primary x-rays. The primary x-rays are produced with a laser activated plasma, and these x-rays strip off the electrons of the high z atoms in the lasing medium, while the low z atoms retain their electrons. The neutral atoms transfer electrons to highly excited states of the highly striped high z ions giving an inverted population which produces the desired coherent x-rays. In one embodiment, a laser, light beam provides a laser spark that produces the intense burst of coherent x-rays that illuminates the mixture of high z and low z gases, whereby the high z atoms are stripped while the low z ones are not, giving the desired mixture of highly ionized and neutral atoms. To this end, the laser spark is produced by injecting a laser light beam, or a plurality of beams, into a first gas in a cylindrical container having an adjacent second gas layer co-axial therewith, the laser producing a plasma and the intense primary x-rays in the first gas, and the second gas containing the high and low atomic number elements for receiving the primary x-rays, whereupon the secondary x-rays are produced therein by stripping desired ions in a neutral gas and transfer of electrons to highly excited states of the stripped ions from the unionized atoms. Means for magnetically confining and stabilizing the plasma are disclosed for controlling the direction of the x-rays.

EIGER detector: application in macromolecular crystallography.

PubMed

Casanas, Arnau; Warshamanage, Rangana; Finke, Aaron D; Panepucci, Ezequiel; Olieric, Vincent; Nöll, Anne; Tampé, Robert; Brandstetter, Stefan; Förster, Andreas; Mueller, Marcus; Schulze-Briese, Clemens; Bunk, Oliver; Wang, Meitian

2016-09-01

The development of single-photon-counting detectors, such as the PILATUS, has been a major recent breakthrough in macromolecular crystallography, enabling noise-free detection and novel data-acquisition modes. The new EIGER detector features a pixel size of 75 × 75 µm, frame rates of up to 3000 Hz and a dead time as low as 3.8 µs. An EIGER 1M and EIGER 16M were tested on Swiss Light Source beamlines X10SA and X06SA for their application in macromolecular crystallography. The combination of fast frame rates and a very short dead time allows high-quality data acquisition in a shorter time. The ultrafine ϕ-slicing data-collection method is introduced and validated and its application in finding the optimal rotation angle, a suitable rotation speed and a sufficient X-ray dose are presented. An improvement of the data quality up to slicing at one tenth of the mosaicity has been observed, which is much finer than expected based on previous findings. The influence of key data-collection parameters on data quality is discussed.

November 15, 1991 X Flare -- The Movie: Hα , Soft X-rays, and Hard X-rays and Magnetic Fields

NASA Astrophysics Data System (ADS)

Wulser, J.-P.; Acton, L.; Sakao, T.; Canfield, R.; Kosugi, T.; Slater, G.; Strong, K.; Tsuneta, S.

1992-05-01

The X1.5/3B flare on 1991 November 15, 22:33 UT was well observed by the Hα Imaging Spectrograph and the Vector Magnetograph (Stokes Polarimeter) at Mees Solar Observatory, and by the Soft- and Hard X-ray Telescopes (SXT and HXT) aboard YOHKOH. We have combined this multispectral dataset into a series of temporally and spatially co-aligned video movies and analyzed the morphological and temporal relationships of the various flare emissions. The earliest manifestations of this flare include unresolved preflare SXR brightenings very close to the magnetic neutral line and preflare motions of filaments seen in Hα . In the flare core, SXR and Hα emission show moving and rotating coronal structures which we interpret as a successive brightening of adjacent loops during the main phase of the flare. The HXR source shows much more dramatic variability than the SXR source, and they are clearly not cospatial. On the other hand, there is a close spatial relationship between the HXR and Hα blue wing emission sites. The Hα , HXR, and SXR images all point to acceleration and heating in a region that starts close to the neutral line and moves outward during each HXR burst and during the gradual phase. Spectacular mass ejections are seen in both SXR and Hα , with clear unwinding of tightly coiled structures, acceleration of X-ray and Hα material to velocities of order 1000 km/s, and a striking thermal bifurcation between hot and cold plasma.

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography.

PubMed

Mueller, C; Marx, A; Epp, S W; Zhong, Y; Kuo, A; Balo, A R; Soman, J; Schotte, F; Lemke, H T; Owen, R L; Pai, E F; Pearson, A R; Olson, J S; Anfinrud, P A; Ernst, O P; Dwayne Miller, R J

2015-09-01

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

PubMed Central

Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; Pai, E. F.; Pearson, A. R.; Olson, J. S.; Anfinrud, P. A.; Ernst, O. P.; Dwayne Miller, R. J.

2015-01-01

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs. PMID:26798825

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

DOE PAGES

Edlund, Petra; Takala, Heikki; Claesson, Elin; ...

2016-10-19

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edlund, Petra; Takala, Heikki; Claesson, Elin

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

PubMed Central

Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

2013-01-01

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

Three-dimensional imaging of nanoscale materials by using coherent x-rays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miao, Jianwei

X-ray crystallography is currently the primary methodology used to determine the 3D structure of materials and macromolecules. However, many nanostructures, disordered materials, biomaterials, hybrid materials and biological specimens are noncrystalline and, hence, their structures are not accessible by X-ray crystallography. Probing these structures therefore requires the employment of different approaches. A very promising technique currently under rapid development is X-ray diffraction microscopy (or lensless imaging), in which the coherent X-ray diffraction pattern of a noncrystalline specimen is measured and then directly phased to obtain a high-resolution image. Through the DOE support over the past three years, we have applied X-raymore » diffraction microscopy to quantitative imaging of GaN quantum dot particles, and revealed the internal GaN-Ga2O3 core shell structure in three dimensions. By exploiting the abrupt change in the scattering cross-section near electronic resonances, we carried out the first experimental demonstration of resonant X-ray diffraction microscopy for element specific imaging. We performed nondestructive and quantitative imaging of buried Bi structures inside a Si crystal by directly phasing coherent X-ray diffraction patterns acquired below and above the Bi M5 edge. We have also applied X-ray diffraction microscopy to nondestructive imaging of mineral crystals inside biological composite materials - intramuscular fish bone - at the nanometer scale resolution. We identified mineral crystals in collagen fibrils at different stages of mineralization and proposed a dynamic mechanism to account for the nucleation and growth of mineral crystals in the collagen matrix. In addition, we have also discovered a novel 3D imaging modality, denoted ankylography, which allows for complete 3D structure determination without the necessity of sample titling or scanning. We showed that when the diffraction pattern of a finite object is sampled at a

Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

DOE PAGES

Hunter, Mark S.; Yoon, Chun Hong; DeMirci, Hasan; ...

2016-11-04

Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity andmore » wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Finally, our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.« less

Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography.

PubMed

Roessler, Christian G; Agarwal, Rakhi; Allaire, Marc; Alonso-Mori, Roberto; Andi, Babak; Bachega, José F R; Bommer, Martin; Brewster, Aaron S; Browne, Michael C; Chatterjee, Ruchira; Cho, Eunsun; Cohen, Aina E; Cowan, Matthew; Datwani, Sammy; Davidson, Victor L; Defever, Jim; Eaton, Brent; Ellson, Richard; Feng, Yiping; Ghislain, Lucien P; Glownia, James M; Han, Guangye; Hattne, Johan; Hellmich, Julia; Héroux, Annie; Ibrahim, Mohamed; Kern, Jan; Kuczewski, Anthony; Lemke, Henrik T; Liu, Pinghua; Majlof, Lars; McClintock, William M; Myers, Stuart; Nelsen, Silke; Olechno, Joe; Orville, Allen M; Sauter, Nicholas K; Soares, Alexei S; Soltis, S Michael; Song, Heng; Stearns, Richard G; Tran, Rosalie; Tsai, Yingssu; Uervirojnangkoorn, Monarin; Wilmot, Carrie M; Yachandra, Vittal; Yano, Junko; Yukl, Erik T; Zhu, Diling; Zouni, Athina

2016-04-05

X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography

DOE PAGES

Roessler, Christian G.; Agarwal, Rakhi; Allaire, Marc; ...

2016-03-17

X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallizationmore » conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. Lastly, we report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). In addition, samples were screened to demonstrate that these methods can be applied to rare samples« less

Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roessler, Christian G.; Agarwal, Rakhi; Allaire, Marc

X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallizationmore » conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.« less

Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roessler, Christian G.; Agarwal, Rakhi; Allaire, Marc

X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallizationmore » conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. Lastly, we report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). In addition, samples were screened to demonstrate that these methods can be applied to rare samples« less

A Newly Designed Microspectrofluorometer for Kinetic Studies on Protein Crystals in Combination with X-Ray Diffraction

PubMed Central

Klink, Björn U.; Goody, Roger S.; Scheidig, Axel J.

2006-01-01

We present a new design for a fluorescence microspectrophotometer for use in kinetic crystallography in combination with x-ray diffraction experiments. The FLUMIX device (Fluorescence spectroscopy to monitor intermediates in x-ray crystallography) is built for 0° fluorescence detection, which has several advantages in comparison to a conventional fluorometer with 90° design. Due to the reduced spatial requirements and the need for only one objective, the system is highly versatile, easy to handle, and can be used for many different applications. In combination with a conventional stereomicroscope, fluorescence measurements or reaction initiation can be performed directly in a hanging drop crystallization setup. The FLUMIX device can be combined with most x-ray sources, normally without the need of a specialized mechanical support. As a biological model system, we have used H-Ras p21 with an artificially introduced photo-labile GTP precursor (caged GTP) and a covalently attached fluorophore (IANBD amide). Using the FLUMIX system, detailed information about the state of photolyzed crystals of the modified H-Ras p21 (p21(mod)) could be obtained. Measurements in combination with a synchrotron beamline showed significant fluorescence changes in p21(mod) crystals even within a few seconds of x-ray exposure at 100 K. PMID:16698776

Development of low temperature and high magnetic field X-ray diffraction facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shahee, Aga; Sharma, Shivani; Singh, K.

2015-06-24

The current progress of materials science regarding multifunctional materials (MFM) has put forward the challenges to understand the microscopic origin of their properties. Most of such MFMs have magneto-elastic correlations. To investigate the underlying mechanism it is therefore essential to investigate the structural properties in the presence of magnetic field. Keeping this in view low temperature and high magnetic field (LTHM) powder x-ray diffraction (XRD), a unique state-of-art facility in the country has been developed at CSR Indore. This setup works on symmetric Bragg Brentano geometry using a parallel incident x-ray beam from a rotating anode source working at 17more » kW. Using this one can do structural studies at non-ambient conditions i.e. at low- temperatures (2-300 K) and high magnetic field (+8 to −8 T). The available scattering angle ranges from 5° to 115° 2θ with a resolution better than 0.1°. The proper functioning of the setup has been checked using Si sample. The effect of magnetic field on the structural properties has been demonstrated on Pr{sub 0.5}Sr{sub 0.5}MnO{sub 3} sample. Clear effect of field induced phase transition has been observed. Moreover, the effect of zero field cooled and field cooled conditions is also observed.« less

Insights into photosystem II from isomorphous difference Fourier maps of femtosecond X-ray diffraction data and quantum mechanics/molecular mechanics structural models

DOE PAGES

Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W.; ...

