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Sample records for normal-mode-based x-ray crystallographic

  1. X-ray Crystallographic Computations Using a Programmable Calculator.

    ERIC Educational Resources Information Center

    Attard, Alfred E.; Lee, Henry C.

    1979-01-01

    Describes six crystallographic programs which have been developed to illustrate the range of usefulness of programmable calculators in providing computational assistance in chemical analysis. These programs are suitable for the analysis of x-ray diffraction data in the laboratory by students. (HM)

  2. X-ray Crystallographic Computations Using a Programmable Calculator.

    ERIC Educational Resources Information Center

    Attard, Alfred E.; Lee, Henry C.

    1979-01-01

    Describes six crystallographic programs which have been developed to illustrate the range of usefulness of programmable calculators in providing computational assistance in chemical analysis. These programs are suitable for the analysis of x-ray diffraction data in the laboratory by students. (HM)

  3. 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

  4. Iron distances in hemoglobin: comparison of x-ray crystallographic and extended x-ray absorption fine structure studies

    SciTech Connect

    Fermi, G.; Perutz, M.F.; Shulman, R.G.

    1987-09-01

    A comparison is presented of the structures obtained around the iron atom in deoxyhemoglobin (Hb). The data come from extended x-ray absorption fine structure (EXAFS) studies of the iron, which gave Fe-porphyrin nitrogen distances of 2.06 +- 0.01 A, and from the most recent high-resolution x-ray crystallographic study, which gave exactly the same distance-2.06 +- 0.02 A. The distance of Fe above the plane of the porphyrin nitrogens was 0.38 +- 0.04 A from the crystallographic study; this value is not far from the upper limit of the distances 0.20 +- /sub 0.20//sup 0.10/ A calculated from the EXAFS experiment by triangulation. These distances above the nitrogen plane are shorter than those estimated in the earliest x-ray structures

  5. Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures

    SciTech Connect

    McLean, Larry R.; Zhang, Ying; Degnen, William; Peppard, Jane; Cabel, Dasha; Zou, Chao; Tsay, Joseph T.; Subramaniam, Arun; Vaz, Roy J.; Li, Yi

    2010-10-28

    Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were found to be structurally different from the corresponding compounds initially identified by virtual screening.

  6. X-ray crystallographic studies of protein-ligand interactions.

    PubMed

    Palmer, R A; Niwa, H

    2003-10-01

    X-ray crystallography enables details of covalent and non-covalent interactions to be analysed quantitatively in three dimensions, thus providing the basis for the understanding of binding of ligands to proteins as well as modes of action such as cell-surface binding. This article is concerned with current methods employed for the X-ray analysis of protein structures complexed with ligands. It deals mainly with 'what can be done' in current research, rather than providing details of 'how to do it'. In recent years significant advances have been made in a variety of techniques: growing protein crystals from very small samples by scanning a wide range of conditions; X-ray intensity data collection and measurement through the use of charge-coupled devices and high-intensity, versatile synchrotron sources; cryo-crystallography which both stabilizes the crystals and provides improved data; methods for analysing and interpreting the structures, dependent, at least in part, on both structural and sequence databases; and improvements in hardware and software. To illustrate the type of results achievable two examples involving protein-sugar interactions are discussed: (i) SNAII (the lectin Sambucus nigra agglutinin-II from elder) N-terminal sugar-binding site where terminal sugar units in a glycosylation chain from a symmetry-related molecule bind and (ii) MLI (mistletoe lectin I) C-terminal sugar-binding site with lactose.

  7. Crystallization and preliminary X-ray crystallographic studies of human cyclophilin J

    SciTech Connect

    Hu, Hao; Huang, Chao-Qun; Liu, He-Li; Han, Yi; Yu, Long; Bi, Ru-Chang

    2005-02-01

    Human cyclophilin J is a member of the cyclophilin family and recent studies have indicated that it plays a role in the formation of liver cancers as a regulation factor or messenger. The preparation, crystallization and preliminary X-ray crystallographic studies of human cyclophilin J are reported.

  8. Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7

    SciTech Connect

    Quesada, Odayme; Gurda, Brittney; Govindasamy, Lakshmanan; McKenna, Robert; Kohlbrenner, Erik; Aslanidi, George; Zolotukhin, Sergei; Muzyczka, Nicholas; Agbandje-McKenna, Mavis

    2007-12-01

    Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids have been produced which diffract X-rays to ∼3.0 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to ∼3.0 Å resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 Å in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R{sub merge} of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of a capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.

  9. Model-building strategies for low-resolution X-ray crystallographic data

    SciTech Connect

    Karmali, Anjum M.; Blundell, Tom L.; Furnham, Nicholas

    2009-02-01

    Interpretation of low-resolution X-ray crystallographic data can prove to be a difficult task. The challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 Å is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.

  10. Crystallization and preliminary X-ray crystallographic analysis of rabbit l-gulonate 3-dehydrogenase

    SciTech Connect

    Asada, Yukuhiko; Kuroishi, Chizu; Ukita, Yoko; Sumii, Rie; Endo, Satoshi; Matsunaga, Toshiyuki; Hara, Akira; Kunishima, Naoki

    2008-03-01

    The preliminary X-ray crystallographic study of rabbit l-gulonate 3-dehydrogenase is described. Rabbit l-gulonate 3-dehydrogenase was crystallized using the oil-microbatch method at 295 K. X-ray diffraction data were collected to 1.70 Å resolution from a crystal at 100 K using synchrotron radiation. The crystal belongs to the C-centred monoclinic space group C2, with unit-cell parameters a = 71.81, b = 69.08, c = 65.64 Å, β = 102.7°. Assuming the presence of a monomeric protomer in the asymmetric unit gives a V{sub M} value of 2.21 Å{sup 3} Da{sup −1} and a solvent content of 44.4%. A cocrystal with NADH, which was isomorphous to the apo form, was also prepared and diffraction data were collected to 1.85 Å resolution using Cu Kα radiation at 100 K.

  11. Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

    SciTech Connect

    Mitchell, M.; Nam, H; Carter, A; McCall, A; Rence, C; Bennett, A; Gurda, B; McKenna, R; Porter, M; et. al.

    2009-01-01

    Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetric unit capsid have been determined by molecular-replacement methods and structure determination is in progress.

  12. The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN compiler

    NASA Technical Reports Server (NTRS)

    Stewart, J. M.; Kruger, G. J.; Ammon, H. L.; Dickinson, C.; Hall, S. R.

    1972-01-01

    A manual is presented for the use of a library of crystallographic programs. This library, called the X-ray system, is designed to carry out the calculations required to solve the structure of crystals by diffraction techniques. It has been implemented at the University of Maryland on the Univac 1108. It has, however, been developed and run on a variety of machines under various operating systems. It is considered to be an essentially machine independent library of applications programs. The report includes definition of crystallographic computing terms, program descriptions, with some text to show their application to specific crystal problems, detailed card input descriptions, mass storage file structure and some example run streams.

  13. Model-building strategies for low-resolution X-ray crystallographic data.

    PubMed

    Karmali, Anjum M; Blundell, Tom L; Furnham, Nicholas

    2009-02-01

    The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 A is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.

  14. Maximum a posteriori estimation of crystallographic phases in X-ray diffraction tomography

    PubMed Central

    Gürsoy, Doĝa; Biçer, Tekin; Almer, Jonathan D.; Kettimuthu, Raj; Stock, Stuart R.; De Carlo, Francesco

    2015-01-01

    A maximum a posteriori approach is proposed for X-ray diffraction tomography for reconstructing three-dimensional spatial distribution of crystallographic phases and orientations of polycrystalline materials. The approach maximizes the a posteriori density which includes a Poisson log-likelihood and an a priori term that reinforces expected solution properties such as smoothness or local continuity. The reconstruction method is validated with experimental data acquired from a section of the spinous process of a porcine vertebra collected at the 1-ID-C beamline of the Advanced Photon Source, at Argonne National Laboratory. The reconstruction results show significant improvement in the reduction of aliasing and streaking artefacts, and improved robustness to noise and undersampling compared to conventional analytical inversion approaches. The approach has the potential to reduce data acquisition times, and significantly improve beamtime efficiency. PMID:25939627

  15. Crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis chorismate mutase

    SciTech Connect

    Qamra, Rohini; Prakash, Prachee; Aruna, Bandi; Hasnain, Seyed E.; Mande, Shekhar C.

    2005-05-01

    Chorismate mutase from M. tuberculosis has been crystallized. Preliminary X-ray crystallographic studies reveal the occurrence of a dimeric molecule in the crystal asymmetric unit. Chorismate mutase catalyzes the first committed step in the biosynthesis of the aromatic amino acids phenylalanine and tyrosine in bacteria, fungi and higher plants. The recent re-annotation of the Mycobacterium tuberculosis genome has revealed the presence of a duplicate set of genes coding for chorismate mutase. The mycobacterial gene Rv1885c bears <20% sequence homology to other bacterial chorismate mutases, thus serving as a potential target for the development of inhibitors specific to the pathogen. The M. tuberculosis chorismate mutase was crystallized in space group C2 and the crystals diffracted to a resolution of 2.2 Å. Matthews coefficient and self-rotation function calculations revealed the presence of two monomers in the asymmetric unit.

  16. Quantification of thin film crystallographic orientation using X-ray diffraction with an area detector.

    PubMed

    Baker, Jessy L; Jimison, Leslie H; Mannsfeld, Stefan; Volkman, Steven; Yin, Shong; Subramanian, Vivek; Salleo, Alberto; Alivisatos, A Paul; Toney, Michael F

    2010-06-01

    As thin films become increasingly popular (for solar cells, LEDs, microelectronics, batteries), quantitative morphological and crystallographic information is needed to predict and optimize the film's electrical, optical, and mechanical properties. This quantification can be obtained quickly and easily with X-ray diffraction using an area detector in two sample geometries. In this paper, we describe a methodology for constructing complete pole figures for thin films with fiber texture (isotropic in-plane orientation). We demonstrate this technique on semicrystalline polymer films, self-assembled nanoparticle semiconductor films, and randomly packed metallic nanoparticle films. This method can be immediately implemented to help understand the relationship between film processing and microstructure, enabling the development of better and less expensive electronic and optoelectronic devices.

  17. Crystallization and preliminary X-ray crystallographic studies of dipeptidyl peptidase 11 from Porphyromonas gingivalis

    PubMed Central

    Sakamoto, Yasumitsu; Suzuki, Yoshiyuki; Iizuka, Ippei; Tateoka, Chika; Roppongi, Saori; Fujimoto, Mayu; Gouda, Hiroaki; Nonaka, Takamasa; Ogasawara, Wataru; Tanaka, Nobutada

    2015-01-01

    Dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) preferentially cleaves substrate peptides with Asp and Glu at the P1 position [NH2–P2–P1(Asp/Glu)–P1′–P2′…]. For crystallographic studies, PgDPP11 was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 1.82 Å resolution were collected from an orthorhombic crystal form belonging to space group C2221, with unit-cell parameters a = 99.33, b = 103.60, c = 177.33 Å. Structural analysis by the multi-wavelength anomalous diffraction method is in progress. PMID:25664797

  18. Preliminary X-ray crystallographic analysis of α-carbonic anhydrase from Thiomicrospira crunogena XCL-2.

    PubMed

    Díaz Torres, Natalia; González, Guillermo; Biswas, Shyamasri; Scott, Kathleen M; McKenna, Robert

    2012-09-01

    Thiomicrospira crunogena XCL-2 is a novel sulfur-oxidizing chemolithoautotroph that plays a significant role in the sustainability of deep-sea hydrothermal vent communities. This recently discovered gammaproteobacterium encodes and expresses four carbonic anhydrases (CAs) from three evolutionarily and structurally distinct CA families: an α-CA, two β-CAs and a γ-CA. In order to characterize and elucidate the physiological roles of these CAs, X-ray crystallographic structural studies have been initiated on the α-CA. The α-CA crystallized in space group C2. The crystals diffracted to a maximum resolution of 2.6 Å, with unit-cell parameters a = 127.1, b = 102.2, c = 105.0 Å, β = 127.3°, and a calculated Matthews coefficient of 2.04 Å(3) Da(-1) with four identical protein molecules in the crystallographic asymmetric unit. A preliminary solution was determined by molecular replacement with the PHENIX AutoMR wizard, which had an initial TFZ score of 17.9. Refinement of the structure is currently in progress.