2017-01-12

Understanding structure–function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metalmore » centers, and different kinetics of the S-state transition in microcrystals compared to solution. Lastly, we summarize recent advances and outstanding challenges in PSII structure–function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.« less

Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models.

PubMed

Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

2017-02-10

Understanding structure-function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metal centers, and different kinetics of the S-state transition in microcrystals compared to solution. Here, we summarize recent advances and outstanding challenges in PSII structure-function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.

Insights into photosystem II from isomorphous difference Fourier maps of femtosecond X-ray diffraction data and quantum mechanics/molecular mechanics structural models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W.

Understanding structure–function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metalmore » centers, and different kinetics of the S-state transition in microcrystals compared to solution. Lastly, we summarize recent advances and outstanding challenges in PSII structure–function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.« less

Multimodal imaging of human cerebellum - merging X-ray phase microtomography, magnetic resonance microscopy and histology

NASA Astrophysics Data System (ADS)

Schulz, Georg; Waschkies, Conny; Pfeiffer, Franz; Zanette, Irene; Weitkamp, Timm; David, Christian; Müller, Bert

2012-11-01

Imaging modalities including magnetic resonance imaging and X-ray computed tomography are established methods in daily clinical diagnosis of human brain. Clinical equipment does not provide sufficient spatial resolution to obtain morphological information on the cellular level, essential for applying minimally or non-invasive surgical interventions. Therefore, generic data with lateral sub-micrometer resolution have been generated from histological slices post mortem. Sub-cellular spatial resolution, lost in the third dimension as a result of sectioning, is obtained using magnetic resonance microscopy and micro computed tomography. We demonstrate that for human cerebellum grating-based X-ray phase tomography shows complementary contrast to magnetic resonance microscopy and histology. In this study, the contrast-to-noise values of magnetic resonance microscopy and phase tomography were comparable whereas the spatial resolution in phase tomography is an order of magnitude better. The registered data with their complementary information permit the distinct segmentation of tissues within the human cerebellum.

Design of Magnetic Shielding and Field Coils for a TES X-Ray Microcalorimeter Test Platform

NASA Technical Reports Server (NTRS)

Miniussi, Antoine R.; Adams, Joseph S.; Bandler, Simon R.; Chervenak, James A.; Datesman, Aaron M.; Doriese, William B.; Eckart, Megan E.; Finkbeiner, Fred M.; Kelley, Richard L.; Kilbourne, Caroline A.;

Applied Crystallography - Proceedings of the XVth Conference

NASA Astrophysics Data System (ADS)

Morawiec, H.; Ströż, D.

1993-06-01

The Table of Contents for the full book PDF is as follows: * Foreword * The International Centre for Diffraction Data and Its Future Developments * The Rietveld Method - A Historical Perspective * Real Structure in Quantitative Powder Diffraction Phase Analysis * Neutron Focusing Optics in Applied Crystallography * The Crystal Structures of Oxygen Deficient Rare Earth Oxides * Short-Range Order in Layer-Structured Ba1-xSrxBi2Nb2O9 Ferroelectrics * Radial Distribution Function as a Tool of Structural Studies on Noncrystalline Materials * Determination of Radial Distribution Function (RDF) of Electrodeposited Cu-Cd Alloys After Annealing * Spheres Packing as a Factor Describing the Local Environment and Structure Stability * X-Ray Stress Measurement of Samples Combined with Diffraction Line Analysis * Phase Stability and Martensitic Transformation in Cu-Zn and Cu-Zn-Al Single Crystals * Order, Defects, Precipitates and the Martensitic Transformation in β Cu-Zn-Al * Effect of γ Precipitates on the Martensitic Transformation in Cu-Zn-Al Alloys * Phase Transitions and Shape Memory Effect in a Thermomechanically Treated NiTi Alloy * Structure of Martensite and Bainite in CuAlMn Alloys * Glass-Ceramics * Mechanism of Texture Formation at the Rolling of Low Stacking Fault Energy Metals and Alloys * Shear Texture of Zinc and the Conditions of Its Occuring * The Development of Texture of ZnAlMg Sheets Depending on Deformation Geometry * Texture Stability of the D.S. NiAlMoCrTi Alloy After Heat Treatment * X-Ray Diffraction Method for Controlling of Texture Evolution in Layers * Texture and Lattice Imperfections Study of Some Low Alloyed Copper Alloys * Selected Examples of the Calculation of the Orientation Distribution Function for Low Crystal and Sample Symmetries * Automatical X-Ray Quantitative Phase Analysis * Application of a PC Computer for Crystallographic Calculations * Electron Diffraction Analysis using a Personal Computer * CA.R.INE Crystallography Version 2

Incoherent Diffractive Imaging via Intensity Correlations of Hard X Rays

NASA Astrophysics Data System (ADS)

Classen, Anton; Ayyer, Kartik; Chapman, Henry N.; Röhlsberger, Ralf; von Zanthier, Joachim

2017-08-01

Established x-ray diffraction methods allow for high-resolution structure determination of crystals, crystallized protein structures, or even single molecules. While these techniques rely on coherent scattering, incoherent processes like fluorescence emission—often the predominant scattering mechanism—are generally considered detrimental for imaging applications. Here, we show that intensity correlations of incoherently scattered x-ray radiation can be used to image the full 3D arrangement of the scattering atoms with significantly higher resolution compared to conventional coherent diffraction imaging and crystallography, including additional three-dimensional information in Fourier space for a single sample orientation. We present a number of properties of incoherent diffractive imaging that are conceptually superior to those of coherent methods.

New Beamlines For Protein Crystallography At The EMBL-Outstation Hamburg

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hermes, C.; Gehrmann, T.; Jahn, D.

2004-05-12

Three new beamlines for Protein Crystallography were built up on a bending magnet fan of the DORIS III storage ring. A 10 mrad wide fan of white Synchrotron Radiation (SR) is evenly distributed among 3 individual stations: X12, a central, wavelength-tunable station intended for anomalous scattering experiments (MAD) and fixed wavelength, high intensity stations symmetrically on either side. The fixed wavelength beamlines X11 and X13 comprise triangular, asymmetrically cut Si (111) monochromators as horizontally focusing optical elements. The tunable station is based on a fixed-exit, horizontally focusing double crystal monochromator system. Vertical focusing is achieved on all three lines bymore » trapezoidal shaped, continuous Rh-coated mirrors which can be dynamically bent. In all three lines the X-ray beam can be examined at various points on its way through the optical system by removable screens and PIN-diode based intensity monitors. Purpose built crystallographic end-stations complete the set-up. The design of individual components and their performance will be described.« less

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakane, Takanori; Song, Changyong; POSTECH, Pohang 790-784

Sulfur SAD phasing facilitates the structure determination of diverse native proteins using femtosecond X-rays from free-electron lasers via serial femtosecond crystallography. Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures.

X-ray studies of neutron stars and their magnetic fields

PubMed Central

MAKISHIMA, Kazuo

2016-01-01

Utilizing results obtained over the past quarter century mainly with Japanese X-ray astronomy satellites, a review is given to some aspects of neutron stars (NSs), with a particular emphasis on the magnetic fields (MFs) of mass-accreting NSs and magnetars. Measurements of electron cyclotron resonance features in binary X-ray pulsars, using the Ginga and Suzaku observatories, clarified that their surface MFs are concentrated in a narrow range of (1–7) × 108 T. Extensive studies of magnetars with Suzaku reinforced their nature as neutron stars with truly strong MFs, and revealed several important clues to their formation, evolution, and physical states. Taking all these results into account, a discussion is made on the origin and evolution of these strong MFs. One possible scenario is that the MF of NSs is a manifestation of some fundamental physics, e.g., neutron spin alignment or chirality violation, and the MF makes transitions from strong to weak states. PMID:27169348

X-ray astronomy from Uhuru to HEAO-1

NASA Technical Reports Server (NTRS)

Clark, G. W.

1981-01-01

The nature of galactic and extragalactic X-ray sources is investigated using observations made with nine satellites and several rockets. The question of X-ray pulsars being neutron stars or white dwarfs is considered, as is the nature of Population II and low-luminosity X-ray stars, the diffuse X-ray emission from clusters of galaxies, the unidentified high-galactic-latitude (UHGL) sources, and the unresolved soft X-ray background. The types of sources examined include binary pulsars, Population II X-ray stars (both nonbursters and bursters) inside and outside globular clusters, coronal X-ray emitters, and active galactic nuclei. It is concluded that: (1) X-ray pulsars are strongly magnetized neutron stars formed in the evolution of massive close binaries; (2) all Population II X-ray stars are weakly magnetized or nonmagnetic neutron stars accreting from low-mass companions in close binary systems; (3) the diffuse emission from clusters is thermal bremsstrahlung of hot matter processed in stars and swept out by ram pressure exerted by the intergalactic gas; (4) most or all of the UHGL sources are active galactic nuclei; and (5) the soft X-ray background is emission from a hot component of the interstellar medium.

Protein crystal structure from non-oriented, single-axis sparse X-ray data

DOE PAGES

Wierman, Jennifer L.; Lan, Ti-Yen; Tate, Mark W.; ...

2016-01-01

X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that aremore » kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases

Protein crystal structure from non-oriented, single-axis sparse X-ray data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wierman, Jennifer L.; Lan, Ti-Yen; Tate, Mark W.

X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that aremore » kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases

Modeling the effect of small-scale magnetic turbulence on the X-ray properties of Pulsar Wind Nebulae

NASA Astrophysics Data System (ADS)

Bucciantini, N.; Bandiera, R.; Olmi, B.; Del Zanna, L.

2017-10-01

Pulsar Wind Nebulae (PWNe) constitute an ideal astrophysical environment to test our current understanding of relativistic plasma processes. It is well known that magnetic fields play a crucial role in their dynamics and emission properties. At present, one of the main issues concerns the level of magnetic turbulence present in these systems, which in the absence of space resolved X-ray polarization measures cannot be directly constrained. In this work, we investigate, for the first time using simulated synchrotron maps, the effect of a small-scale fluctuating component of the magnetic field on the emission properties in X-ray. We illustrate how to include the effects of a turbulent component in standard emission models for PWNe and which consequences are expected in terms of net emissivity and depolarization, showing that the X-ray surface brightness maps can provide already some rough constraints. We then apply our analysis to the Crab and Vela nebulae and by comparing our model with Chandra and Vela data, we found that the typical energies in the turbulent component of the magnetic field are about 1.5-3 times the one in the ordered field.

X-ray resonant magnetic scattering ellipsometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Z.; Randall, K.J.; Gluskin, E.

1996-09-01

It is very difficult to characterize the polarization of a synchrotron radiation source in the soft and/or intermediate x-ray energy region particularly from 1 to 2 keV. Conventional multilayer mirror or single-crystal polarimeters do not work over this energy region because their throughput (the reflectivities combined with the phase shift) becomes insignificant. In this paper, we present a new ellipsometer scheme that is able to fully characterize the polarization of synchrotron radiation sources in this energy region. It is based on the dichroic x-ray resonant ferromagnetic scattering that yields information on both the polarization of the x-ray and the materialmore » (element specific) dielectric-constant tensor [C.-C. Kao {ital et} {ital al}., Phys. Rev. B {bold 50}, 9599 (1994)] due to the interband ferromagnetic Kerr effect [B.R. Cooper, Phys. Rev. A {bold 139}, 1504 (1965)]. {copyright} {ital 1996 American Institute of Physics.}« less

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mueller, C.; Marx, A.; Epp, S. W.