  19. Sterically Hindered Chiral Organometallic Complexes: AN X-Ray Crystallographic, NMR Spectroscopic and Ehmo Study.

    NASA Astrophysics Data System (ADS)

    Malisza, Krisztina Laura

    results in elimination of water to yield 2-methylcyclopentene derivatives of which the dimolybdenum cluster has been characterized by x-ray crystallography. The sterically crowded complexes rm(C _6H_5)_3SiOH[ Cr(CO)_3 ]_{n}, where n = 1,2,3, have also been characterized X-ray crystallographically and all three have propellor-type geometries. The question of whether the phenyl ring rotations are correlated has been studied by variable-temperature NMR spectroscopy. These systems do not yield stable silicenium cations, but the analogous Cr(CO)_3 complex of triphenylcarbinol not only shows fluxional behaviour but also yields a metal -stabilized cation. The pathway for phenyl rotations in such systems can be followed via a Dunitz-type trajectory approach in which a number of x-ray structures were analyzed.

  20. An EXAFS, and preliminary X-ray crystallographic, investigation of an iron-containing product from the lichen Cladonia deformis.

    PubMed

    Alagna, L; Prosperi, T; Tomlinson, A A; Kjøsen, H; Mo, F

    1990-10-12

    An iron-containing product in the acetone extract from the lichen Cladonia deformis has been investigated using chemical, spectroscopic and X-ray crystallographic methods. Visible-near UV, EPR and IR spectra indicate that the iron is present as high-spin Fe(III) and coordinates in an oxygen-containing environment arising from graciliformin (or graciliformin-like) ligands. This has been confirmed by an XAS (X-ray absorption) study using synchrotron radiation. Comparison of the EXAFS and XANES results with those obtained from a model, tris(pent-2,4-dionato)Fe(III), and detailed fitting using the single-scattering, curved-wave formalism for the EXAFS strongly supports the presence of a Fe(III) coordinated to five oxygen atoms from the graciliformin.

  1. (1)H, (13)C NMR and X-ray crystallographic studies of highly polyhalogenated derivatives of costunolide lactone.

    PubMed

    Corona, D; Díaz, E; Nava, J L; Guzmán, A; Barrios, H; Fuentes, A; Hernandez-Plata, S A; Allard, J; Jankowski, C K

    2005-11-01

    The costunolide lactone, a sesquiterpene compound isolated from Zaluzania triiloba species, reacted with several dihalocarbene sources produced by trihaloform-NaOH under successive phase transfer reactions yielding mono-, bis- and tris-dihalocyclopropane adducts. The structures, as well as the configurational assignments of the different derivatives, were established by (1)H and (13)C NMR spectroscopy and assisted by X-ray crystallographic and molecular modelling studies. The specific shielding of protons in the neighbourhood of different halogens on the cyclopropane moieties was correlated to the pseudocontact interactions.

  2. Improving Beamline X-ray Optics by Analyzing the Damage to Crystallographic Structure

    SciTech Connect

    Zientek, John J.; Maj, Jozef; Navrotski, Gary; Srajer, George; Harmata, Charles M.; Maj, Lech; Lazarski, Krystofer; mikula, Stanislaw

    2015-01-01

    The mission of the X-ray Characterization Laboratory in the X-ray Science Division (XSD) at the Advanced Photon Source (APS) is to support both the users and the Optics Fabrication Facility that produces high performance optics for synchrotron X-ray beamlines. The Topography Test Unit (TTU) in the X-ray Lab has been successfully used to characterize diffracting crystals and test monochromators by quantifying residual surface stresses. This topographic method has also been adapted for testing standard X-ray mirrors, characterizing concave crystal optics and in principle, can be used to visualize residual stresses on any optic made from single crystalline material. The TTU has been instrumental in quantitatively determining crystal mounting stresses which are mechanically induced by positioning, holding, and cooling fixtures. It is this quantitative aspect that makes topography so useful since the requirements and responses for crystal optics and X-ray mirrors are quite different. In the case of monochromator crystals, even small residual or induced stresses, on the order of tens of kPa, can cause detrimental distortions to the perfect crystal rocking curves. Mirrors, on the other hand, are much less sensitive to induced stresses where stresses that are an order of magnitude greater can be tolerated. This is due to the fact that the surface rather than the lattice-spacing determines a mirror’s performance. For the highly sensitive crystal optics, it is essential to measure the in-situ rocking curves using topographs as mounting fixtures are adjusted. In this way, high heat-load monochromator crystals can be successfully mounted with minimum stress. Topographical analysis has been shown to be a highly effective method to visualize and quantify the distribution of stresses, to help identify methods that mitigate stresses, and most notably to improve diffractive crystal optic rocking curves.

  3. A Practical Synthesis and X-ray Crystallographic Analysis of Dithymoquinone, a Photodimer of Thymoquinone

    PubMed Central

    Myers, Alan L.; Zhang, Yan-Ping; Kramer, Mark A.; Bornmann, William G.; Kaseb, Ahmed; Yang, Peiying; Tran, Hai T.

    2014-01-01

    An updated and practical approach to the synthesis of dithymoquinone via one-step photoirradiation of thymoquinone (2-methyl-5-isopropyl-1,4-benzoquinone) is described. Synthesis resulted in a 55% yield of one structural isomer (trans-anti derivative), as confirmed by HPLC, NMR spectroscopy and first ever single-crystal X-ray diffraction analyses. PMID:24883052

  4. Preliminary X-ray crystallographic analysis of glutathione transferase zeta 1 (GSTZ1a-1a)

    SciTech Connect

    Boone, Christopher D.; Zhong, Guo; Smeltz, Marci; James, Margaret O. McKenna, Robert

    2014-01-21

    Crystals of glutathione transferase zeta 1 were grown and shown to diffract X-rays to 3.1 Å resolution. They belonged to space group P1, with unit-cell parameters a = 42.0, b = 49.6, c = 54.6 Å, α = 82.9, β = 69.9, γ = 73.4°.

  5. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling.

    PubMed

    Knight, Jennifer L; Zhou, Zhiyong; Gallicchio, Emilio; Himmel, Daniel M; Friesner, Richard A; Arnold, Eddy; Levy, Ronald M

    2008-04-01

    Modeling structural variability is critical for understanding protein function and for modeling reliable targets for in silico docking experiments. Because of the time-intensive nature of manual X-ray crystallographic refinement, automated refinement methods that thoroughly explore conformational space are essential for the systematic construction of structurally variable models. Using five proteins spanning resolutions of 1.0-2.8 A, it is demonstrated how torsion-angle sampling of backbone and side-chain libraries with filtering against both the chemical energy, using a modern effective potential, and the electron density, coupled with minimization of a reciprocal-space X-ray target function, can generate multiple structurally variable models which fit the X-ray data well. Torsion-angle sampling as implemented in the Protein Local Optimization Program (PLOP) has been used in this work. Models with the lowest R(free) values are obtained when electrostatic and implicit solvation terms are included in the effective potential. HIV-1 protease, calmodulin and SUMO-conjugating enzyme illustrate how variability in the ensemble of structures captures structural variability that is observed across multiple crystal structures and is linked to functional flexibility at hinge regions and binding interfaces. An ensemble-refinement procedure is proposed to differentiate between variability that is a consequence of physical conformational heterogeneity and that which reflects uncertainty in the atomic coordinates.

  6. Crystallographic Characterization of Extraterrestrial Materials by Energy-Scanning X-ray Diffraction

    NASA Technical Reports Server (NTRS)

    Hagiya, Kenji; Mikouchi, Takashi; Ohsumi, Kazumasa; Terada, Yasuko; Yagi, Naoto; Komatsu, Mutsumi; Yamaguchi, Shoki; Hirata, Arashi; Kurokawa, Ayaka; Zolensky, Michael E. (Principal Investigator)

    2016-01-01

    We have continued our long-term project using X-ray diffraction to characterize a wide range of extraterrestrial samples. The stationary sample method with polychromatic X-rays is advantageous because the irradiated area of the sample is always same and fixed, meaning that all diffraction spots occur from the same area of the sample, however, unit cell parameters cannot be directly obtained by this method though they are very important for identification of mineral and for determination of crystal structures. In order to obtain the cell parameters even in the case of the sample stationary method, we apply energy scanning of a micro-beam of monochromatic SR at SPring-8.

  7. Crystallization and preliminary X-ray crystallographic study of disproportionating enzyme from potato

    SciTech Connect

    Imamura, Kayo; Matsuura, Takanori; Ye, Zhengmao; Takaha, Takeshi; Fujii, Kazutoshi; Kusunoki, Masami; Nitta, Yasunori

    2005-01-01

    Disproportionating enzyme from potato was crystallized and preliminarily analyzed using X-ray diffraction. Disproportionating enzyme (D-enzyme; EC 2.4.1.25) is a 59 kDa protein that belongs to the α-amylase family. D-enzyme catalyses intramolecular and intermolecular transglycosylation reactions of α-1,4 glucan. A crystal of the D-enzyme from potato was obtained by the hanging-drop vapour-diffusion method. Preliminary X-ray data showed that the crystal diffracts to 2.0 Å resolution and belongs to space group C222{sub 1}, with unit-cell parameters a = 69.7, b = 120.3, c = 174.2 Å.

  8. Crystallographic texture of straight-rolled ?-uranium foils via neutron and X-ray diffraction

    DOE PAGES

    Einhorn, J. R.; Steiner, M. A.; Vogel, S. C.; ...

    2017-05-25

    The texture of recrystallized straight-rolled ?-uranium foils, a component in prospective irradiation target designs for medical isotope production, has been measured by neutron diffraction, as well as X-ray diffraction using both Cu and Mo sources. Variations in the penetration depth of neutron and X-ray radiation allow for determination of both the bulk and surface textures. The bulk ?-uranium foil texture is similar to the warm straight-rolled plate texture, with the addition of a notable splitting of the (001) poles along the transverse direction. The surface texture of the foils is similar to the bulk, with an additional (001) texture componentmore » that is oriented between the rolling and normal directions. Differences between the surface and bulk textures are expected to arise from shear forces during the rolling process and the influence that distinct strain histories have on subsequent texture evolution during recrystallization.« less

  9. Crystallization and preliminary X-ray crystallographic analysis of squalene-hopene cyclase from Alicyclobacillus acidocaldarius.

    PubMed Central

    Wendt, K. U.; Feil, C.; Lenhart, A.; Poralla, K.; Schulz, G. E.

    1997-01-01

    The membrane-associated protein squalene-hopene cyclase from Alicyclobacillus acidocaldarius was overexposed in Escherichia coli and purified by ion exchange and gel permeation chromatography. Crystals of three interrelated forms were grown by vapor diffusion under identical conditions. The crystals diffract to about 2.3 A resolution, but they are unstable in the X-ray beam. An interpretable heavy-atom derivative was obtained. PMID:9070455

  10. X-RAY AND CRYSTALLOGRAPHIC STUDIES OF PLANT VIRUS PREPARATIONS. III

    PubMed Central

    Bernal, J. D.; Fankuchen, I.