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore » Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

DOE PAGES

Mueller, C.; Marx, A.; Epp, S. W.; ...

2015-08-18

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore » Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

Future directions of electron crystallography.

PubMed

Fujiyoshi, Yoshinori

2013-01-01

In biological science, there are still many interesting and fundamental yet difficult questions, such as those in neuroscience, remaining to be answered. Structural and functional studies of membrane proteins, which are key molecules of signal transduction in neural and other cells, are essential for understanding the molecular mechanisms of many fundamental biological processes. Technological and instrumental advancements of electron microscopy have facilitated comprehension of structural studies of biological components, such as membrane proteins. While X-ray crystallography has been the main method of structure analysis of proteins including membrane proteins, electron crystallography is now an established technique to analyze structures of membrane proteins in the lipid bilayer, which is close to their natural biological environment. By utilizing cryo-electron microscopes with helium-cooled specimen stages, structures of membrane proteins were analyzed at a resolution better than 3 Å. Such high-resolution structural analysis of membrane proteins by electron crystallography opens up the new research field of structural physiology. Considering the fact that the structures of integral membrane proteins in their native membrane environment without artifacts from crystal contacts are critical in understanding their physiological functions, electron crystallography will continue to be an important technology for structural analysis. In this chapter, I will present several examples to highlight important advantages and to suggest future directions of this technique.

Identification of Hard X-ray Sources in Galactic Globular Clusters: Simbol-X Simulations

NASA Astrophysics Data System (ADS)

Servillat, M.

2009-05-01

Globular clusters harbour an excess of X-ray sources compared to the number of X-ray sources in the Galactic plane. It has been proposed that many of these X-ray sources are cataclysmic variables that have an intermediate magnetic field, i.e. intermediate polars, which remains to be confirmed and understood. We present here several methods to identify intermediate polars in globular clusters from multiwavelength analysis. First, we report on XMM-Newton, Chandra and HST observations of the very dense Galactic globular cluster NGC 2808. By comparing UV and X-ray properties of the cataclysmic variable candidates, the fraction of intermediate polars in this cluster can be estimated. We also present the optical spectra of two cataclysmic variables in the globular cluster M 22. The HeII (4868 Å) emission line in these spectra could be related to the presence of a magnetic field in these objects. Simulations of Simbol-X observations indicate that the angular resolution is sufficient to study X-ray sources in the core of close, less dense globular clusters, such as M 22. The sensitivity of Simbol-X in an extended energy band up to 80 keV will allow us to discriminate between hard X-ray sources (such as magnetic cataclysmic variables) and soft X-ray sources (such as chromospherically active binaries).

UCSD High Energy X-ray Timing Experiment magnetic shield design and test results

NASA Technical Reports Server (NTRS)

Rothschild, Richard E.; Pelling, Michael R.; Hink, Paul L.

1991-01-01

Results are reported from an effort to define a passive magnetic field concept for the High Energy X-ray Timing Experiment (HEXTE), in the interest of reducing the detector-gain variations due to 0.5-1.0-sec timescale magnetic field variations. This will allow a sensitivity of the order of 1 percent of the HEXTE background. While aperture modulation and automatic gain control will minimize effects on timescales of tens of seconds and longer, passive magnetic shielding of the photomultiplier tubes will address 1-sec timescale variations due to aperture motions.

Performance of Magnetic Penetration Thermometers for X-Ray Astronomy

NASA Technical Reports Server (NTRS)

Nagler, P. C.; Adams, J. S.; Balvin, M. A.; Bandler, S. R.; Denis, K. L.; Hsieh, W. T.; Kelly, D. P.; Porst, J. P.; Sadleir, J. E.; Seidel, G. M.;

Magnetic field strength of a neutron-star-powered ultraluminous X-ray source

NASA Astrophysics Data System (ADS)

Brightman, M.; Harrison, F. A.; Fürst, F.; Middleton, M. J.; Walton, D. J.; Stern, D.; Fabian, A. C.; Heida, M.; Barret, D.; Bachetti, M.

2018-04-01

Ultraluminous X-ray sources (ULXs) are bright X-ray sources in nearby galaxies not associated with the central supermassive black hole. Their luminosities imply they are powered by either an extreme accretion rate onto a compact stellar remnant, or an intermediate mass ( 100-105M⊙) black hole1. Recently detected coherent pulsations coming from three bright ULXs2-5 demonstrate that some of these sources are powered by accretion onto a neutron star, implying accretion rates significantly in excess of the Eddington limit, a high degree of geometric beaming, or both. The physical challenges associated with the high implied accretion rates can be mitigated if the neutron star surface field is very high (1014 G)6, since this suppresses the electron scattering cross-section, reducing the radiation pressure that chokes off accretion for high luminosities. Surface magnetic field strengths can be determined through cyclotron resonance scattering features7,8 produced by the transition of charged particles between quantized Landau levels. Here, we present the detection at a significance of 3.8σ of an absorption line at 4.5 keV in the Chandra spectrum of a ULX in M51. This feature is likely to be a cyclotron resonance scattering feature produced by the strong magnetic field of a neutron star. Assuming scattering off electrons, the magnetic field strength is implied to be 1011 G, while protons would imply a magnetic field of B 1015 G.

Soft X-Ray Emissions from Planets and Moons

NASA Technical Reports Server (NTRS)

Bhardwaj, A.; Gladstone, G. R.; Elsner, R. F.; Waite, J. H., Jr.; Grodent, D.; Lewis, W. S.; Crary, F. J.; Weisskopf, M. C.; Howell, R. R.; Johnson, R. E.;

The superslow pulsation X-ray pulsars in high mass X-ray binaries

NASA Astrophysics Data System (ADS)

Wang, Wei

2013-03-01

There exists a special class of X-ray pulsars that exhibit very slow pulsation of P spin > 1000 s in the high mass X-ray binaries (HMXBs). We have studied the temporal and spectral properties of these superslow pulsation neutron star binaries in hard X-ray bands with INTEGRAL observations. Long-term monitoring observations find spin period evolution of two sources: spin-down trend for 4U 2206+54 (P spin ~ 5560 s with Ṗ spin ~ 4.9 × 10-7 s s-1) and long-term spin-up trend for 2S 0114+65 (P spin ~ 9600 s with Ṗ spin ~ -1 × 10-6 s s-1) in the last 20 years. A Be X-ray transient, SXP 1062 (P spin ~ 1062 s), also showed a fast spin-down rate of Ṗ spin ~ 3 × 10-6 s s-1 during an outburst. These superslow pulsation neutron stars cannot be produced in the standard X-ray binary evolution model unless the neutron star has a much stronger surface magnetic field (B > 1014 G). The physical origin of the superslow spin period is still unclear. The possible origin and evolution channels of the superslow pulsation X-ray pulsars are discussed. Superslow pulsation X-ray pulsars could be younger X-ray binary systems, still in the fast evolution phase preceding the final equilibrium state. Alternatively, they could be a new class of neutron star system - accreting magnetars.

Design of High Resolution Soft X-Ray Microcalorimeters Using Magnetic Penetration Thermometers

NASA Technical Reports Server (NTRS)

Busch. Sarah; Balvin, Manuel; Bandler, Simon; Denis, Kevin; Finkbeiner, Fred; Porst, Jan-Patrick; Sadlier, Jack; Smith, Stephen; Stevenson, Thomas

2012-01-01

We have designed high-resolution soft x-ray microcalorimeters using magnetic penetration thermometers (MPTs) in an array of pixels covering a total of 2 square centimeters to have a resolving power of 300 at energies around 300 eV. This performance is desirable for studying the soft x-ray background from the warm hot intergalactic medium. MPT devices have small sensor heat capacity and high responsivities, which makes them excellent detector technology for attempting to attain sub-eV resolution. We are investigating the feasibility of pixels with absorbers that are 625 x 625 square micrometers, up to 1 x 1 square millimeters in area and 0.35 micrometer thick and thinner. Our tests have shown that suspended gold absorbers 0.35 micrometers thick (RRR = 6.7) are feasible to fabricate. We modeled the thermal diffusion from such thin gold over the size of a 625 x 625 square micrometer absorber, and conclude that the effect of the thermalization on the resolution of a 300 eV photon is an additional approximately 0.2 eV FWHM of broadening. We discuss the thermal effects of small absorber attachment sterns on solid substrate, as well as considerations for multiplexed readout. We will present the progress we have made towards building and testing this soft x-ray detector.

Plain X-ray, computed tomography and magnetic resonance imaging findings of telangiectatic osteosarcoma: a case report.

PubMed

Skiadas, Vasilios; Koutoulidis, Vasilios; Koureas, Andreas; Moulopoulos, Lia; Gouliamos, Athanasios

2009-09-16

An 18-year-old male patient presented with chronic nonspecific pain of three months located at his left proximal tibia. The patient was admitted to our department for plain X-ray, computed tomography and magnetic resonance imaging examination. Plain X-ray and computed tomography revealed a geographic lytic lesion at the medial aspect of the proximal tibia. Biopsy of the lesion showed telangiectatic osteosarcoma. Image findings of all modalities are presented.

First-principles analysis of X-ray magnetic circular dichroism for transition metal complex oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ikeno, Hidekazu, E-mail: h-ikeno@21c.osakafu-u.ac.jp

2016-10-14

X-ray magnetic circular dichroism (XMCD) is widely used for the characterization of magnetism of materials. However, information from XMCD related to the atomic, electronic, and magnetic structures is not fully utilized due to the lack of reliable theoretical tools for spectral analysis. In this work, the first-principles configuration interaction (CI) calculations for X-ray absorption spectra developed by the author were extended for the calculation of XMCD, where the Zeeman energy was taken into the Hamiltonian of the CI to mimic magnetic polarization in the solid state. This technique was applied to interpret the L{sub 2,3} XMCD from 3d transition metalmore » complex oxides, such as NiFe{sub 2}O{sub 4} and FeTiO{sub 3}. The experimental XMCD spectra were quantitatively reproduced using this method. The oxidation states as well as the magnetic ordering between transition metal ions on crystallographically different sites in NiFe{sub 2}O{sub 4} can be unambiguously determined. A first-principles analysis of XMCD in FeTiO{sub 3} revealed the presence of Fe{sup 3+} and Ti{sup 3+} ions, which indicates that the charge transfer from Fe to Ti ions occurs. The origin of magnetic polarization of Ti ions in FeTiO{sub 3} was also discussed.« less

Serial Femtosecond Crystallography of G Protein-Coupled Receptors

PubMed Central

Liu, Wei; Wacker, Daniel; Gati, Cornelius; Han, Gye Won; James, Daniel; Wang, Dingjie; Nelson, Garrett; Weierstall, Uwe; Katritch, Vsevolod; Barty, Anton; Zatsepin, Nadia A.; Li, Dianfan; Messerschmidt, Marc; Boutet, Sébastien; Williams, Garth J.; Koglin, Jason E.; Seibert, M. Marvin; Wang, Chong; Shah, Syed T.A.; Basu, Shibom; Fromme, Raimund; Kupitz, Christopher; Rendek, Kimberley N.; Grotjohann, Ingo; Fromme, Petra; Kirian, Richard A.; Beyerlein, Kenneth R.; White, Thomas A.; Chapman, Henry N.; Caffrey, Martin; Spence, John C.H.; Stevens, Raymond C.; Cherezov, Vadim

2014-01-01

X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. Here we used an x-ray free-electron laser (XFEL) with individual 50-fs duration x-ray pulses to minimize radiation damage and obtained a high-resolution room temperature structure of a human serotonin receptor using sub-10 µm microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared to the structure solved by traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment. PMID:24357322

X-ray magneto-optic KERR effect studies of spring magnet heterostructures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kortright, J. B.; Kim, S.-K.; Fullerton, E. E.

2000-11-01

The complex 3-dimensional magnetization reversal behavior of Sin-Co/Fe exchange spring films is used to test the sensitivity of different resonant soft x-ray magneto-optical Kerr effect (MOKE) measurements to changes in longitudinal and transverse moments within the SOIIFe layer and to changes in these moments in depth within the Fe layer. As in the visible MOKE, changes in longitudinal and net transverse moments are resolved by measuring both Kerr rotation and intensity loops in the near the Fe 2p core resonance. These x-ray MOKE signals measured using linear incident polarization are more directly interpreted in terms of longitudinal and transverse momentsmore » than are the same signals measured using elliptical polarization. Varying photon energy near the Fe L3line is shown to be an effective means of resolving distinctly different reversal behavior at the top and bottom of the 20 nm thick Fe layer resulting from the strong exchange coupling at the Sin-Co/Fe interface. Measured x-ray MOKE spectra and signals are in qualitative agreement with those calculated using standard magneto-optical formalisms incorporating interference between different layers and measured helicity-dependent magneto-optical constants for Fe.« less

Searching for X-ray emission from AGB stars

NASA Astrophysics Data System (ADS)

Ramstedt, S.; Montez, R.; Kastner, J.; Vlemmings, W. H. T.

2012-07-01

Context. Magnetic fields have been measured around asymptotic giant branch (AGB) stars of all chemical types using maser polarization observations. If present, a large-scale magnetic field would lead to X-ray emission, which should be observable using current X-ray observatories. Aims: The aim is to search the archival data for AGB stars that are intrinsic X-ray emitters. Methods: We have searched the ROSAT, CXO, and XMM-Newton archives for serendipitous X-ray observations of a sample of ~500 AGB stars. We specifically searched for the AGB stars detected with GALEX. The data is calibrated, analyzed and the X-ray luminosities and temperatures are estimated as functions of the circumstellar absorption. Results: We identify 13 AGB stars as having either serendipitous or targeted observations in the X-ray data archives, however for a majority of the sources the detailed analysis show that the detections are questionable. Two new sources are detected by ROSAT: T Dra and R UMa. The spectral analysis suggests that the emission associated with these sources could be due to coronal activity or interaction across a binary system. Conclusions: Further observations of the detected sources are necessary to clearly determine the origin of the X-ray emission. Moreover, additional objects should be subject to targeted X-ray observations in order to achieve better constraints for the magnetic fields around AGB stars. Appendices are available in electronic form at http://www.aanda.org

Structural investigation of oxovanadium(IV) Schiff base complexes: X-ray crystallography, electrochemistry and kinetic of thermal decomposition.

PubMed

Asadi, Mozaffar; Asadi, Zahra; Savaripoor, Nooshin; Dusek, Michal; Eigner, Vaclav; Shorkaei, Mohammad Ranjkesh; Sedaghat, Moslem

2015-02-05

A series of new VO(IV) complexes of tetradentate N2O2 Schiff base ligands (L(1)-L(4)), were synthesized and characterized by FT-IR, UV-vis and elemental analysis. The structure of the complex VOL(1)⋅DMF was also investigated by X-ray crystallography which revealed a vanadyl center with distorted octahedral coordination where the 2-aza and 2-oxo coordinating sites of the ligand were perpendicular to the "-yl" oxygen. The electrochemical properties of the vanadyl complexes were investigated by cyclic voltammetry. A good correlation was observed between the oxidation potentials and the electron withdrawing character of the substituents on the Schiff base ligands, showing the following trend: MeO5-H>5-Br>5-Cl. Furthermore, the kinetic parameters of thermal decomposition were calculated by using the Coats-Redfern equation. According to the Coats-Redfern plots the kinetics of thermal decomposition of studied complexes is of the first-order in all stages, the free energy of activation for each following stage is larger than the previous one and the complexes have good thermal stability. The preparation of VOL(1)⋅DMF yielded also another compound, one kind of vanadium oxide [VO]X, with different habitus of crystals, (platelet instead of prisma) and without L(1) ligand, consisting of a V10O28 cage, diaminium moiety and dimethylamonium as a counter ions. Because its crystal structure was also new, we reported it along with the targeted complex. Copyright © 2014 Elsevier B.V. All rights reserved.

Plain X-ray, computed tomography and magnetic resonance imaging findings of telangiectatic osteosarcoma: a case report

PubMed Central

Koutoulidis, Vasilios; Koureas, Andreas; Moulopoulos, Lia; Gouliamos, Athanasios

2009-01-01

An 18-year-old male patient presented with chronic nonspecific pain of three months located at his left proximal tibia. The patient was admitted to our department for plain X-ray, computed tomography and magnetic resonance imaging examination. Plain X-ray and computed tomography revealed a geographic lytic lesion at the medial aspect of the proximal tibia. Biopsy of the lesion showed telangiectatic osteosarcoma. Image findings of all modalities are presented. PMID:19918488

Serial femtosecond crystallography: A revolution in structural biology.

PubMed

Martin-Garcia, Jose M; Conrad, Chelsie E; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

2016-07-15

Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. Published by Elsevier Inc.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

NASA Astrophysics Data System (ADS)

Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; Berntsen, Peter; Bielecki, Johan; Daurer, Benedikt J.; DeMirci, Hasan; Fromme, Petra; Hantke, Max Felix; Maia, Filipe R. N. C.; Munke, Anna; Nettelblad, Carl; Pande, Kanupriya; Reddy, Hemanth K. N.; Sellberg, Jonas A.; Sierra, Raymond G.; Svenda, Martin; van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu; Aquila, Andrew; Zwart, Peter H.; Mancuso, Adrian P.

2017-10-01

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

Synthesis, X-ray characterisation and reactions of a trigonal planar palladium(0) carbonyl complex, (tbpx)PdCO.

PubMed

Bellabarba, Ronan M; Tooze, Robert P; Slawin, Alexandra M Z

2003-08-07

The novel complex (tbpx)PdCO (1), the first example of a structurally characterised sixteen electron, trigonal planar palladium(0) carbonyl complex, was prepared, characterised by NMR spectroscopy and X-ray crystallography, and some unusual aspects of its reactivity were studied.

Magnetic and chemical nonuniformity in Ga{sub 1-x}Mn{sub x}As films as probed by polarized neutron and x-ray reflectometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirby, B. J.; Borchers, J. A.; Rhyne, J. J.

We have used complementary neutron and x-ray reflectivity techniques to examine the depth profiles of a series of as-grown and annealed Ga{sub 1-x}Mn{sub x}As thin films. A magnetization gradient is observed for two as-grown films and originates from a nonuniformity of Mn at interstitial sites, and not from local variations in Mn at Ga sites. Furthermore, we see that the depth-dependent magnetization can vary drastically among as-grown Ga{sub 1-x}Mn{sub x}As films despite being deposited under seemingly similar conditions. These results imply that the depth profile of interstitial Mn is dependent not only on annealing, but is also extremely sensitive tomore » initial growth conditions. We observe that annealing improves the magnetization by producing a surface layer that is rich in Mn and O, indicating that the interstitial Mn migrates to the surface. Finally, we expand upon our previous neutron reflectivity study of Ga{sub 1-x}Mn{sub x}As, by showing how the depth profile of the chemical composition at the surface and through the film thickness is directly responsible for the complex magnetization profiles observed in both as-grown and annealed films.« less

Mix-and-diffuse serial synchrotron crystallography

DOE PAGES

Beyerlein, Kenneth R.; Dierksmeyer, Dennis; Mariani, Valerio; ...

2017-10-09

Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzymemore » at a high level of detail. Here, the success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.« less

Mix-and-diffuse serial synchrotron crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beyerlein, Kenneth R.; Dierksmeyer, Dennis; Mariani, Valerio

Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzymemore » at a high level of detail. Here, the success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.« less

Development of Superconducting Insertion Device Magnets at NSRRC

NASA Astrophysics Data System (ADS)

Hwang, C. S.; Chang, C. H.; Chen, H. H.; Jan, J. C.; Lin, F. Y.; Fan, T. C.; Chen, J.; Hsu, S. N.; Hsu, K. T.; Huang, M. H.; Chang, H. P.; Hsiung, G. Y.; Chien, Y. C.; Chen, J. R.; Kuo, C. C.; Chen, C. T.

2007-01-01

A superconducting wavelength shifter (SWLS) with a magnetic field of 6.5 T in cryogen-free operation provides X-rays for high-resolution X-ray microscopy, EXAFS, and medical imaging beamlines. A 32-pole superconducting wiggler (SW) with a period of 6.1 cm and a magnetic field of 3.2 T in a liquid helium bath provides for three dedicated protein crystallography beamlines. Additionally, three 16-pole in-achromatic superconducting wigglers (IASW) with a period of 6.1 cm and a field strength of 3.1 T were constructed in-house and installed between the first and second bending magnets of a TBA arc section. Development of a prototype superconducting undulator (SU15) with a period of 15 mm and a field strength of 1.4 T is currently underway at National Synchrotron Radiation Research Center (MSRRC).

The X-Ray View of Young Stellar Objects

NASA Astrophysics Data System (ADS)

Guedel, Manuel

2007-08-01

X-rays offer ideal access to high-energy phenomena in young, accreting stars. The energy released in magnetic flares has profound effects on the stellar environment. Star-disk magnetic reconnection has been suggested as a possible origin of bipolar jets. Such jets from have been detected at X-ray wavelengths, offering new diagnostics for the energy release and jet shock physics. Finally, eruptive phenomena of FU Ori and EX Lup-type stars have been monitored in X-rays. I will discuss observations and suggest simple models for high-energy eruptive phenomena in young stars.

Construction of a magnetic bottle spectrometer and its application to pulse duration measurement of X-ray laser using a pump-probe method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Namba, S., E-mail: namba@hiroshima-u.ac.jp; Hasegawa, N.; Kishimoto, M.