    1941-01-01

    These papers give an account of an optical and x-ray examination of preparations of plant virus substances isolated by Bawden and Pirie, in particular of those of tobacco mosaic disease. They open with a historical survey of the work, indicating the order in which new phenomena were discovered. The subsequent treatment is divided into three parts: I. Introduction and preparation of specimens. II. Modes of aggregation of virus particles. III. (1) The structure of the particles. (2) Biological implications. Part I, after an historical introduction, describes the method of preparation, from solutions of the virus, of optically oriented specimens of different concentrations. For their examination special x-ray apparatus was developed, in particular cameras working with very low angles and capable of indicating spacings up to 1000 Å. In Part III, Section 1 deals with the x-ray evidence on the internal structure of the particles. Even in solution, they have an inner regularity like that of a crystal. Virus preparations are thus in a sense doubly crystalline. Closer analysis reveals that the x-ray patterns are not directly comparable to those of a crystal as many of the reflections do not obey Bragg's law, but can be understood on the theory of gratings of limited size. The structure seems to consist of sub-units of the dimensions of approximately 11 Å cube, fitted together in a hexagonal or pseudohexagonal lattice of dimensions—a = 87 Å, c = 68 Å. Contrary to what earlier observations seemed to indicate, the particle seems to be virtually unchanged by drying and must therefore contain little water. There are marked resemblances with the structure of both crystalline and fibrous protein, but the virus structure does not belong to any of the classes hitherto studied. There are indications that the inner structure is of a simpler character than that of the molecules of crystalline proteins. Part III, Section 2 contains a comparative study of the optical and x-ray

  11. Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

    SciTech Connect

    Hughes, Ronny C.; McFeeters, Hana; Coates, Leighton; McFeeters, Robert L.

    2014-10-15

    The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6122 with unit-cell parameters a = b = 63.62,c = 155.20 Å, α = β = 90, γ = 120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da-1. The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.

  12. Purification, crystallization and preliminary X-ray crystallographic studies of Rv3705c from Mycobacterium tuberculosis

    SciTech Connect

    Lu, Feifei; Gao, Feng; Li, Honglin; Gong, Weimin; Zhou, Lin; Bi, Lijun

    2014-07-23

    The cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of Rv3705c from M. tuberculosis are described. The conserved protein Rv3705c from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant. The Rv3705c crystals exhibited space group P6{sub 1}22 or P6{sub 5}22, with unit-cell parameters a = b = 198.0, c = 364.1 Å, α = β = 90, γ = 120°, and diffracted to a resolution of 3.3 Å.

  13. Crystallization and preliminary X-ray crystallographic study of disproportionating enzyme from potato.

    PubMed

    Imamura, Kayo; Matsuura, Takanori; Ye, Zhengmao; Takaha, Takeshi; Fujii, Kazutoshi; Kusunoki, Masami; Nitta, Yasunori

    2005-01-01

    Disproportionating enzyme (D-enzyme; EC 2.4.1.25) is a 59 kDa protein that belongs to the alpha-amylase family. D-enzyme catalyses intramolecular and intermolecular transglycosylation reactions of alpha-1,4 glucan. A crystal of the D-enzyme from potato was obtained by the hanging-drop vapour-diffusion method. Preliminary X-ray data showed that the crystal diffracts to 2.0 A resolution and belongs to space group C222(1), with unit-cell parameters a = 69.7, b = 120.3, c = 174.2 A.

  14. Crystallization and preliminary X-ray crystallographic analysis of importin-α from Neurospora crassa.

    PubMed

    Bernardes, Natalia E; Takeda, Agnes A S; Freitas, Fernanda Z; Bertolini, Maria Célia; Fontes, Marcos R M

    2014-04-01

    Importin-α recognizes cargo proteins that contain classical nuclear localization sequences (NLS) and, in complex with importin-β, is able to translocate nuclear proteins through the nuclear pore complex. The filamentous fungus Neurospora crassa is a well studied organism that has been widely used as a model organism for fundamental aspects of eukaryotic biology, and is important for understanding the specific mechanisms of protein transport to the cell nucleus. In this work, the crystallization and preliminary X-ray diffraction analysis of importin-α from N. crassa (IMPα-Nc) complexed with a classical NLS peptide (SV40 NLS) are reported. IMPα-Nc-SV40 NLS crystals diffracted X-rays to 2.0 Å resolution and the structure was solved by molecular-replacement techniques, leading to a monomeric structure. The observation of the electron-density map indicated the presence of SV40 NLSs interacting at both the minor and major NLS-binding sites of the protein.

  15. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis

    SciTech Connect

    Das, Satyabrata; Kumar, Parimal; Bhor, Vikrant; Surolia, A. Vijayan, M.

    2005-01-01

    Pantothenate kinase, the first enzyme of the universal coenzyme A biosynthetic pathway, from M. tuberculosis H37Rv has been cloned, expressed, purified and X-ray analysed in two different crystal forms. Pantothenate kinase is an essential enzyme in the bacterial life cycle. It catalyzes the phosphorylation of pantothenate (vitamin B{sub 5}) to 4′-phosphopantothenate, the first step in the coenzyme A biosynthetic pathway. The enzyme from Mycobacterium tuberculosis, MW 35.7 kDa, has been cloned, expressed, purified and crystallized in two different trigonal crystal forms, both belonging to space group P3{sub 1}21. Two complete data sets of resolution 2.5 Å (form I) and 2.9 Å (form II) from crystals with unit-cell parameters a = b = 78.3, c = 115.45 Å and a = b = 107.63, c = 89.85 Å, respectively, were collected at room temperature on a home X-ray source. Structures of both crystal forms were solved for one subunit in the asymmetric unit by molecular replacement.

  16. Overexpression, crystallization and preliminary X-ray crystallographic analysis of phosphopantetheine adenylyltransferase from Enterococcus faecalis

    SciTech Connect

    Kang, Ji Yong; Lee, Hyung Ho; Yoon, Hye Jin; Kim, Hyoun Sook; Suh, Se Won

    2006-11-01

    Phosphopantetheine adenylyltransferase from En. faecalis was crystallized and X-ray diffraction data were collected to 2.70 Å resolution. Phosphopantetheine adenylyltransferase, an essential enzyme in the coenzyme A biosynthetic pathway, catalyzes the reversible transfer of an adenylyl group from ATP to 4′-phosphopantetheine, yielding 3′-dephospho-CoA and pyrophosphate. Enterococcus faecalis PPAT has been overexpressed in Escherichia coli as a fusion with a C-terminal purification tag and crystallized at 297 K using a reservoir solution consisting of 0.1 M sodium HEPES pH 7.5, 0.8 M sodium dihydrogen phosphate and 0.8 M potassium dihydrogen phosphate. X-ray diffraction data were collected to 2.70 Å at 100 K. The crystals belong to the primitive tetragonal space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 160.81, c = 225.68 Å. Four copies of the hexameric molecule are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (V{sub M}) of 3.08 Å{sup 3} Da{sup −1} and a solvent content of 60.1%.

  17. Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.

    PubMed Central

    Byron, O

    1997-01-01

    Computer software such as HYDRO, based upon a comprehensive body of theoretical work, permits the hydrodynamic modeling of macromolecules in solution, which are represented to the computer interface as an assembly of spheres. The uniqueness of any satisfactory resultant model is optimized by incorporating into the modeling procedure the maximal possible number of criteria to which the bead model must conform. An algorithm (AtoB, for atoms to beads) that permits the direct construction of bead models from high resolution x-ray crystallographic or nuclear magnetic resonance data has now been formulated and tested. Models so generated then act as informed starting estimates for the subsequent iterative modeling procedure, thereby hastening the convergence to reasonable representations of solution conformation. Successful application of this algorithm to several proteins shows that predictions of hydrodynamic parameters, including those concerning solvation, can be confirmed. PMID:8994627

  18. X-ray crystallographic and kinetic investigations of 6-sulfamoyl-saccharin as a carbonic anhydrase inhibitor.

    PubMed

    Alterio, V; Tanc, M; Ivanova, J; Zalubovskis, R; Vozny, I; Monti, S M; Di Fiore, A; De Simone, G; Supuran, C T

    2015-04-07

    6-Sulfamoyl-saccharin was investigated as an inhibitor of 11 α-carbonic anhydrase (CA, EC 4.2.1.1) isoforms of human (h) origin, hCA I-XIV, and X-ray crystallographic data were obtained for its adduct with hCA II, the physiologically dominant isoform. This compound possesses two potential zinc-binding groups, the primary sulfamoyl one and the secondary, acylatedsulfonamide. Saccharin itself binds to the Zn(II) ion from the CA active site coordinating with this last group, in deprotonated (SO2N(-)CO) form. Here we explain why 6-sulfamoyl-saccharin, unlike saccharin, binds to the metal ion from the hCA II active site by its primary sulfonamide moiety and not the secondary one as saccharin itself. Our study is useful for shedding new light to the structure-based drug design of isoform-selective CA inhibitors of the sulfonamide type.

  19. Discovery of Pyrrolopyridine−Pyridone Based Inhibitors of Met Kinase: Synthesis, X-ray Crystallographic Analysis, and Biological Activities

    SciTech Connect

    Kim, Kyoung Soon; Zhang, Liping; Schmidt, Robert; Cai, Zhen-Wei; Wei, Donna; Williams, David K.; Lombardo, Louis J.; Trainor, George L.; Xie, Dianlin; Zhang, Yaquan; An, Yongmi; Sack, John S.; Tokarski, John S.; Darienzo, Celia; Kamath, Amrita; Marathe, Punit; Zhang, Yueping; Lippy, Jonathan; Jeyaseelan, Sr., Robert; Wautlet, Barri; Henley, Benjamin; Gullo-Brown, Johnni; Manne, Veeraswamy; Hunt, John T.; Fargnoli, Joseph; Borzilleri, Robert M.

    2008-10-02

    Conformationally constrained 2-pyridone analogue 2 is a potent Met kinase inhibitor with an IC50 value of 1.8 nM. Further SAR of the 2-pyridone based inhibitors of Met kinase led to potent 4-pyridone and pyridine N-oxide inhibitors such as 3 and 4. The X-ray crystallographic data of the inhibitor 2 bound to the ATP binding site of Met kinase protein provided insight into the binding modes of these inhibitors, and the SAR of this series of analogues was rationalized. Many of these analogues showed potent antiproliferative activities against the Met dependent GTL-16 gastric carcinoma cell line. Compound 2 also inhibited Flt-3 and VEGFR-2 kinases with IC{sub 50} values of 4 and 27 nM, respectively. It possesses a favorable pharmacokinetic profile in mice and demonstrates significant in vivo antitumor activity in the GTL-16 human gastric carcinoma xenograft model.

  20. Identification, SAR studies, and X-ray co-crystallographic analysis of a novel furanopyrimidine aurora kinase A inhibitor.

    PubMed

    Coumar, Mohane Selvaraj; Tsai, Ming-Tsung; Chu, Chang-Ying; Uang, Biing-Jiun; Lin, Wen-Hsing; Chang, Chun-Yu; Chang, Teng-Yuan; Leou, Jiun-Shyang; Teng, Chi-Huang; Wu, Jian-Sung; Fang, Ming-Yu; Chen, Chun-Hwa; Hsu, John T-A; Wu, Su-Ying; Chao, Yu-Sheng; Hsieh, Hsing-Pang

    2010-02-01

    Herein we reveal a simple method for the identification of novel Aurora kinase A inhibitors through substructure searching of an in-house compound library to select compounds for testing. A hydrazone fragment conferring Aurora kinase activity and heterocyclic rings most frequently reported in kinase inhibitors were used as substructure queries to filter the in-house compound library collection prior to testing. Five new series of Aurora kinase inhibitors were identified through this strategy, with IC(50) values ranging from approximately 300 nM to approximately 15 microM, by testing only 133 compounds from a database of approximately 125,000 compounds. Structure-activity relationship studies and X-ray co-crystallographic analysis of the most potent compound, a furanopyrimidine derivative with an IC(50) value of 309 nM toward Aurora kinase A, were carried out. The knowledge gained through these studies could help in the future design of potent Aurora kinase inhibitors.

  1. Discovery of pyrrolopyridine-pyridone based inhibitors of Met kinase: synthesis, X-ray crystallographic analysis, and biological activities.

    PubMed

    Kim, Kyoung Soon; Zhang, Liping; Schmidt, Robert; Cai, Zhen-Wei; Wei, Donna; Williams, David K; Lombardo, Louis J; Trainor, George L; Xie, Dianlin; Zhang, Yaquan; An, Yongmi; Sack, John S; Tokarski, John S; Darienzo, Celia; Kamath, Amrita; Marathe, Punit; Zhang, Yueping; Lippy, Jonathan; Jeyaseelan, Robert; Wautlet, Barri; Henley, Benjamin; Gullo-Brown, Johnni; Manne, Veeraswamy; Hunt, John T; Fargnoli, Joseph; Borzilleri, Robert M

    2008-09-11

    Conformationally constrained 2-pyridone analogue 2 is a potent Met kinase inhibitor with an IC50 value of 1.8 nM. Further SAR of the 2-pyridone based inhibitors of Met kinase led to potent 4-pyridone and pyridine N-oxide inhibitors such as 3 and 4. The X-ray crystallographic data of the inhibitor 2 bound to the ATP binding site of Met kinase protein provided insight into the binding modes of these inhibitors, and the SAR of this series of analogues was rationalized. Many of these analogues showed potent antiproliferative activities against the Met dependent GTL-16 gastric carcinoma cell line. Compound 2 also inhibited Flt-3 and VEGFR-2 kinases with IC50 values of 4 and 27 nM, respectively. It possesses a favorable pharmacokinetic profile in mice and demonstrates significant in vivo antitumor activity in the GTL-16 human gastric carcinoma xenograft model.

  2. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the mannose 6-phosphate isomerase from Salmonella typhimurium

    SciTech Connect

    Gowda, Giri; Sagurthi, Someswar Rao; Savithri, H. S.; Murthy, M. R. N.

    2008-02-01

    The cloning, expression, purification, crystallization and preliminary X-ray crystallographic studies of mannose 6-phosphate isomerase from S. typhimurium are reported. Mannose 6-phosphate isomerase (MPI; EC 5.3.1.8) catalyzes the reversible isomerization of d-mannose 6-phosphate (M6P) and d-fructose 6-phosphate (F6P). In the eukaryotes and prokaryotes investigated to date, the enzyme has been reported to play a crucial role in d-mannose metabolism and supply of the activated mannose donor guanosine diphosphate d-mannose (GDP-d-mannose). In the present study, MPI was cloned from Salmonella typhimurium, overexpressed in Escherichia coli and purified using Ni–NTA affinity column chromatography. Purified MPI crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 36.03, b = 92.2, c = 111.01 Å. A data set extending to 1.66 Å resolution was collected with 98.8% completeness using an image-plate detector system mounted on a rotating-anode X-ray generator. The asymmetric unit of the crystal cell was compatible with the presence of a monomer of MPI. A preliminary structure solution of the enzyme has been obtained by molecular replacement using Candida albicans MPI as the phasing model and the program Phaser. Further refinement and model building are in progress.

  3. Synthesis, X-Ray Crystallographic Analysis and BSA Interaction of a New α-Aminophosphonate

    NASA Astrophysics Data System (ADS)

    Wang, Q.-M.; Gao, W.; Song, J.-L.; Liu, Y.; Qi, H.; Tang, X.-H.

    2016-09-01

    A new α-aminophosphonate ( 1) was synthesized and its composition and structure were established by EA, FT-IR, ESI-MS, NMR (1H, 13C, and 31P), and X-ray crystallography. Compound 1 crystallizes in a monoclinic system with space group C2/c. The interaction between α-aminophosphonate ( 1) and bovine serum albumin (BSA) at three different temperatures (298, 303, and 310 K) under simulated physiological condition were studied by fluorescence spectroscopy. The results showed that the fluorescence quenching mechanism between 1 and BSA was a static quenching procedure. The binding constant (Ka) and binding sites (n) were obtained. The corresponding thermodynamic parameters (ΔH, ΔS, and ΔG) of the interaction system were calculated at different temperatures. The results revealed that the binding process was spontaneous; hydrogen bonds and van der Waals forces were the main forces that stabilize the complex.

  4. Preliminary neutron and X-ray crystallographic studies of equine cyanomethemoglobin

    SciTech Connect

    Kovalevsky, A.Y.; Fisher, S.Z.; Seaver, S.; Mustyakimov, M.; Sukumar, N.; Langan, P.; Mueser, T.C.; Hanson, B.L.

    2010-08-18

    Room-temperature and 100 K X-ray and room-temperature neutron diffraction data have been measured from equine cyanomethemoglobin to 1.7 {angstrom} resolution using a home source, to 1.6 {angstrom} resolution on NE-CAT at the Advanced Photon Source and to 2.0 {angstrom} resolution on the PCS at Los Alamos Neutron Science Center, respectively. The cyanomethemoglobin is in the R state and preliminary room-temperature electron and neutron scattering density maps clearly show the protonation states of potential Bohr groups. Interestingly, a water molecule that is in the vicinity of the heme group and coordinated to the distal histidine appears to be expelled from this site in the low-temperature structure.

  5. Crystallization and preliminary X-ray crystallographic studies of pig heart carbonyl reductase

    SciTech Connect

    Aoki, Ken-ichi; Tanaka, Nobutada; Ishikura, Shuhei; Araki, Naoko; Imamura, Yorishige; Hara, Akira; Nakamura, Kazuo T.

    2006-10-01

    Pig heart carbonyl reductase has been crystallized in the presence of NADPH. Diffraction data have been collected using synchrotron radiation. Pig heart carbonyl reductase (PHCR), which belongs to the short-chain dehydrogenase/reductase (SDR) family, has been crystallized by the hanging-drop vapour-diffusion method. Two crystal forms (I and II) have been obtained in the presence of NADPH. Form I crystals belong to the tetragonal space group P4{sub 2}, with unit-cell parameters a = b = 109.61, c = 94.31 Å, and diffract to 1.5 Å resolution. Form II crystals belong to the tetragonal space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 120.10, c = 147.00 Å, and diffract to 2.2 Å resolution. Both crystal forms are suitable for X-ray structure analysis at high resolution.

  6. Purification, crystallization and preliminary X-ray crystallographic analysis of rice lectin from Oryza sativa

    SciTech Connect

    Huang, Yen-Chieh; Lin, Yi-Hung; Shih, Chia-Hao; Shih, Chun-Liang; Chang, Tschining; Chen, Chun-Jung

    2006-02-01

    Rice lectin was crystallized and analyzed by X-ray crystallography. Lectins with sugar-binding specificity are widely distributed in higher plants and various other species. The expression of rice lectin from Oryza sativa is up-regulated in the growing coleoptile when anaerobic stress persists. A rice lectin of molecular weight 15.2 kDa has been crystallized using the hanging-drop vapour-diffusion method. From the diffraction of the lectin crystals at 1.93 Å resolution, the unit cell belongs to space group P3{sub 1}, with unit-cell parameters a = 98.58, b = 98.58, c = 44.72 Å. Preliminary analysis indicates that there are two lectin molecules in an asymmetric unit with a large solvent content, 70.1%.

  7. Crystallization and preliminary X-ray crystallographic studies of the CARD domain of human CARMA1.

    PubMed

    Park, Jin Hee; Park, Hyun Ho

    2013-04-01

    The CARMA1 signalosome, which is composed of CARMA1 [caspase recruitment domain (CARD) containing MAGUK protein 1], BCL10 (B-cell lymphoma 10) and MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), is a molecular-signalling complex that performs pivotal functions in T-cell receptor (TCR) and B-cell receptor (BCR) mediated NF-κB activation. In this study, the CARD domain of human CARMA1 (CARMA1 CARD), corresponding to amino acids 14-109, was overexpressed in Escherichia coli using an engineered C-terminal His tag. CARMA1 CARD was then purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 3.2 Å from a crystal belonging to space group P2(1)2(1)2(1) with unit-cell parameters a = 45.73, b = 53.37, c = 91.89 Å.

  8. Quantification of thin film crystallographic orientation using X-ray diffraction with an area detector

    SciTech Connect

    Baker, Jessica L; Jimison, Leslie H; Mannsfeld, Stefan; Volkman, Steven; Yin, Shong; Subramanian, Vivek; Salleo, Alberto; Alivisatos, A Paul; Toney, Michael F

    2010-02-19

    As thin films become increasingly popular (for solar cells, LEDs, microelectronics, batteries), quantitative morphological information is needed to predict and optimize the film's electronic, optical and mechanical properties. This quantification can be obtained quickly and easily with X-ray diffraction using an area detector and synchrotron radiation in two simple geometries. In this paper, we describe a methodology for constructing complete pole figures for thin films with fiber texture (isotropic in-plane orientation). We demonstrate this technique on semicrystalline polymer films, self-assembled nanoparticle semiconductor films, and randomly-packed metallic nanoparticle films. This method can be immediately implemented to help understand the relationship between film processing and microstructure, enabling the development of better and less expensive electronic and optoelectronic devices.

  9. Crystallization and Preliminary X-Ray Crystallographic Analysis of Human Plasma Platelet Activating Factor Acetylhydrolase

    SciTech Connect

    Samanta, U.; Wilder, C; Bahnson, B

    2009-01-01

    The plasma form of the human enzyme platelet activating factor acetylhydrolase (PAF-AH) has been crystallized, and X-ray diffraction data were collected at a synchrotron source to a resolution of 1.47 {angstrom}. The crystals belong to space group C2, with unit cell parameters of a = 116.18, b = 83.06, c = 96.71 {angstrom}, and {beta} = 115.09 and two molecules in the asymmetric unit. PAF-AH functions as a general anti-inflammatory scavenger by reducing the levels of the signaling molecule PAF. Additionally, the LDL bound enzyme has been linked to atherosclerosis due to its hydrolytic activities of pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids.

  10. Crystallization and preliminary X-ray crystallographic analysis of zebrafish prototype galectin Drgal1-L2

    PubMed Central

    Scott, Stacy A.; Cozier, Matthew O.; Dubar, Pauline D. I.; Ramakrishna, Manasa; Scott, Ken; Blanchard, Helen

    2010-01-01

    Zebrafish (Danio rerio) are an important developmental and embryological model given the optical clarity of the embryos and larvae, which permits real-time viewing of developing pathologies. More recently, a broader scope for these vertebrates to model a range of human diseases, including some cancers, has been indicated. Zebrafish Drgal1-L2 has been identified as an orthologue of mammalian galectin-1, which is is a carbohydrate-binding protein that exhibits β-galactoside-binding specificity and which is overexpressed by many aggressive human cancers. This study describes the cloning, expression in Escherichia coli, purification and crystallization of recombinant Drgal1-L2 protein in the presence of lactose (ligand). X-ray diffraction data from these novel crystals of zebrafish Drgal1-L2 were collected to a resolution of 1.5 Å using a synchrotron-radiation source, enabling their characterization. PMID:21139216

  11. Crystallization and preliminary X-ray crystallographic studies of the axin DIX domain

    SciTech Connect

    Shibata, Naoki; Tomimoto, Yusuke; Hanamura, Toru; Yamamoto, Ryo; Ueda, Mai; Ueda, Yasufumi; Mizuno, Nobuhiro; Ogata, Hideaki; Komori, Hirofumi; Shomura, Yasuhito; Kataoka, Michihiko; Shimizu, Sakayu; Kondo, Jun; Yamamoto, Hideki; Kikuchi, Akira; Higuchi, Yoshiki

    2007-06-01

    The DIX domain of rat axin has been purified and crystallized. Crystals diffracted to 2.9 Å resolution using synchrotron radiation. Axin is a negative regulator of the canonical Wnt signalling pathway that mediates the phosphorylation of β-catenin by glycogen synthase kinase 3β. The DIX domain of rat axin, which is important for its homooligomerization and interactions with other regulators in the Wnt pathway, was purified and crystallized by the sitting-drop vapour-diffusion technique using polyethylene glycol 6000 and lithium sulfate as crystallization agents. Crystals belong to space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 91.49, c = 84.92 Å. An X-ray diffraction data set has been collected to a nominal resolution of 2.9 Å.