To characterize the temporal evolution of ultrashort X-ray pulses emitted by laser plasmas using a pump-probe method, a magnetic bottle time-of-flight electron spectrometer is constructed. The design is determined by numerical calculations of a mirror magnetic field and of the electron trajectory in a flight tube. The performance of the spectrometer is characterized by measuring the electron spectra of xenon atoms irradiated with a laser-driven plasma X-ray pulse. In addition, two-color above-threshold ionization (ATI) experiment is conducted for measurement of the X-ray laser pulse duration, in which xenon atoms are simultaneously irradiated with an X-ray laser pump and an IRmore » laser probe. The correlation in the intensity of the sideband spectra of the 4d inner-shell photoelectrons and in the time delay of the two laser pulses yields an X-ray pulse width of 5.7 ps, in good agreement with the value obtained using an X-ray streak camera.« less

Visualizing chemical states and defects induced magnetism of graphene oxide by spatially-resolved-X-ray microscopy and spectroscopy.

PubMed

Wang, Y F; Singh, Shashi B; Limaye, Mukta V; Shao, Y C; Hsieh, S H; Chen, L Y; Hsueh, H C; Wang, H T; Chiou, J W; Yeh, Y C; Chen, C W; Chen, C H; Ray, Sekhar C; Wang, J; Pong, W F; Takagi, Y; Ohigashi, T; Yokoyama, T; Kosugi, N

2015-10-20

This investigation studies the various magnetic behaviors of graphene oxide (GO) and reduced graphene oxides (rGOs) and elucidates the relationship between the chemical states that involve defects therein and their magnetic behaviors in GO sheets. Magnetic hysteresis loop reveals that the GO is ferromagnetic whereas photo-thermal moderately reduced graphene oxide (M-rGO) and heavily reduced graphene oxide (H-rGO) gradually become paramagnetic behavior at room temperature. Scanning transmission X-ray microscopy and corresponding X-ray absorption near-edge structure spectroscopy were utilized to investigate thoroughly the variation of the C 2p(π*) states that are bound with oxygen-containing and hydroxyl groups, as well as the C 2p(σ*)-derived states in flat and wrinkle regions to clarify the relationship between the spatially-resolved chemical states and the magnetism of GO, M-rGO and H-rGO. The results of X-ray magnetic circular dichroism further support the finding that C 2p(σ*)-derived states are the main origin of the magnetism of GO. Based on experimental results and first-principles calculations, the variation in magnetic behavior from GO to M-rGO and to H-rGO is interpreted, and the origin of ferromagnetism is identified as the C 2p(σ*)-derived states that involve defects/vacancies rather than the C 2p(π*) states that are bound with oxygen-containing and hydroxyl groups on GO sheets.

Visualizing chemical states and defects induced magnetism of graphene oxide by spatially-resolved-X-ray microscopy and spectroscopy

PubMed Central

Wang, Y. F.; Singh, Shashi B.; Limaye, Mukta V.; Shao, Y. C.; Hsieh, S. H.; Chen, L. Y.; Hsueh, H. C.; Wang, H. T.; Chiou, J. W.; Yeh, Y. C.; Chen, C. W.; Chen, C. H.; Ray, Sekhar C.; Wang, J.; Pong, W. F.; Takagi, Y.; Ohigashi, T.; Yokoyama, T.; Kosugi, N.

2015-01-01

This investigation studies the various magnetic behaviors of graphene oxide (GO) and reduced graphene oxides (rGOs) and elucidates the relationship between the chemical states that involve defects therein and their magnetic behaviors in GO sheets. Magnetic hysteresis loop reveals that the GO is ferromagnetic whereas photo-thermal moderately reduced graphene oxide (M-rGO) and heavily reduced graphene oxide (H-rGO) gradually become paramagnetic behavior at room temperature. Scanning transmission X-ray microscopy and corresponding X-ray absorption near-edge structure spectroscopy were utilized to investigate thoroughly the variation of the C 2p(π*) states that are bound with oxygen-containing and hydroxyl groups, as well as the C 2p(σ*)-derived states in flat and wrinkle regions to clarify the relationship between the spatially-resolved chemical states and the magnetism of GO, M-rGO and H-rGO. The results of X-ray magnetic circular dichroism further support the finding that C 2p(σ*)-derived states are the main origin of the magnetism of GO. Based on experimental results and first-principles calculations, the variation in magnetic behavior from GO to M-rGO and to H-rGO is interpreted, and the origin of ferromagnetism is identified as the C 2p(σ*)-derived states that involve defects/vacancies rather than the C 2p(π*) states that are bound with oxygen-containing and hydroxyl groups on GO sheets. PMID:26481557

Uranium Hydridoborates: Synthesis, Magnetism, and X-ray/Neutron Diffraction Structures.

PubMed

Braunschweig, H; Gackstatter, A; Kupfer, T; Radacki, K; Franke, S; Meyer, K; Fucke, K; Lemée-Cailleau, M-H

2015-08-17

While uranium hydridoborate complexes containing the [BH4](-) moiety have been well-known in the literature for many years, species with functionalized borate centers remained considerably rare. We were now able to prepare several uranium hydridoborates (1-4) with amino-substituted borate moieties with high selectivity by smooth reaction of [Cp*2UMe2] (Cp* = C5Me5) and [Cp'2UMe2] (Cp' = 1,2,4-tBu3C5H2) with the aminoborane H2BN(SiMe3)2. A combination of nuclear magnetic resonance spectroscopy, deuteration experiments, magnetic SQUID measurements, and X-ray/neutron diffraction studies was used to verify the anticipated molecular structures and oxidation states of 1-4 and helped to establish a linear tridentate coordination mode of the borate anions.

Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology.

PubMed

Mizohata, Eiichi; Nakane, Takanori; Fukuda, Yohta; Nango, Eriko; Iwata, So

2018-04-01

X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca. 200-50 μm). In recent years, one of the most important technological innovations in structural biology has been the development of X-ray free electron lasers (XFELs). The SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan generates the XFEL beam by accelerating electrons to relativistic speeds and directing them through in-vacuum, short-period undulators. Since user operation started in 2012, we have been involved in the development of serial femtosecond crystallography (SFX) measurement systems using XFEL at the SACLA. The SACLA generates X-rays a billion times brighter than SPring-8. The extremely bright XFEL pulses enable data collection with microcrystals (ca. 50-1 μm). Although many molecular analysis techniques exist, SFX is the only technique that can visualize radiation-damage-free structures of biological macromolecules at room temperature in atomic resolution and fast time resolution. Here, we review the achievements of the SACLA-SFX Project in the past 5 years. In particular, we focus on: (1) the measurement system for SFX; (2) experimental phasing by SFX; (3) enzyme chemistry based on damage-free room-temperature structures; and (4) molecular movie taken by time-resolved SFX.

Synthesis, characterization, X-ray crystallography, acetyl cholinesterase inhibition and antioxidant activities of some novel ketone derivatives of gallic hydrazide-derived Schiff bases.

PubMed

Gwaram, Nura Suleiman; Ali, Hapipah Mohd; Abdulla, Mahmood Ameen; Buckle, Michael J C; Sukumaran, Sri Devi; Chung, Lip Yong; Othman, Rozana; Alhadi, Abeer A; Yehye, Wageeh A; Hadi, A Hamid A; Hassandarvish, Pouya; Khaledi, Hamid; Abdelwahab, Siddig Ibrahim

2012-02-28

Alzheimer's disease (AD) is the most common form of dementia among older people and the pathogenesis of this disease is associated with oxidative stress. Acetylcholinesterase inhibitors with antioxidant activities are considered potential treatments for AD. Some novel ketone derivatives of gallic hydrazide-derived Schiff bases were synthesized and examined for their antioxidant activities and in vitro and in silico acetyl cholinesterase inhibition. The compounds were characterized using spectroscopy and X-ray crystallography. The ferric reducing antioxidant power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays revealed that all the compounds have strong antioxidant activities. N-(1-(5-bromo-2-hydroxyphenyl)-ethylidene)-3,4,5-trihydroxybenzohydrazide (2) was the most potent inhibitor of human acetyl cholinesterase, giving an inhibition rate of 77% at 100 μM. Molecular docking simulation of the ligand-enzyme complex suggested that the ligand may be positioned in the enzyme's active-site gorge, interacting with residues in the peripheral anionic subsite (PAS) and acyl binding pocket (ABP). The current work warrants further preclinical studies to assess the potential for these novel compounds for the treatment of AD.

Analyzing the Spectra of Accreting X-Ray Pulsars

NASA Astrophysics Data System (ADS)

Wolff, Michael

This proposal seeks funding for the analysis of accretion-powered X-ray pulsar spectra from NASA/ HEASARC archived X-ray data. Spectral modeling of accreting X-ray pulsars can tell us a great deal about the physical conditions in and near high mass X-ray binary systems. Such systems have accretion flows where plasma is initially channeled from an accretion disk by the strong neutron star magnetic field, eventually falling onto the magnetic polar cap of the neutron star compact object. Many of these accreting X-ray pulsars have X-ray spectra that consist of broad power-law continua with superposed cyclotron resonant scattering features indicating magnetic field strengths above 10^12 G. The energies of these cyclotron line features have recently been shown to vary with X-ray luminosity in a number of sources such as Her X-1 and V 0332+53, a phenomenon not well understood. Another recent development is the relatively new analytic model for the spectral continuum formation in accretion-powered pulsar systems developed by Becker & Wolff. In their formalism the accretion flows are assumed to go through radiation- dominated radiative shocks and settle onto the neutron star surface. The radiation field consists of strongly Comptonized bremsstrahlung emission from the entire plasma, Comptonized cyclotron emission from the de-excitations of Landau-excited electrons in the neutron star magnetic field, and Comptonized black-body emission from a thermal mound near the neutron star surface. We seek to develop the data analysis tools to apply this model framework to the X-ray data from a wide set of sources to make progress characterizing the basic accretion properties (e.g., magnetic field strength, plasma temperatures, polar cap size, accretion rate per unit area, dominance of bulk vs. thermal Comptonization) as well as understanding the variations of the cyclotron line energies with X-ray luminosity. The three major goals of our proposed work are as follows: In the first year

Measuring and modeling diffuse scattering in protein X-ray crystallography

PubMed Central

Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; Brewster, Aaron S.; Sauter, Nicholas K.; Wall, Michael E.

2016-01-01

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering. PMID:27035972

Measuring and modeling diffuse scattering in protein X-ray crystallography

DOE PAGES

Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; ...

2016-03-28

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practicesmore » for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. In conclusion, these results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.« less

X-ray magnetic circular dichroism measured at the Fe K-edge with a reduced intrinsic broadening: x-ray absorption spectroscopy versus resonant inelastic x-ray scattering measurements

NASA Astrophysics Data System (ADS)

Juhin, Amélie; Sainctavit, Philippe; Ollefs, Katharina; Sikora, Marcin; Filipponi, Adriano; Glatzel, Pieter; Wilhelm, Fabrice; Rogalev, Andrei

2016-12-01

X-ray magnetic circular dichroism is measured at the Fe K pre-edge in yttrium iron garnet using two different procedures that allow reducing the intrinsic broadening due to the 1s corehole lifetime. First, deconvolution of XMCD data measured in total fluorescence yield (TFY) with an extremely high signal-to-noise ratio enables a factor of 2.4 to be gained in the XMCD intensity. Ligand field multiplet calculations performed with different values of intrinsic broadening show that deconvolving such high quality XMCD data is similar to reducing the lifetime broadening from a 1s corehole to a 2p corehole. Second, MCD is measured by resonant inelastic x-ray scattering spectroscopy as a function of incident energy and emission energy. Selection of a fixed emission energy, instead of using the TFY, allows enhancing the MCD intensity up to a factor of  ˜4.7. However, this significantly changes the spectral shape of the XMCD signal, which cannot be interpreted any more as an absorption spectrum.