  12. Purification, crystallization and preliminary X-ray crystallographic analysis of xylose reductase from Candida tropicalis

    PubMed Central

    Chen, Li-Chun; Huang, Sheng-Cih; Chuankhayan, Phimonphan; Chen, Chung-Der; Huang, Yen-Chieh; Jeyakanthan, Jeyaraman; Pang, Hsiao-Fang; Men, Lee-Chung; Chen, Yu-Ching; Wang, Yu-Kuo; Liu, Ming-Yih; Wu, Tung-Kung; Chen, Chun-Jung

    2009-01-01

    Xylose reductase (XR), which requires NADPH as a co-substrate, catalyzes the reduction of d-xylose to xylitol, which is the first step in the metabolism of d-­xylose. The detailed three-dimensional structure of XR will provide a better understanding of the biological significance of XR in the efficient production of xylitol from biomass. XR of molecular mass 36.6 kDa from Candida tropicalis was crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction data from C. tropicalis XR crystals at 2.91 Å resolution, the unit cell belongs to space group P31 or P32. Preliminary analysis indicated the presence of four XR molecules in the asymmetric unit, with 68.0% solvent content. PMID:19342796

  13. Crystallization and preliminary X-ray crystallographic analysis of zebrafish prototype galectin Drgal1-L2.

    PubMed

    Scott, Stacy A; Cozier, Matthew O; Dubar, Pauline D I; Ramakrishna, Manasa; Scott, Ken; Blanchard, Helen

    2010-12-01

    Zebrafish (Danio rerio) are an important developmental and embryological model given the optical clarity of the embryos and larvae, which permits real-time viewing of developing pathologies. More recently, a broader scope for these vertebrates to model a range of human diseases, including some cancers, has been indicated. Zebrafish Drgal1-L2 has been identified as an orthologue of mammalian galectin-1, which is is a carbohydrate-binding protein that exhibits β-galactoside-binding specificity and which is overexpressed by many aggressive human cancers. This study describes the cloning, expression in Escherichia coli, purification and crystallization of recombinant Drgal1-L2 protein in the presence of lactose (ligand). X-ray diffraction data from these novel crystals of zebrafish Drgal1-L2 were collected to a resolution of 1.5 Å using a synchrotron-radiation source, enabling their characterization.

  14. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Zucchini from Drosophila melanogaster.

    PubMed

    Fukuhara, Satoshi; Nishimasu, Hiroshi; Bonnefond, Luc; Matsumoto, Naoki; Ishitani, Ryuichiro; Nureki, Osamu

    2012-11-01

    PIWI-interacting RNAs (piRNAs) bind PIWI proteins and silence transposons to maintain the genomic integrity of germ cells. Zucchini (Zuc), a phospholipase D superfamily member, is conserved among animals and is implicated in piRNA biogenesis. However, the underlying mechanism by which Zuc participates in piRNA biogenesis remains elusive. Drosophila melanogaster Zuc (DmZuc) was expressed in Escherichia coli, purified and crystallized. X-ray diffraction data were collected to 1.75 Å resolution. The crystal belonged to space group P2(1), with unit-cell parameters a=55.0, b=71.2, c=56.3 Å, β=107.9°.

  15. Preliminary X-ray crystallographic studies of mouse UPR responsive protein P58(IPK) TPR fragment.

    PubMed

    Tao, Jiahui; Wu, Yunkun; Ron, David; Sha, Bingdong

    2008-02-01

    Endoplasmic reticulum (ER) stress induces the unfolded protein response (UPR), which can promote protein folding and misfolded protein degradation and attenuate protein translation and protein translocation into the ER. P58(IPK) has been proposed to function as a molecular chaperone to maintain protein-folding homeostasis in the ER under normal and stressed conditions. P58(IPK) contains nine TPR motifs and a C-terminal J-domain within its primary sequence. To investigate the mechanism by which P58(IPK) functions to promote protein folding within the ER, a P58(IPK) TPR fragment without the C-terminal J-domain was crystallized. The crystals diffract to 2.5 A resolution using a synchrotron X-ray source. The crystals belong to space group P2(1), with unit-cell parameters a = 83.53, b = 92.75, c = 84.32 A, alpha = 90.00, beta = 119.36, gamma = 90.00 degrees. There are two P58(IPK) molecules in the asymmetric unit, which corresponds to a solvent content of approximately 60%. Structure determination by MAD methods is under way.

  16. Preliminary X-ray crystallographic studies of yeast mitochondrial protein Tom70p

    SciTech Connect

    Wu, Yunkun; McCombs, Debbie; Nagy, Lisa; DeLucas, Lawrence; Sha, Bingdong

    2006-03-01

    Tom70p is an important translocase of the outer membrane complex member and a major surface receptor of the protein-translocation machinery in the outer mitochondrial membrane. To investigate the mechanism by which Tom70p functions to deliver the mitochondrial protein precursors, the cytosolic fragment of yeast Tom70p (cTom70p) has been crystallized. Protein translocations across mitochondrial membranes play critical roles in mitochondrion biogenesis. Protein transport from the cell cytosol to the mitochondrial matrix is carried out by the translocase of the outer membrane (TOM) complex and the translocase of the inner membrane (TIM) complexes. Tom70p is an important TOM-complex member and a major surface receptor of the protein-translocation machinery in the outer mitochondrial membrane. To investigate the mechanism by which Tom70p functions to deliver the mitochondrial protein precursors, the cytosolic fragment of yeast Tom70p (cTom70p) was crystallized. The crystals diffract to 3.2 Å using a synchrotron X-ray source and belong to space group P2{sub 1}, with unit-cell parameters a = 44.89, b = 168.78, c = 83.41 Å, α = 90.00, β = 102.74, γ = 90.00°. There are two Tom70p molecules in one asymmetric unit, which corresponds to a solvent content of approximately 51%. Structure determination by MAD methods is under way.

  17. Expression, crystallization and preliminary X-ray crystallographic analysis of human agmatinase.

    PubMed

    Kim, Kyoung Hoon; Ahn, Hyung Jun; Kim, Do Jin; Lee, Hyung Ho; Ha, Jun-Yong; Kim, Hye-Kyung; Yoon, Hye-Jin; Suh, Se Won

    2005-10-01

    Agmatine, which results from the decarboxylation of L-arginine by arginine decarboxylase, is a metabolic intermediate in the biosynthesis of putresine and higher polyamines (spermidine and spermine). Recent studies indicate that agmatine can have several important biochemical effects in humans, ranging from effects on the central nervous system to cell proliferation in cancer and viral replication. Agmatinase catalyses the hydrolysis of agmatine to putresine and urea and is a major target for drug action and development. The human agmatinase gene encodes a 352-residue protein with a putative mitochondrial targeting sequence at the N-terminus. Human agmatinase (residues Ala36-Val352) has been overexpressed as a fusion with both N- and C-terminal purification tags in Escherichia coli and crystallized in the presence of Mn2+ and 1,6-diaminohexane at 297 K using polyethylene glycol 4000 as a precipitant. X-ray diffraction data were collected at 100 K to 2.49 A from a flash-frozen crystal. The crystals are tetragonal, belonging to space group P4(2), with unit-cell parameters a = b = 114.54, c = 125.65 A, alpha = beta = gamma = 90 degrees. Three monomers are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (VM) of 3.66 A3 Da(-1) and a solvent content of 66.4%.

  18. Preliminary X-ray crystallographic studies of mouse UPR responsive protein P58(IPK) TPR fragment

    PubMed Central

    Tao, Jiahui; Wu, Yunkun; Ron, David; Sha, Bingdong

    2008-01-01

    Endoplasmic reticulum (ER) stress induces the unfolded protein response (UPR), which can promote protein folding and misfolded protein degradation and attenuate protein translation and protein translocation into the ER. P58(IPK) has been proposed to function as a molecular chaperone to maintain protein-folding homeostasis in the ER under normal and stressed conditions. P58(IPK) contains nine TPR motifs and a C-terminal J-domain within its primary sequence. To investigate the mechanism by which P58(IPK) functions to promote protein folding within the ER, a P58(IPK) TPR fragment without the C-terminal J-domain was crystallized. The crystals diffract to 2.5 Å resolution using a synchrotron X-ray source. The crystals belong to space group P21, with unit-cell parameters a = 83.53, b = 92.75, c = 84.32 Å, α = 90.00, β = 119.36, γ = 90.00°. There are two P58(IPK) molecules in the asymmetric unit, which corresponds to a solvent content of approximately 60%. Structure determination by MAD methods is under way. PMID:18259061

  19. Synthesis, X-ray crystallographic, spectroscopic and computational studies of aminothiazole derivatives

    NASA Astrophysics Data System (ADS)

    Adeel, Muhammad; Braga, Ataualpa A. C.; Tahir, Muhammad Nawaz; Haq, Fazal; Khalid, Muhammad; Halim, Mohammad A.

    2017-03-01

    Aminothiazole organic compounds have diverse biological applications. Herein we report the synthesis of two aminothiazole derivatives: 4-(biphenyl-4-yl)thiazol-2-amine (1) and 4-(2‧,4‧-difluorobiphenyl-4-yl)thiazol-2-amine (2) via Suzuki-Miyaura cross coupling reaction. The chemical structures of 1 and 2 are confirmed using 1HNMR, 13CNMR, FT-IR, UV-Vis and single crystal x-ray studies. The XRD study reveals that the both solid state structures (1) and (2) are diffused to form poly chain structures due to presence of intra molecular hydrogen bonding (H.B). Furthermore, these compounds were analysed by density functional theory (DFT) at M06-2X/6-311G(d,p), B3LYP/6-31G(d) B3LYP/6-31G(d,p) and B3LYP/6-311G(2d,p) level of theories to obtain optimized geometry, electronic and spectroscopic properties. DFT optimized geometry supports the experimental XRD parameters. Natural bond orbital (NBO) calculation predicted the hyper conjugative interaction and hydrogen bonding in all derivatives. The FT-IR and thermodynamic studies also confirm the presence of hydrogen bonding network in the dimers which agrees well with the XRD results. Moreover, UV-Vis analysis reveals that maximum excitations take place in 1 and 2 due to HOMO → LUMO(98%) and HOMO → LUMO(97%) respectively which show good agreement to experimental data. The first order hyperpolarizability of both molecules is remarkably greater than the value of urea. The global reactivity parameters which are obtained by frontier molecular orbitals disclose that the molecules might be bioactive.

  20. Crystallization and preliminary X-ray crystallographic analysis of a blue-light-absorbing proteorhodopsin.

    PubMed

    Wang, Ning; Wang, Meitian; Gao, Yanyan; Ran, Tingting; Lan, Yanli; Wang, Jian; Xu, Langlai; Wang, Weiwu

    2012-03-01

    Proteorhodopsins (PRs), seven-transmembrane chromoproteins with retinal as a chromophore, are light-driven proton pumps. To elucidate the light-driven proton-pumping mechanism of PRs, a pET28a vector containing the blue-light-absorbing proteorhodopsin (BPR) gene was constructed and the protein was overexpressed in Escherichia coli. The protein was purified by immobilized metal-ion affinity chromatography (IMAC). The purified BPR D97N mutant protein (BPR_D97N) was crystallized using the vapour-diffusion method. Preliminary X-ray diffraction data analysis showed that the crystal belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 161.6, b = 168.6, c = 64.7 Å. A complete data set was collected to 3.3 Å resolution using synchrotron radiation on beamline X06 of the Swiss Light Source (SLS). Molecular replacement was unsuccessful. To solve the structure of BPR_D97N by experimental phasing, selenomethionine-substituted protein crystals were prepared. These crystals diffracted to 3.0 Å resolution and a complete data set was collected on beamline BL17U of the Shanghai Synchrotron Radiation Facility (SSRF). Heavy-atom substructure determination and phasing by SAD clearly showed that the crystal contained five molecules in the asymmetric unit, with a V(M) of 3.26 Å(3) Da(-1) and a solvent content of 62.3%. © 2012 International Union of Crystallography

  1. Overexpression, crystallization and preliminary X-ray crystallographic analysis of Nudix hydrolase Orf141 from Escherichia coli K-1

    SciTech Connect

    Jung, Junho; Ahn, Yeh-Jin; Kang, Lin-Woo

    2007-09-01

    A novel Nudix hydrolase Orf141 from E. coli, which cleaves pyrimidine deoxynucleoside triphosphates, was recently cloned. In order to illuminate the structural and functional features of the novel Nudix hydrolase Orf141, it was expressed, purified and crystallized and a preliminary X-ray crystallographic analysis was conducted. Nudix hydrolases are a family of proteins that contain the characteristic amino-acid sequence GX{sub 5}EX{sub 7}REUXEEXGU (where U is usually I, L or V), the Nudix signature sequence. They catalyze the hydrolysis of a variety of nucleoside diphosphate derivatives such as nucleoside triphosphates, nucleotide sugars, ADP-ribose, dinucleotide coenzymes, diadenosine oligophosphates and capped RNAs. Recently, three new Nudix hydrolases have been found from Escherichia coli; one of them is Orf141, which cleaves pyrimidine deoxynucleoside triphosphates. Orf141 was cloned directly from E. coli K1 strain and was overexpressed in E. coli without any extra residues. Orf141 crystals were successfully obtained using polyethylene glycol 1500 as a precipitant at 285 K. X-ray diffraction data were collected to 3.1 Å resolution using synchrotron radiation. The crystal is a member of the rhombohedral space group H32, with unit-cell parameters a = b = 182.2, c = 62.3 Å, α = 90, β = 90, γ = 120° (hexagonal setting). Two or three monomers are likely to be present in the asymmetric unit, with corresponding V{sub M} values of 2.92 and 1.95 Å{sup 3} Da{sup −1} and solvent contents of 57.9 and 36.9%, respectively.

  2. Crystallization and preliminary X-ray crystallographic analysis of polyphenol oxidase from Juglans regia (jrPPO1)

    SciTech Connect

    Zekiri, Florime; Bijelic, Aleksandar; Molitor, Christian; Rompel, Annette

    2014-05-28

    The crystallization and preliminary X-ray crystallographic analysis of a plant PPO exhibiting monophenolase activity from J. regia (jrPPO1) in its active form (Asp{sup 101}–Arg{sup 445}) are reported. Tyrosinase is a type 3 copper enzyme that catalyzes the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones, which are precursors for the biosynthesis of melanins. The first plant tyrosinase from walnut leaves (Juglans regia) was purified to homogeneity and crystallized. During the purification, two forms of the enzyme differing only in their C-termini [jrPPO1(Asp{sup 101}–Pro{sup 444}) and jrPPO1(Asp{sup 101}–Arg{sup 445})] were obtained. The most abundant form jrPPO1(Asp{sup 101}–Arg{sup 445}), as described in Zekiri et al. [Phytochemistry (2014 ▶), 101, 5–15], was crystallized, resulting in crystals that belonged to space group C121, with unit-cell parameters a = 115.56, b = 91.90, c = 86.87 Å, α = 90, β = 130.186, γ = 90°, and diffracted to 2.39 Å resolution. Crystals were only obtained from solutions containing at least 30% polyethylene glycol 5000 monomethyl ether in a close-to-neutral pH range.

  3. Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin.

    PubMed

    Matsuno, Asuka; Gai, Zuoqi; Tanaka, Miyuki; Kato, Koji; Kato, Sanae; Katoh, Tsuyoshi; Shimizu, Takeshi; Yoshioka, Takeya; Kishimura, Hideki; Tanaka, Yoshikazu; Yao, Min

    2015-06-01

    Many molluscs transport oxygen using a very large cylindrical multimeric copper-containing protein named hemocyanin. The molluscan hemocyanin forms a decamer (cephalopods) or multidecamer (gastropods) of approximately 330-450kDa subunits, resulting in a molecular mass >3.3MDa. Therefore, molluscan hemocyanin is one of the largest proteins. The reason why these organisms use such a large supermolecule for oxygen transport remains unclear. Atomic-resolution X-ray crystallographic analysis is necessary to unveil the detailed molecular structure of this mysterious large molecule. However, its propensity to dissociate in solution has hampered the crystallization of its intact form. In the present study, we successfully obtained the first crystals of an intact decameric molluscan hemocyanin. The diffraction dataset at 3.0-Å resolution was collected by merging the datasets of two isomorphic crystals. Electron microscopy analysis of the dissolved crystals revealed cylindrical particles. Furthermore, self-rotation function analysis clearly showed the presence of a fivefold symmetry with several twofold symmetries perpendicular to the fivefold axis. The absorption spectrum of the crystals showed an absorption peak around 345nm. These results indicated that the crystals contain intact hemocyanin decamers in the oxygen-bound form.

  4. Characterization of the phosphoserine of pepsinogen using /sup 31/P nuclear magnetic resonance: corroboration of X-ray crystallographic results

    SciTech Connect

    Williams, S.P.; Bridger, W.A.; James, M.N.G.

    1986-10-21

    The endogenous phosphoserine residue in porcine pepsinogen has been titrated with use of phosphorus-31 nuclear magnetic resonance (/sup 31/P NMR). It has an observed pK/sub a/sub 2// of 6.7 and a narrow line width (approx. =10 Hz). The phosphate can be readily removed by an acid phosphatase from potato; however, it is resistant to hydrolysis by several alkaline phosphatases. The X-ray crystal structure of porcine pepsinogen at 1.8-A resolution shows a rather weak and diffuse region of electron density in the vicinity of the phosphorylated serine residue. This suggests considerable dynamic mobility or conformational disorder of the phosphate. In order to define more fully this behavior the NMR data have been used to corroborate these crystallographic results. All these physical data are consistent with a highly mobile phosphoserine residue on the surface of the zymogen and freely exposed to solvent. In addition, certain properties of this phosphoserine moiety on pepsinogen are similar to those of one of the phosphorylated residues of ovalbumin. The possible significance of this is discussed.

  5. Overexpression, crystallization and preliminary X-ray crystallographic analysis of the variable lymphocyte receptor 2913 ectodomain fused with internalin B

    PubMed Central

    Lee, Ji Yeon; Kim, Hyoun Sook; Baek, In Wha; Back, Jang Mi; Han, Mi Ra; Kong, Sun-Young; Kim, Ji Hyeon; Kirchdoerfer, Robert N.; Kim, Jae-Ouk; Cooper, Max D.; Wilson, Ian A.; Kim, Hyun-Jung; Han, Byung Woo

    2013-01-01

    In jawless vertebrates, variable lymphocyte receptors (VLRs) play a crucial role in the recognition of antigens as part of the adaptive immune system. Leucine-rich repeat (LRR) modules and the highly variable insert (HVI) of VLRs contribute to the specificity and diversity of antigen recognition. VLR2913, the antigen of which is not known, contains the same HVI amino-acid sequence as that of VLR RBC36, which recognizes the H-trisaccharide from human blood type O erythrocytes. Since the HVI sequence is rarely identical among all known VLRs, identification of the antigen for VLR2913 and the main contributing factors for antigen recognition based on a comparison of VLR2913 and VLR RBC36 has been attempted. To initiate and facilitate this structural approach, the ectodomain of VLR2913 was fused with the N-terminal domain of internalin B (InlB-VLR2913-ECD). Three amino-acid residues on the concave surface of the LRR modules of InlB-VLR2913-ECD were mutated, considering important residues for hydrogen bonds in the recognition of H-trisaccharide by VLR RBC36. InlB-VLR2913-ECD was overexpressed in Escherichia coli and was crystallized at 295 K using the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 2.04 Å resolution and could be indexed in the tetragonal space group P41212 (or P43212), with unit-cell parameters a = 91.12, b = 91.12, c = 62.87 Å. Assuming that one monomer molecule was present in the crystallographic asymmetric unit, the calculated Matthews coefficient (V M) was 2.75 Å3 Da−1 and the solvent content was 55.2%. Structural determination of InlB-VLR2913-ECD by molecular replacement is in progress. PMID:23295483

  6. X-ray Crystallographic and Steady State Fluorescence Characterization of the Protein Dynamics of Yeast Polyadenylate Polymerase.

    SciTech Connect

    Balbo,P.; Toth, J.; Bohm, A.

    2007-01-01

    Polyadenylate polymerase (PAP) catalyzes the synthesis of poly(A) tails on the 3'-end of pre-mRNA. PAP is composed of three domains: an N-terminal nucleotide-binding domain (homologous to the palm domain of DNA and RNA polymerases), a middle domain (containing other conserved, catalytically important residues), and a unique C-terminal domain (involved in protein-protein interactions required for 3'-end formation). Previous X-ray crystallographic studies have shown that the domains are arranged in a V-shape such that they form a central cleft with the active site located at the base of the cleft at the interface between the N-terminal and middle domains. In the previous studies, the nucleotides were bound directly to the N-terminal domain and exhibited a conspicuous lack of adenine-specific interactions that would constitute nucleotide recognition. Furthermore, it was postulated that base-specific contacts with residues in the middle domain could occur either as a result of a change in the conformation of the nucleotide or domain movement. To address these issues and to better characterize the structural basis of substrate recognition and catalysis, we report two new crystal structures of yeast PAP. A comparison of these structures reveals that the N-terminal and C-terminal domains of PAP move independently as rigid bodies along two well defined axes of rotation. Modeling of the nucleotide into the most closed state allows us to deduce specific nucleotide interactions involving residues in the middle domain (K215, Y224 and N226) that are proposed to be involved in substrate binding and specificity. To further investigate the nature of PAP domain flexibility, 2-aminopurine labeled molecular probes were employed in steady state fluorescence and acrylamide quenching experiments. The results suggest that the closed domain conformation is stabilized upon recognition of the correct substrate, MgATP, in an enzyme-substrate ternary complex. The implications of these results

  7. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase.

    PubMed

    Daughtry, Kelly D; Xiao, Youli; Stoner-Ma, Deborah; Cho, Eunsun; Orville, Allen M; Liu, Pinghua; Allen, Karen N

    2012-02-08

    Herein, the structure resulting from in situ turnover in a chemically challenging quaternary ammonium oxidative demethylation reaction was captured via crystallographic analysis and analyzed via single-crystal spectroscopy. Crystal structures were determined for the Rieske-type monooxygenase, stachydrine demethylase, in the unliganded state (at 1.6 Å resolution) and in the product complex (at 2.2 Å resolution). The ligand complex was obtained from enzyme aerobically cocrystallized with the substrate stachydrine (N,N-dimethylproline). The ligand electron density in the complex was interpreted as proline, generated within the active site at 100 K by the absorption of X-ray photon energy and two consecutive demethylation cycles. The oxidation state of the Rieske iron-sulfur cluster was characterized by UV-visible spectroscopy throughout X-ray data collection in conjunction with resonance Raman spectra collected before and after diffraction data. Shifts in the absorption band wavelength and intensity as a function of absorbed X-ray dose demonstrated that the Rieske center was reduced by solvated electrons generated by X-ray photons; the kinetics of the reduction process differed dramatically for the liganded complex compared to unliganded demethylase, which may correspond to the observed turnover in the crystal.