Normal incidence X-ray telescope power spectra of X-ray emission from solar active regions. I - Observations. II - Theory

NASA Technical Reports Server (NTRS)

Gomez, Daniel O.; Martens, Petrus C. H.; Golub, Leon

1993-01-01

Fourier analysis is applied to very high resolution image of coronal active regions obtained by the Normal Incidence X-Ray Telescope is used to find a broad isotropic power-law spectrum of the spatial distribution of soft X-ray intensities. Magnetic structures of all sizes are present down to the resolution limit of the instrument. Power spectra for the X-ray intensities of a sample of topologically different active regions are found which fall off with increasing wavenumber as 1/k-cubed. A model is presented that relates the basic features of coronal magnetic fluctuations to the subphotospheric hydrodynamic turbulence that generates them. The model is used to find a theoretical power spectrum for the X-ray intensity which falls off with increasing wavenumber as 1/k-cubed. The implications of a turbulent regime in active regions are discussed.

Fab Chaperone-Assisted RNA Crystallography (Fab CARC).

PubMed

Sherman, Eileen; Archer, Jennifer; Ye, Jing-Dong

2016-01-01

Recent discovery of structured RNAs such as ribozymes and riboswitches shows that there is still much to learn about the structure and function of RNAs. Knowledge learned can be employed in both biochemical research and clinical applications. X-ray crystallography gives unparalleled atomic-level structural detail from which functional inferences can be deduced. However, the difficulty in obtaining high-quality crystals and their phasing information make it a very challenging task. RNA crystallography is particularly arduous due to several factors such as RNA's paucity of surface chemical diversity, lability, repetitive anionic backbone, and flexibility, all of which are counterproductive to crystal packing. Here we describe Fab chaperone assisted RNA crystallography (CARC), a systematic technique to increase RNA crystallography success by facilitating crystal packing as well as expediting phase determination through molecular replacement of conserved Fab domains. Major steps described in this chapter include selection of a synthetic Fab library displayed on M13 phage against a structured RNA crystallization target, ELISA for initial choice of binding Fabs, Fab expression followed by protein A affinity then cation exchange chromatography purification, final choice of Fab by binding specificity and affinity as determined by a dot blot assay, and lastly gel filtration purification of a large quantity of chosen Fabs for crystallization.

1,3-Oxazole-based selective picomolar inhibitors of cytosolic human carbonic anhydrase II alleviate ocular hypertension in rabbits: Potency is supported by X-ray crystallography of two leads.

PubMed

Ferraroni, Marta; Lucarini, Laura; Masini, Emanuela; Korsakov, Mikhail; Scozzafava, Andrea; Supuran, Claudiu T; Krasavin, Mikhail

2017-09-01

Two lead 1,3-oxazole-based carbonic anhydrase inhibitors (CAIs) earlier identified as selective, picomolar inhibitors of hCA II (a cytosolic target for treatment of glaucoma) have been investigated further. Firstly, they were found to be conveniently synthesized on multigram scale, which enables further development. These compounds were found to be comparable in efficacy to dorzolamide eye drops when applied in the eye drop form as well. Finally, the reasons for unusually high potency of these compounds became understood from their high-resolution X-ray crystallography structures. These data significantly expand our understanding of heterocycle-based primary sulfonamides, many of which have recently emerged from our labs - particularly, from the corneal permeability standpoint. Copyright © 2017 Elsevier Ltd. All rights reserved.

Magnetic properties of Co/Rh (001) multilayers studied by x-ray magnetic-circular dichroism

NASA Astrophysics Data System (ADS)

Tomaz, M. A.; Mayo, E.; Lederman, D.; Hallin, E.; Sham, T. K.; O'brien, W. L.; Harp, G. R.

1998-11-01

The layer-averaged magnetic moments of Co and Rh have been measured in sputter deposited Co/Rh (001) multilayer thin films using the x-ray magnetic circular dichroism. The Rh moments were measured at both the L and M absorption edges, where we find that the Rh moment decreases as a function of increasing Rh layer thickness (tRh). The decline of the layer-averaged Rh moment is well described in terms of a simple dilution, implying that the Rh moment is confined to the interfacial region. We find that the Co moment remains largely unaffected, maintaining a bulklike value of 1.7μB in the region preceding the first antiferromagnetic coupling peak where tRh ranges from 0 to 4 Å. We also find, via application of the dichroism sum rules, that the ratio / for Co increases ~10% for this same region. Finally, we contrast the magnetic behavior of the Co/Rh (001) and Fe/Rh (001) multilayer systems.

Soft x-ray resonant diffraction study of magnetic structure in magnetoelectric Y-type hexaferrite

NASA Astrophysics Data System (ADS)

Ueda, H.; Tanaka, Y.; Wakabayashi, Y.; Kimura, T.

2018-05-01

The effect of magnetic field on the magnetic structure associated with magnetoelectric properties in a Y-type hexaferrite, Ba1.3Sr0.7CoZnFe11AlO22, was investigated by utilizing the soft x-ray resonant diffraction technique. In this hexaferrite, the so-called alternating longitudinal conical phase is stabilized at room temperature and zero magnetic field. Below room temperature, however, this phase is transformed into the so-called transverse conical phase by applying an in-plane magnetic field (≈ 0.3 T). The transverse conical phase persists even after removing the magnetic field. The magnetoelectricity, which is magnetically-induced electric polarization, observed in the hexaferrite is discussed in terms of the temperature-dependent magnetic structure at zero field.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

NASA Astrophysics Data System (ADS)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

PubMed

Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2016-04-12

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

PubMed Central

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-01-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

History of Chandra X-Ray Observatory

NASA Image and Video Library

2002-12-18

At a distance of 6,000 light years from Earth, the star cluster RCW 38 is a relatively close star-forming region. This area is about 5 light years across, and contains thousands of hot, very young stars formed less than a million years ago, 190 of which exposed x-rays to Chandra. Enveloping the star cluster, the diffused cloud of x-rays shows an excess of high energy x-rays, which indicates that the x-rays come from trillion-volt electrons moving in a magnetic field. Such particles are typically produced by exploding stars, or in the strong magnetic fields around neutron stars or black holes, none of which are evident in RCW 38. One possible origin for the particles, could be an undetected supernova that occurred in the cluster, possibly thousands of years ago, producing a shock wave that is interacting with the young stars. Regardless of the origin of these energetic electrons, their presence could change the chemistry of the disks that will eventually form planets around the stars in the cluster.

X-ray Observations of Neutron Stars

NASA Astrophysics Data System (ADS)

Enoto, Teruaki

A large diversity of neutron stars has been discovered by recent multi-wavelength observations from the radio band to the X-ray and gamma-ray energy range. Among different manifestation of neutron stars, magnetars are strongly magnetised objects with the magnetic field strength of B = 1014-15 G. Some of magnetars exhibit transient behaviours, in which activated state the magnetars radiate sporadic short bursts and enhanced persistent X-ray emission for a couple of weeks or more. The Suzaku X-ray satellite has observed 15 magnetars among 23 known sources in 2006-2013, including persistently bright sources and transient objects. We showed that the broadband magnetar spectra, including both of surface emission below 10 keV and magnetospheric power-law radiation above 10 keV, follow spectral evolution as a function of the magnetic field, in terms of wide-band spectral hardness ratio and of power-law photon index. Magnetars are also compared with other rotation powered pulsars on the correlation between X-ray luminosity and the spin-down luminosity. I will address future missions related with investigation of the nature of neutron stars.

From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography.

PubMed

Dods, Robert; Båth, Petra; Arnlund, David; Beyerlein, Kenneth R; Nelson, Garrett; Liang, Mengling; Harimoorthy, Rajiv; Berntsen, Peter; Malmerberg, Erik; Johansson, Linda; Andersson, Rebecka; Bosman, Robert; Carbajo, Sergio; Claesson, Elin; Conrad, Chelsie E; Dahl, Peter; Hammarin, Greger; Hunter, Mark S; Li, Chufeng; Lisova, Stella; Milathianaki, Despina; Robinson, Joseph; Safari, Cecilia; Sharma, Amit; Williams, Garth; Wickstrand, Cecilia; Yefanov, Oleksandr; Davidsson, Jan; DePonte, Daniel P; Barty, Anton; Brändén, Gisela; Neutze, Richard

2017-09-05

Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RC vir ). We first crushed these crystals prior to multiple rounds of microseeding. Each cycle of microseeding facilitated improvements in the RC vir serial femtosecond crystallography (SFX) structure from 3.3-Å to 2.4-Å resolution. This approach may allow known crystallization conditions for other proteins to be adapted to exploit novel scientific opportunities created by serial crystallography. Copyright © 2017 Elsevier Ltd. All rights reserved.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

DOE PAGES

Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; ...

2017-10-12

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates frommore » the expected perfect icosahedral symmetry. Lastly, our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.« less

Optical identification of X-ray source 1RXS J180431.1-273932 as a magnetic cataclysmic variable

NASA Astrophysics Data System (ADS)

Masetti, N.; Nucita, A. A.; Parisi, P.

2012-08-01

The X-ray source 1RXS J180431.1-273932 has been proposed as a new member of the symbiotic X-ray binary (SyXB) class of systems, which are composed of a late-type giant that loses matter to an extremely compact object, most likely a neutron star. In this paper, we present an optical campaign of imaging plus spectroscopy on selected candidate counterparts of this object. We also reanalyzed the available archival X-ray data collected with XMM-Newton. We find that the brightest optical source inside the 90% X-ray positional error circle is spectroscopically identified as a magnetic cataclysmic variable (CV), most likely of intermediate polar type, through the detection of prominent Balmer, He i, He ii, and Bowen blend emissions. On either spectroscopic or statistical grounds, we discard as counterparts of the X-ray source the other optical objects in the XMM-Newton error circle. A red giant star of spectral type M5 III is found lying just outside the X-ray position: we consider this latter object as a fore-/background one and likewise rule it out as a counterpart of 1RXS J180431.1-273932. The description of the X-ray spectrum of the source using a bremsstrahlung plus black-body model gives temperatures of kTbr ~ 40 keV and kTbb ~ 0.1 keV for these two components. We estimate a distance of d ~ 450 pc and a 0.2-10 keV X-ray luminosity of LX ~ 1.7 × 1032 erg s-1 for this system and, using the information obtained from the X-ray spectral analysis, a mass MWD ~ 0.8 M⊙ for the accreting white dwarf (WD). We also confirm an X-ray periodicity of 494 s for this source, which we interpret as the spin period of the WD. In summary, 1RXS J180431.1-273932 is identified as a magnetic CV and its SyXB nature is excluded. Partly based on observations collected at the Italian Telescopio Nazionale Galileo, located at the Observatorio del Roque de los Muchachos (Canary Islands, Spain).Reduced data used for imaging and spectra is only available at the CDS via anonymous ftp to cdsarc

Review: Serial Femtosecond Crystallography: A Revolution in Structural Biology

PubMed Central

Martin-Garcia, Jose M.; Conrad, Chelsie E.; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

2016-01-01

Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. PMID:27143509

High-energy magnetic excitations in overdoped La 2-xSr xCuO 4 studied by neutron and resonant inelastic X-ray scattering

DOE PAGES

Wakimoto, S.; Ishii, K.; Kimura, H.; ...

2015-05-21

We have performed neutron inelastic scattering and resonant inelastic x-ray scattering (RIXS) at the Cu-L 3 edge to study high-energy magnetic excitations at energy transfers of more than 100 meV for overdoped La 2₋xSr xCuO 4 with x=0.25 (T c=15 K) and x=0.30 (nonsuperconducting) using identical single-crystal samples for the two techniques. From constant-energy slices of neutron-scattering cross sections, we have identified magnetic excitations up to ~250 meV for x=0.25. Although the width in the momentum direction is large, the peak positions along the (π,π) direction agree with the dispersion relation of the spin wave in the nondoped La 2CuOmore » 4 (LCO), which is consistent with the previous RIXS results of cuprate superconductors. Using RIXS at the Cu-L 3 edge, we have measured the dispersion relations of the so-called paramagnon mode along both (π,π) and (π,0) directions. Although in both directions the neutron and RIXS data connect with each other and the paramagnon along (π,0) agrees well with the LCO spin-wave dispersion, the paramagnon in the (π,π) direction probed by RIXS appears to be less dispersive and the excitation energy is lower than the spin wave of LCO near (π/2,π/2). Thus, our results indicate consistency between neutron inelastic scattering and RIXS, and elucidate the entire magnetic excitation in the (π,π) direction by the complementary use of two probes. The polarization dependence of the RIXS profiles indicates that appreciable charge excitations exist in the same energy range of magnetic excitations, reflecting the itinerant character of the overdoped sample. Lastly, we find a possible anisotropy in the charge excitation intensity might explain the apparent differences in the paramagnon dispersion in the (π,π) direction as detected by the x-ray scattering.« less

Thermonuclear ignition by Z-pinch X-ray radiation produced by current of an explosive magnetic generator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garanin, S. G.; Ivanovskiy, A. V., E-mail: ivanovsky@elph.vniief.ru

2015-12-15

The scheme of a device based a superpower disk-type magnetic explosion generator to produce a pulse of X-ray radiation with the energy exceeding the target ignition threshold is described and validated.

Thermonuclear ignition by Z-pinch X-ray radiation produced by current of an explosive magnetic generator

NASA Astrophysics Data System (ADS)

Garanin, S. G.; Ivanovskiy, A. V.

2015-12-01

The scheme of a device based a superpower disk-type magnetic explosion generator to produce a pulse of X-ray radiation with the energy exceeding the target ignition threshold is described and validated.

Calibration standard of body tissue with magnetic nanocomposites for MRI and X-ray imaging

NASA Astrophysics Data System (ADS)

Rahn, Helene; Woodward, Robert; House, Michael; Engineer, Diana; Feindel, Kirk; Dutz, Silvio; Odenbach, Stefan; StPierre, Tim

2016-05-01

We present a first study of a long-term phantom for Magnetic Resonance Imaging (MRI) and X-ray imaging of biological tissues with magnetic nanocomposites (MNC) suitable for 3-dimensional and quantitative imaging of tissues after, e.g. magnetically assisted cancer treatments. We performed a cross-calibration of X-ray microcomputed tomography (XμCT) and MRI with a joint calibration standard for both imaging techniques. For this, we have designed a phantom for MRI and X-ray computed tomography which represents biological tissue enriched with MNC. The developed phantoms consist of an elastomer with different concentrations of multi-core MNC. The matrix material is a synthetic thermoplastic gel, PermaGel (PG). The developed phantoms have been analyzed with Nuclear Magnetic Resonance (NMR) Relaxometry (Bruker minispec mq 60) at 1.4 T to obtain R2 transverse relaxation rates, with SQUID (Superconducting QUantum Interference Device) magnetometry and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to verify the magnetite concentration, and with XμCT and 9.4 T MRI to visualize the phantoms 3-dimensionally and also to obtain T2 relaxation times. A specification of a sensitivity range is determined for standard imaging techniques X-ray computed tomography (XCT) and MRI as well as with NMR. These novel phantoms show a long-term stability over several months up to years. It was possible to suspend a particular MNC within the PG reaching a concentration range from 0 mg/ml to 6.914 mg/ml. The R2 relaxation rates from 1.4 T NMR-relaxometry show a clear connection (R2=0.994) with MNC concentrations between 0 mg/ml and 4.5 mg/ml. The MRI experiments have shown a linear correlation of R2 relaxation and MNC concentrations as well but in a range between MNC concentrations of 0 mg/ml and 1.435 mg/ml. It could be shown that XμCT displays best moderate and high MNC concentrations. The sensitivity range for this particular XμCT apparatus yields from 0.569 mg/ml to 6.914 mg/ml. The

Magnetically Assisted Remote-controlled Endovascular Catheter for Interventional MR Imaging: In Vitro Navigation at 1.5 T versus X-ray Fluoroscopy

PubMed Central

Losey, Aaron D.; Lillaney, Prasheel; Martin, Alastair J.; Cooke, Daniel L.; Wilson, Mark W.; Thorne, Bradford R. H.; Sincic, Ryan S.; Arenson, Ronald L.; Saeed, Maythem

2014-01-01

Purpose To compare in vitro navigation of a magnetically assisted remote-controlled (MARC) catheter under real-time magnetic resonance (MR) imaging with manual navigation under MR imaging and standard x-ray guidance in endovascular catheterization procedures in an abdominal aortic phantom. Materials and Methods The 2-mm-diameter custom clinical-grade microcatheter prototype with a solenoid coil at the distal tip was deflected with a foot pedal actuator used to deliver 300 mA of positive or negative current. Investigators navigated the catheter into branch vessels in a custom cryogel abdominal aortic phantom. This was repeated under MR imaging guidance without magnetic assistance and under conventional x-ray fluoroscopy. MR experiments were performed at 1.5 T by using a balanced steady-state free precession sequence. The mean procedure times and percentage success data were determined and analyzed with a linear mixed-effects regression analysis. Results The catheter was clearly visible under real-time MR imaging. One hundred ninety-two (80%) of 240 turns were successfully completed with magnetically assisted guidance versus 144 (60%) of 240 turns with nonassisted guidance (P < .001) and 119 (74%) of 160 turns with standard x-ray guidance (P = .028). Overall mean procedure time was shorter with magnetically assisted than with nonassisted guidance under MR imaging (37 seconds ± 6 [standard error of the mean] vs 55 seconds ± 3, P < .001), and time was comparable between magnetically assisted and standard x-ray guidance (37 seconds ± 6 vs 44 seconds ± 3, P = .045). When stratified by angle of branch vessel, magnetic assistance was faster than nonassisted MR guidance at turns of 45°, 60°, and 75°. Conclusion In this study, a MARC catheter for endovascular navigation under real-time MR imaging guidance was developed and tested. For catheterization of branch vessels arising at large angles, magnetically assisted catheterization was faster than manual catheterization

Magnetically assisted remote-controlled endovascular catheter for interventional MR imaging: in vitro navigation at 1.5 T versus X-ray fluoroscopy.

PubMed

Losey, Aaron D; Lillaney, Prasheel; Martin, Alastair J; Cooke, Daniel L; Wilson, Mark W; Thorne, Bradford R H; Sincic, Ryan S; Arenson, Ronald L; Saeed, Maythem; Hetts, Steven W

2014-06-01

To compare in vitro navigation of a magnetically assisted remote-controlled (MARC) catheter under real-time magnetic resonance (MR) imaging with manual navigation under MR imaging and standard x-ray guidance in endovascular catheterization procedures in an abdominal aortic phantom. The 2-mm-diameter custom clinical-grade microcatheter prototype with a solenoid coil at the distal tip was deflected with a foot pedal actuator used to deliver 300 mA of positive or negative current. Investigators navigated the catheter into branch vessels in a custom cryogel abdominal aortic phantom. This was repeated under MR imaging guidance without magnetic assistance and under conventional x-ray fluoroscopy. MR experiments were performed at 1.5 T by using a balanced steady-state free precession sequence. The mean procedure times and percentage success data were determined and analyzed with a linear mixed-effects regression analysis. The catheter was clearly visible under real-time MR imaging. One hundred ninety-two (80%) of 240 turns were successfully completed with magnetically assisted guidance versus 144 (60%) of 240 turns with nonassisted guidance (P < .001) and 119 (74%) of 160 turns with standard x-ray guidance (P = .028). Overall mean procedure time was shorter with magnetically assisted than with nonassisted guidance under MR imaging (37 seconds ± 6 [standard error of the mean] vs 55 seconds ± 3, P < .001), and time was comparable between magnetically assisted and standard x-ray guidance (37 seconds ± 6 vs 44 seconds ± 3, P = .045). When stratified by angle of branch vessel, magnetic assistance was faster than nonassisted MR guidance at turns of 45°, 60°, and 75°. In this study, a MARC catheter for endovascular navigation under real-time MR imaging guidance was developed and tested. For catheterization of branch vessels arising at large angles, magnetically assisted catheterization was faster than manual catheterization under MR imaging guidance and was comparable to

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.

PubMed

Gardberg, Anna S; Del Castillo, Alexis Rae; Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew P; Myles, Dean A A

2010-05-01

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

Serial Millisecond Crystallography of Membrane Proteins.

PubMed

Jaeger, Kathrin; Dworkowski, Florian; Nogly, Przemyslaw; Milne, Christopher; Wang, Meitian; Standfuss, Joerg

2016-01-01

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a powerful method to determine high-resolution structures of pharmaceutically relevant membrane proteins. Recently, the technology has been adapted to carry out serial millisecond crystallography (SMX) at synchrotron sources, where beamtime is more abundant. In an injector-based approach, crystals grown in lipidic cubic phase (LCP) or embedded in viscous medium are delivered directly into the unattenuated beam of a microfocus beamline. Pilot experiments show the application of microjet-based SMX for solving the structure of a membrane protein and compatibility of the method with de novo phasing. Planned synchrotron upgrades, faster detectors and software developments will go hand-in-hand with developments at free-electron lasers to provide a powerful methodology for solving structures from microcrystals at room temperature, ligand screening or crystal optimization for time-resolved studies with minimal or no radiation damage.

Does crystallography need a new name?

DOE PAGES

Argryriou, Dimitri

2017-07-01

The discovery of X-rays and their use in the observation of diffraction from crystals placed crystallography at the forefront of science at the beginning of the last century. The combination of this new tool, together with the emerging understanding of the symmetry of crystals, exposed the locations of atoms in matter and allowed us to start understanding macroscopic properties from an atomic perspective for the first time. These discoveries transformed physics and chemistry bringing to light new scientific fields such as materials science and structural biology.