  8. Local Strain, Defects and Crystallographic Tilt in GaN(0001) Layers Grown by Maskless Pendeo-epitaxy from X-ray Microdiffraction

    SciTech Connect

    Barabash, R.I.; Ice, G.E.; Liu, W.; Einfeldt, S.; Roskovski, A.M.; Davis, R.F.

    2010-07-13

    Polychromatic x-ray microdiffraction, high-resolution monochromatic x-ray diffraction, and finite element simulations have been used to determine the distribution of strain, defects, and crystallographic tilt in uncoalesced GaN layers grown by maskless pendeo-epitaxy. An important materials parameter was the width-to-height ratio of the etched columns of GaN from which occurred the lateral growth of the wings. Tilt boundaries formed at the column/wing interface for samples with a large ratio. Formation of the tilt boundary can be avoided by using smaller ratios. The strain and tilt across the stripe increased with the width-to-height ratio. The wings were tilted upward at room temperature.

  9. Kinetic and X-ray crystallographic investigations of substituted 2-thio-6-oxo-1,6-dihydropyrimidine-benzenesulfonamides acting as carbonic anhydrase inhibitors.

    PubMed

    Vullo, Daniela; Supuran, Claudiu T; Scozzafava, Andrea; De Simone, Giuseppina; Monti, Simona Maria; Alterio, Vincenzo; Carta, Fabrizio

    2016-08-15

    Herein we report an in vitro kinetic evaluation against the most relevant human carbonic anhydrase (hCA, EC 4.2.1.1) isoforms (I, II, IX and XII) of a small series of lactate dehydrogenase (LDH, EC 1.1.1.27) inhibitors. All compounds contain a primary sulfonamide zinc-binding group (ZBG) substituted with the 2-thio-6-oxo-1,6-dihydropyrimidine scaffold. By means of X-ray crystallographic experiments we explored the ligand-enzyme binding modes, thus highlighting the contribution of the 2-thio-6-oxo-1,6-dihydropyrimidine moiety to the stabilization of the complex.

  10. Crystallographic parameters of magnetic Pr2Fe14-xCoxB-type alloys determined using anomalous x-ray diffraction with synchrotron radiation

    NASA Astrophysics Data System (ADS)

    Galego, E.; Serna, M. M.; Ramanathan, L. V.; Faria, R. N.

    2017-02-01

    Anomalous x-ray synchrotron diffraction was used to determine the crystallographic parameters of PrFeCoB-based magnetic alloys. The effect of cobalt concentration on the crystallographic parameters of the magnetically hard Pr2Fe14-xCoxB phase was studied. The results indicate that addition of cobalt has a marked effect on crystal structure. Variation of the c parameter decreased twice as much as the a parameter with increase in Co content. The positions of inequivalent atoms of the magnetically hard matrix phase ϕ in the Pr-based alloys were determined using Rietveld refinement. This permitted determination of the relative distance of each inequivalent atom from its nearest neighbors. Cobalt occupied the 16k2 site and Fe had a tendency to occupy the 8j2 sites located between the Kagomé layers.

  11. Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+.

    PubMed

    Wan, Qun; Kovalevsky, Andrey Y; Wilson, Mark A; Bennett, Brad C; Langan, Paul; Dealwis, Chris

    2014-06-01

    A crystal of Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ of 4×1.3×0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR-folate-NADP+ ternary-complex structure in order to examine the protonation state, protein dynamics and solvent structure of the complex, furthering understanding of the catalytic mechanism.

  12. Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+

    PubMed Central

    Wan, Qun; Kovalevsky, Andrey Y.; Wilson, Mark A.; Bennett, Brad C.; Langan, Paul; Dealwis, Chris

    2014-01-01

    A crystal of Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ of 4 × 1.3 × 0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR–folate–NADP+ ternary-complex structure in order to examine the protonation state, protein dynamics and solvent structure of the complex, furthering understanding of the catalytic mechanism. PMID:24915100

  13. Crystallization and preliminary X-ray crystallographic analysis of a galactose-specific lectin from Dolichos lablab

    SciTech Connect

    Lavanya Latha, V.; Kulkarni, Kiran A.; Nagender Rao, R.; Siva Kumar, N.; Suguna, K.

    2006-02-01

    The galactose-specific lectin from the seeds of a leguminous plant, D. lablab, has been crystallized. Molecular-replacement solution using 3.0 Å X-ray diffraction data showed the lectin to be a tetramer. The galactose-specific lectin from the seeds of Dolichos lablab has been crystallized using the hanging-drop vapour-diffusion technique. The crystals belong to space group P1, with unit-cell parameters a = 73.99, b = 84.13, c = 93.15 Å, α = 89.92, β = 76.01, γ = 76.99°. X-ray diffraction data to a resolution of 3.0 Å have been collected under cryoconditions (100 K) using a MAR imaging-plate detector system mounted on a rotating-anode X-ray generator. Molecular-replacement calculations carried out using the available structures of legume lectins as search models revealed that the galactose-specific lectin from D. lablab forms a tetramer similar to soybean agglutinin; two such tetramers are present in the asymmetric unit.

  14. Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study.

    PubMed Central

    Bolognesi, M; Rosano, C; Losso, R; Borassi, A; Rizzi, M; Wittenberg, J B; Boffi, A; Ascenzi, P

    1999-01-01

    The x-ray crystal structures of the cyanide derivative of Lucina pectinata monomeric hemoglobin I (L. pectinata HbI) and sperm whale (Physeter catodon) myoglobin (Mb), generally taken as reference models for monomeric hemoproteins carrying hydrogen sulfide and oxygen, respectively, have been determined at 1.9 A (R-factor = 0. 184), and 1.8 A (R-factor = 0.181) resolution, respectively, at room temperature (lambda = 1.542 A). Moreover, the x-ray crystal structure of the L. pectinata HbI:cyanide derivative has been studied at 1.4-A resolution (R-factor = 0.118) and 100 K (on a synchrotron source lambda = 0.998 A). At room temperature, the cyanide ligand is roughly parallel to the heme plane of L. pectinata HbI, being located approximately 2.5 A from the iron atom. On the other hand, the crystal structure of the L. pectinata HbI:cyanide derivative at 100 K shows that the diatomic ligand is coordinated to the iron atom in an orientation almost perpendicular to the heme (the Fe-C distance being 1.95 A), adopting a coordination geometry strictly reminescent of that observed in sperm whale Mb, at room temperature. The unusual cyanide distal site orientation observed in L. pectinata HbI, at room temperature, may reflect reduction of the heme Fe(III) atom induced by free radical species during x-ray data collection using Cu Kalpha radiation. PMID:10423453

  15. Bacterial expression, purification and preliminary X-ray crystallographic characterization of the invertase inhibitor Nt-CIF from tobacco.

    PubMed

    Hothorn, Michael; Bonneau, Fabien; Stier, Gunter; Greiner, Steffen; Scheffzek, Klaus

    2003-12-01

    Acid invertases catalyzing the breakdown of sucrose are regulated at the post-translational level by extracellular inhibitory proteins of 16-20 kDa molecular weight in a pH-dependent manner. Little is known about the characteristics of the underlying protein-protein interaction. Here, the expression, purification, characterization, crystallization and initial X-ray analysis of a biologically active invertase inhibitor Nt-CIF from tobacco is reported. Four crystal forms covering a wide pH range have been obtained and data sets at resolutions higher than 2.5 A have been collected.

  16. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of ScpB (Rv1710) from Mycobacterium tuberculosis

    SciTech Connect

    Kwon, Soo-Young; Kang, Beom Sik; Kim, Myung Hee; Kim, Kyung Jin

    2007-12-01

    ScpB from M. tuberculosis was crystallized using the sitting-drop vapour-diffusion method in the presence of 2 M NaCl and 10% PEG 6000 at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.3 Å at a synchrotron beamline. Structural maintenance of chromosome (SMC) proteins play diverse roles in cellular DNA reassembly by directly interacting with DNA. They require non-SMC proteins for their proper function; these include the conserved segregation and condensation proteins (Scps) in prokaryotes. ScpB from Mycobacterium tuberculosis was crystallized using the sitting-drop vapour-diffusion method in the presence of 2 M NaCl and 10% PEG 6000 at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.3 Å at a synchrotron beamline. The crystal belongs to the hexagonal space group R32, with unit-cell parameters a = b = 136.69, c = 78.55 Å, γ = 120°. With one molecule per asymmetric unit, the crystal volume per unit protein weight (V{sub M}) is 2.95 Å{sup 3} Da{sup −1}. The structure was solved by the single anomalous dispersion method and structure refinement is in progress.

  17. Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation

    SciTech Connect

    Kobayashi, Kan; Suzuki, Takehiro; Dohmae, Naoshi; Ishitani, Ryuichiro; Nureki, Osamu

    2014-08-27

    E. coli YfcM was expressed, purified and crystallized. Crystals of YfcM were obtained by the in situ proteolysis crystallization method. Using these crystals, an X-ray diffraction data set was collected at 1.45 Å resolution. Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein from Escherichia coli was overexpressed, purified and crystallized. The crystal of YfcM was obtained by the in situ proteolysis crystallization method and diffracted X-rays to 1.45 Å resolution. It belonged to space group C2, with unit-cell parameters a = 124.4, b = 37.0, c = 37.6 Å, β = 101.2°. The calculated Matthews coefficient (V{sub M}) of the crystal was 1.91 Å{sup 3} Da{sup −1}, indicating that one YfcM molecule is present in the asymmetric unit with a solvent content of 35.7%.

  18. Protein Conformational Changes in the Bacteriorhodopsin Photocycle: Comparison of Findings from Electron and X-Ray Crystallographic Analyses

    PubMed Central

    Hirai, Teruhisa; Subramaniam, Sriram

    2009-01-01

    Light-driven conformational changes in the membrane protein bacteriorhodopsin have been studied extensively using X-ray and electron crystallography, resulting in the deposition of >30 sets of coordinates describing structural changes at various stages of proton transport. Using projection difference Fourier maps, we show that coordinates reported by different groups for the same photocycle intermediates vary considerably in the extent and nature of conformational changes. The different structures reported for the same intermediate cannot be reconciled in terms of differing extents of change on a single conformational trajectory. New measurements of image phases obtained by cryo-electron microscopy of the D96G/F171C/F219L triple mutant provide independent validation for the description of the large protein conformational change derived at 3.2 Å resolution by electron crystallography of 2D crystals, but do not support atomic models for light-driven conformational changes derived using X-ray crystallography of 3D crystals. Our findings suggest that independent determination of phase information from 2D crystals can be an important tool for testing the accuracy of atomic models for membrane protein conformational changes. PMID:19488399

  19. X-ray Crystallographic Analysis of α-Ketoheterocycle Inhibitors Bound to a Humanized Variant of Fatty Acid Amide Hydrolase

    PubMed Central

    Mileni, Mauro; Garfunkle, Joie; Ezzili, Cyrine; Kimball, F. Scott; Cravatt, Benjamin F.; Stevens, Raymond C.; Boger, Dale L.

    2009-01-01

    Three cocrystal X-ray structures of the α-ketoheterocycle inhibitors 3–5 bound to a humanized variant of fatty acid amide hydrolase (FAAH) are disclosed and comparatively discussed alongside those of 1 (OL-135) and its isomer 2. These five X-ray structures systematically probe each of the three active site regions key to substrate or inhibitor binding: (1) the conformationally mobile acyl chain-binding pocket and membrane access channel responsible for fatty acid amide substrate and inhibitor acyl chain binding, (2) the atypical active site catalytic residues and surrounding oxyanion hole that covalently binds the core of the α-ketoheterocycle inhibitors captured as deprotonated hemiketals mimicking the tetrahedral intermediate of the enzyme catalyzed reaction, and (3) the cytosolic port and its uniquely important imbedded ordered water molecules and a newly identified anion binding site. The detailed analysis of their key active site interactions and their implications on the interpretation of the available structure–activity relationships are discussed providing important insights for future design. PMID:19924997

  20. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement

    PubMed Central

    Borbulevych, Oleg; Martin, Roger I.; Tickle, Ian J.; Westerhoff, Lance M.