Does crystallography need a new name?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Argryriou, Dimitri

The discovery of X-rays and their use in the observation of diffraction from crystals placed crystallography at the forefront of science at the beginning of the last century. The combination of this new tool, together with the emerging understanding of the symmetry of crystals, exposed the locations of atoms in matter and allowed us to start understanding macroscopic properties from an atomic perspective for the first time. These discoveries transformed physics and chemistry bringing to light new scientific fields such as materials science and structural biology.

Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography.

PubMed

Akter, Mahfuza; Inoue, Chika; Komori, Hirofumi; Matsuda, Nana; Sakurai, Takeshi; Kataoka, Kunishige; Higuchi, Yoshiki; Shibata, Naoki

2016-10-01

Multicopper oxidases oxidize various phenolic and nonphenolic compounds by using molecular oxygen as an electron acceptor to produce water. A multicopper oxidase protein, CueO, from Escherichia coli is involved in copper homeostasis in the bacterial cell. Although X-ray crystallographic studies have been conducted, the reduction mechanism of oxygen and the proton-transfer pathway remain unclear owing to the difficulty in identifying H atoms from X-ray diffraction data alone. To elucidate the reaction mechanism using neutron crystallography, a preparation system for obtaining large, high-quality single crystals of deuterated CueO was developed. Tiny crystals were obtained from the deuterated CueO initially prepared from the original construct. The X-ray crystal structure of the deuterated CueO showed that the protein contained an incompletely truncated signal sequence at the N-terminus, which resulted in the heterogeneity of the protein sample for crystallization. Here, a new CueO expression system that had an HRV3C cleavage site just after the signal sequence was constructed. Deuterated CueO from the new construct was expressed in cells cultured in deuterated algae-extract medium and the signal sequence was completely eliminated by HRV3C protease. The deuteration level of the purified protein was estimated by MALDI-TOF mass spectrometry to be at least 83.2% compared with nondeuterated protein. Nondeuterated CueO crystallized in space group P2 1 , with unit-cell parameters a = 49.51, b = 88.79, c = 53.95 Å, β = 94.24°, and deuterated CueO crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 49.91, b = 106.92, c = 262.89 Å. The crystallographic parameters for the crystals of the new construct were different from those previously reported for nondeuterated crystals. The nondeuterated and deuterated CueO from the new construct had similar UV-Vis spectra, enzymatic activities and overall structure and geometry of the ligands of the Cu atoms

Performance and Characterization of Magnetic Penetration Thermometer Devices for X-Ray Spectroscopy

NASA Technical Reports Server (NTRS)

Porst, J. -P.; Adams, J. S.; Bandler, S. R.; Balvin, M.; Busch, S. E.; Denis, K. L.; Kelly, D.; Nagler, P.; Sadleir, J. E.; Seidel, G. M.;

High resolution projection X-ray microscope equipped with fluorescent X-ray analyzer and its applications

NASA Astrophysics Data System (ADS)

Minami, K.; Saito, Y.; Kai, H.; Shirota, K.; Yada, K.

2009-09-01

We have newly developed an open type fine-focus X-ray tube "TX-510" to realize a spatial resolution of 50nm and to radiate low energy characteristic X-rays for giving high absorption contrast to images of microscopic organisms. The "TX-510" employs a ZrO/W(100) Schottky emitter and an "In-Lens Field Emission Gun". The key points of the improvements are (1) reduced spherical aberration coefficient of magnetic objective lens, (2) easy and accurate focusing, (3) newly designed astigmatism compensator, (4) segmented thin film target for interchanging the target materials by electron beam shift and (5) fluorescent X-ray analysis system.

Microbeam X-ray analysis in Poland - past and future

NASA Astrophysics Data System (ADS)

Kusinski, J.

2010-02-01

The article provides an overview of the development of electron beam X-ray microanalysis (EPMA) in Poland. Since the introduction by Prof. Bojarski of EMPA over 45 years ago, tremendous advances in methodologies and in instrumentation have been made in order to improve the precision of quantitative compositional analysis, spatial resolution and analytical sensitivity. This was possible due to the activity of Applied Crystallography Committee at the Polish Academy of Sciences, as well as the groups of researches working in the Institute for Ferrous Metallurgy (Gliwice), the Technical University of Warsaw, the Silesian Technical University (Katowice), the AGH-University of Sciences and Technology (Krakow), and the Institute of Materials Science and Metallurgy Polish Academy of Sciences (Krakow). Based on the research examples realized by these teams, conferences, seminars and congresses organized, as well as books and academic textbooks issued, the evolution of electron beam X-ray microanalysis in Poland is demonstrated.

Development of an alternating magnetic-field-assisted finishing process for microelectromechanical systems micropore x-ray optics.

PubMed

Riveros, Raul E; Yamaguchi, Hitomi; Mitsuishi, Ikuyuki; Takagi, Utako; Ezoe, Yuichiro; Kato, Fumiki; Sugiyama, Susumu; Yamasaki, Noriko; Mitsuda, Kazuhisa

2010-06-20

X-ray astronomy research is often limited by the size, weight, complexity, and cost of functioning x-ray optics. Micropore optics promises an economical alternative to traditional (e.g., glass or foil) x-ray optics; however, many manufacturing difficulties prevent micropore optics from being a viable solution. Ezoe et al. introduced microelectromechanical systems (MEMS) micropore optics having curvilinear micropores in 2008. Made by either deep reactive ion etching or x-ray lithography, electroforming, and molding (LIGA), MEMS micropore optics suffer from high micropore sidewall roughness (10-30nmrms) which, by current standards, cannot be improved. In this research, a new alternating magnetic-field-assisted finishing process was developed using a mixture of ferrofluid and microscale abrasive slurry. A machine was built, and a set of working process parameters including alternating frequency, abrasive size, and polishing time was selected. A polishing experiment on a LIGA-fabricated MEMS micropore optic was performed, and a change in micropore sidewall roughness of 9.3+/-2.5nmrms to 5.7+/-0.7nmrms was measured. An improvement in x-ray reflectance was also seen. This research shows the feasibility and confirms the effects of this new polishing process on MEMS micropore optics.

X-ray absorption fine structure and X-ray excited optical luminescence studies of II-VI semiconducting nanostructures

NASA Astrophysics Data System (ADS)

Murphy, Michael Wayne

2010-06-01

of 0, 1,3, and 10% and annealed at 400, 600 and 800°C in air. XAFS spectra show that low dopant concentrations and low processing temperatures limit the amount of secondary phase formation. The nanopowders did not show roomtemperature ferromagnetism and increased secondary phase formation increases the paramagnetic character of the hysteresis curves at 5°K. Keywords: X-ray absorption fine structures (XAFS), X-ray absorption near-edge structures (XANES), extended X-ray absorption fine structure (EXAFS), X-ray absorption spectroscopy(XAS), X-ray excited optical luminescence (XEOL), time-resolved, II-VI semiconductors, nanostructure, nanomaterial, nanoribbon, nanowire, nanopartic1e, heterostructure, ZnO, ZnS, ZnO-ZnS, CdS, CdSe, CdSSe, ZnO:Mn, ZnO:Co, ZnS:Mn, dilute magnetic semiconductor (DMS), dilute magnetic oxide (DMO), spintronics, magnetism, paramagnetism, ferromagnetism.

Projection x-ray topography system at 1-BM x-ray optics test beamline at the advanced photon source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoupin, Stanislav, E-mail: sstoupin@aps.anl.gov; Liu, Zunping; Trakhtenberg, Emil

2016-07-27

Projection X-ray topography of single crystals is a classic technique for the evaluation of intrinsic crystal quality of large crystals. In this technique a crystal sample and an area detector (e.g., X-ray film) collecting intensity of a chosen crystallographic reflection are translated simultaneously across an X-ray beam collimated in the diffraction scattering plane (e.g., [1, 2]). A bending magnet beamline of a third-generation synchrotron source delivering x-ray beam with a large horizontal divergence, and therefore, a large horizontal beam size at a crystal sample position offers an opportunity to obtain X-ray topographs of large crystalline samples (e.g., 6-inch wafers) inmore » just a few exposures. Here we report projection X-ray topography system implemented recently at 1-BM beamline of the Advanced Photon Source. A selected X-ray topograph of a 6-inch wafer of 4H-SiC illustrates capabilities and limitations of the technique.« less

Energy Dependence of Synchrotron X-Ray Rims in Tycho's Supernova Remnant

NASA Technical Reports Server (NTRS)

Tran, Aaron; Williams, Brian J.; Petre, Robert; Ressler, Sean M.; Reynolds, Stephen P.

2015-01-01

Several young supernova remnants exhibit thin X-ray bright rims of synchrotron radiation at their forward shocks. Thin rims require strong magnetic field amplification beyond simple shock compression if rim widths are only limited by electron energy losses. But, magnetic field damping behind the shock could produce similarly thin rims with less extreme field amplification. Variation of rim width with energy may thus discriminate between competing influences on rim widths. We measured rim widths around Tycho's supernova remnant in 5 energy bands using an archival 750 ks Chandra observation. Rims narrow with increasing energy and are well described by either loss-limited or damped scenarios, so X-ray rim width-energy dependence does not uniquely specify a model. But, radio counterparts to thin rims are not loss-limited and better reflect magnetic field structure. Joint radio and X-ray modeling favors magnetic damping in Tycho's SNR with damping lengths approximately 1-5% of remnant radius and magnetic field strengths approximately 50-400 micron G assuming Bohm diffusion. X-ray rim widths are approximately 1% of remnant radius, somewhat smaller than inferred damping lengths. Electron energy losses are important in all models of X-ray rims, suggesting that the distinction between loss-limited and damped models is blurred in soft X-rays. All loss-limited and damping models require magnetic fields approximately greater than 20 micron G, arming the necessity of magnetic field amplification beyond simple compression.

Sub-arcsecond observations of the solar X-ray corona

NASA Technical Reports Server (NTRS)

Golub, L.; Nystrom, G.; Herant, M.; Kalata, K.; Lovas, I.

1990-01-01

Results from a high-resolution multi-layer-coated X-ray imaging telescope, part of the Normal Incidence X-ray Telescope sounding rocket payload are presented. Images of the peak of a two-ribbon flare showed detailed structure within each ribbon, as well as the expected bright arches of emission connecting the ribbons. The number of X-ray bright points is small, consistent with predictions based on the previous solar cycle. Topology of the magnetic structure is complex and highly tangled, implying that the magnetic complexity of the photosphere is paralleled in the corona.

The effect of vacuum birefringence on the polarization of X-ray binaries and pulsars

NASA Technical Reports Server (NTRS)

Novick, R.; Weisskopf, M. C.; Angel, J. R. P.; Sutherland, P. G.

1977-01-01

In a strong magnetic field the vacuum becomes birefringent. This effect is especially important for pulsars at X-ray wavelengths. Any polarized X-ray emission from the surface of a magnetic neutron star becomes depolarized as it propagates through the magnetic field. The soft X-ray emission from AM Her, believed to be a magnetic white dwarf, may show about one radian of phase retardation. In this case, circular polarization of the X-ray flux would be a characteristic signature of vacuum birefringence.