    2016-01-01

    Gaining an understanding of the protein–ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  1. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.

    PubMed

    Borbulevych, Oleg; Martin, Roger I; Tickle, Ian J; Westerhoff, Lance M

    2016-04-01

    Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  2. Crystallization and preliminary X-ray crystallographic studies of the outer membrane cytochrome OmcA from Shewanella oneidensis MR-1

    SciTech Connect

    Tomanicek, S.J.; Johs, A.; Sawhney, M.S.; Shi, L.; Liang, L.

    2012-05-24

    The outer membrane cytochrome OmcA functions as a terminal metal reductase in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. The ten-heme centers shuttle electrons from the transmembrane donor complex to extracellular electron acceptors. Here, the crystallization and preliminary crystallographic analysis of OmcA are reported. Crystals of OmcA were grown by the sitting-drop vapor-diffusion method using PEG 20 000 as a precipitant. The OmcA crystals belonged to space group P2{sub 1}, with unit-cell parameters a = 93.0, b = 246.0, c = 136.6 {angstrom}, = 90, {beta} = 97.8, {gamma} = 90{sup o}. X-ray diffraction data were collected to a maximum resolution of 3.25 {angstrom}.

  3. Crystallization and preliminary X-ray crystallographic studies of the outer membrane cytochrome OmcA from Shewanella oneidensis MR-1

    SciTech Connect

    Tomanicek, S. J.; Johs, Alexander; Sawhney, M. S.; Shi, Liang; Liang, L.

    2012-01-01

    The outer membrane cytochrome OmcA functions as a terminal metal reductase in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. The ten-heme centers shuttle electrons from the transmembrane donor complex to extracellular electron acceptors. Here, the crystallization and preliminary crystallographic analysis of OmcA are reported. Crystals of OmcA were grown by the sitting-drop vapor-diffusion method using PEG 20 000 as a precipitant. The OmcA crystals belonged to space group P21, with unit-cell parameters a = 93.0, b = 246.0, c = 136.6 A ° , * = 90, * = 97.8, * = 90*. X-ray diffraction data were collected to a maximum resolution of 3.25 A ° .

  4. Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide.

    PubMed

    Saravanan, R R; Seshadri, S; Gunasekaran, S; Mendoza-Meroño, R; Garcia-Granda, S

    2015-03-15

    Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT-B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.

    PubMed

    Dong, Danghong; Ihara, Tokuo; Motoshima, Hiroyuki; Watanabe, Keiichi

    2005-03-01

    The psychrophilic alkaline serine protease Apa1 secreted by the Antarctic psychrotroph Pseudoalteromonas sp. strain AS-11 consists of a subtilisin-like region (293 residues) and an additional insert region (148 residues) that does not show a sequence homology to any proteins in the RCSB Protein Data Bank. Apa1 inhibited with phenylmethanesulfonyl fluoride has been crystallized and X-ray diffraction data have been collected to 1.78 A resolution. The crystals belong to space group C2, with unit-cell parameters a = 122.94, b = 138.48, c = 64.77 A, alpha = gamma = 90, beta = 97.5 degrees. A molecular-replacement solution has been found using the structure of the mesophilic counterpart subtilisin DY with 38% sequence identity to the catalytic domain of Apa1 as a search model. This is the first crystallographic study of a cold-adapted subtilisin-like protease.

  6. X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide

    SciTech Connect

    Feng, Youjun; Qi, Jianxun; Zhang, Huimin; Wang, Jinzi; Liu, Jinhua; Jiang, Fan; Gao, Feng

    2006-01-01

    X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide. Simian immunodeficiency virus (SIV) in the rhesus macaque is regarded as a classic animal model, playing a crucial role in HIV vaccine strategies and therapeutics by characterizing various cytotoxic T-lymphocyte (CTL) responses in macaque monkeys. However, the availability of well documented structural reports focusing on rhesus macaque major histocompatibility complex class I (MHC I) molecules remains extremely limited. Here, a complex of the rhesus macaque MHC I molecule (Mamu-A*02) with human β{sub 2}m and an immunodominant SIV-Gag nonapeptide, GESNLKSLY (GY9), has been crystallized. The crystal diffracts X-rays to 2.7 Å resolution and belongs to space group C2, with unit-cell parameters a = 124.11, b = 110.45, c = 100.06 Å, and contains two molecules in the asymmetric unit. The availability of the structure, which is being solved by molecular replacement, will provide new insights into rhesus macaque MHC I (Mamu-A*02) presenting pathogenic SIV peptides.

  7. Combined microspectrophotometric and crystallographic examination of chemically-reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus

    PubMed Central

    Liu, Bin; Chen, Ying; Doukov, Tzanko; Soltis, S. Michael; Stout, C. David; Fee, James A.

    2009-01-01

    Three paths are described to obtain crystals of reduced (II-E4Q/I-K258R) cytochrome ba3, and the structures of these are reported at ∼2.8 to 3.0 Å resolution. Microspectrophotometry of single crystals of Thermus ba3 oxidase at 100 K was used to show that crystals of the oxidized enzyme are reduced in an intense X-ray (beam line 7-1 at the Stanford Synchrotron Radiation Laboratory, U.S.A) being nearly complete in one minute. The previously reported structures of ba3 (PDB codes 1EHK and 1XME), having a crystallographically detectable water between the CuB and Fea3 metals of the dinuclear center, actually represent the X-ray radiation-reduced enzyme. Dithionite reduced crystals or crystals formed from dithionite reduced enzyme revealed the absence of the above mentioned water and an increase in the CuB - Fea3 distance of ∼0.3 A. The new structures are discussed in terms of enzyme function. An unexpected optical absorption envelope at ∼590 nm is also reported. This spectral feature is tentatively thought to arise from a 5-coordinate, low-spin, ferrous heme-a3 that is trapped in the frozen crystals. PMID:19140675

  8. Structure and conformation of (dibenzyldiaza-18-crown-6)-Nd(III) and Eu(III) thiocyanates: infrared spectroscopic and X-ray crystallographic studies

    NASA Astrophysics Data System (ADS)

    Saleh, Muhammad Idiris; Salhin, Abdussalam; Saad, Bahruddin; Fun, Hoong-Kun

    1999-01-01

    Dibenzyldiaza-18-crown-6 was utilised as a host to accommodate Nd(III) and Eu(III) metal ions together with thiocyanate as counter ion. The crystalline complexes formed were studied for their absorption in the infrared region and their crystalline structure by X-ray diffraction. The coordination of the metal ions to the counter ion and also to the donor atoms of the crown ether was clearly seen from the shift of the absorption band of the pure compound by up to nearly 15 cm -1. From these absorption it was found that each lanthanide ion was coordinated to six donor atoms (2 N and 4 O) from crown ether and three donor atoms, N from NCS -. This nine coordination number complex was found to have the stoichiometry of 1:1:3 (crown ether:lanthanide; NCS -). This ratio was further confirmed by X-ray crystallographic method. The lanthanide thiocyanate salts existed as an isolated (separate) entity in the center of the macrocyclic cavity. The three N atoms surrounded the Ln cation in a nearly planar trigonal arrangement with Ln ion being slightly out of plane. The trigonal plane was perpendicular to and bisects the plane of the macrocycle.

  9. Protein expression, crystallization and preliminary X-ray crystallographic analysis of chicken interferon-γ receptor α chain.

    PubMed

    Ping, Zhiguang; Shi, Yi; Sun, Yanling; Ma, Liping; Wang, Ming

    2012-01-01

    The activity of interferon-γ (IFN-γ) relies on signal transduction, which is triggered by combination with the receptors interferon-γ receptor α chain (IFNGR1) and β chain (IFNGR2). Native recombinant chicken IFNGR1 (chIFNGR1; residues 25-237) was overexpressed in Escherichia coli, purified by refolding and crystallized using the vapour-diffusion technique. The crystals belonged to space group P6(5)22, with unit-cell parameters a = b = 64.1, c = 216.3 Å, α = β = 90, γ = 120°. The Matthews coefficient and solvent content were calculated as 2.67 Å(3) Da(-1) and 53.97%, respectively. X-ray diffraction data for chIFNGR1 were collected to 2.0 Å resolution at a synchrotron source.

  10. Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional α-amylase/subtilisin inhibitor from Oryza sativa

    SciTech Connect

    Lin, Yi-Hung; Peng, Wen-Yan; Huang, Yen-Chieh; Guan, Hong-Hsiang; Hsieh, Ying-Cheng; Liu, Ming-Yih; Chang, Tschining; Chen, Chun-Jung

    2006-08-01

    The crystallization of rice α-amylase/subtilisin bifunctional inhibitor is reported. Rice bifunctional α-amylase/subtilisin inhibitor (RASI) can inhibit both α-amylase from larvae of the red flour beetle (Tribolium castaneum) and subtilisin from Bacillus subtilis. The synthesis of RASI is up-regulated during the late milky stage in developing seeds. The 8.9 kDa molecular-weight RASI from rice has been crystallized using the hanging-drop vapour-diffusion method. According to 1.81 Å resolution X-ray diffraction data from rice RASI crystals, the crystal belongs to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 79.99, b = 62.95, c = 66.70 Å. Preliminary analysis indicates two RASI molecules in an asymmetric unit with a solvent content of 44%.

  11. Crystallization and preliminary X-ray crystallographic analysis of the CARD domain of apoptosis repressor with CARD (ARC).

    PubMed

    Kim, Seong Hyun; Park, Hyun Ho

    2015-01-01

    Apoptosis repressor with caspase-recruiting domain (ARC) is an apoptosis repressor that inhibits both intrinsic and extrinsic apoptosis signalling. Human ARC contains an N-terminal caspase-recruiting domain (CARD domain) and a C-terminal proline- and glutamic acid-rich (P/E-rich) domain. The CARD domain in ARC is the domain that is directly involved in inhibition of the extrinsic pathway. In this study, the N-terminal CARD domain of ARC was overexpressed, purified and crystallized. X-ray diffraction data were collected to a resolution of 2.1 Å and the crystals were found to belong to space group P6(1) or P65, with unit-cell parameters a=98.28, b=98.28, c=51.86 Å, α=90, β=90, γ=120°.

  12. Preliminary X-ray crystallographic studies of the TIR domain of human Toll-like receptor 6.

    PubMed

    Jang, Tae-ho; Park, Hyun Ho

    2014-08-01

    Toll-like receptor (TLR) proteins have been identified and shown to play a role in the innate immune response. TLR6 associated with TLR2 can recognize diacylated lipoprotein. In this study, the human TLR6 TIR domain corresponding to amino acids 640-796 was overexpressed in Escherichia coli using engineered C-terminal His tags. The TLR6 TIR domain was then purified to homogeneity and crystallized at 20°C. Finally, X-ray diffraction data were collected to a resolution of 2.2 Å from a crystal belonging to space group C2, with unit-cell parameters a = 127.60, b = 44.20, c = 75.72 Å, β = 118.89°

  13. Cloning, expression, purification, crystallization and preliminary X-ray diffraction crystallographic study of human synaptotagmin 5 C2A domain.

    PubMed

    Qiu, Xiaoting; Huang, Kai; Liu, Yiwei; Zhang, Xiao; Gao, Yongxiang

    2011-11-01

    Synaptotagmin acts as the Ca(2+) sensor for neural and endocrine exocytosis. Synaptotagmin 5 has been demonstrated to play a key role in the acquisition of cathepsin D and the vesicular proton ATPase and in Ca(2+)-dependent insulin exocytosis. The C2 domains modulate the interaction of synaptotagmin with the phospholipid bilayer of the presynaptic terminus and effector proteins such as the SNARE complex. This study reports the cloning, expression in Escherichia coli, purification, crystallization and preliminary X-ray analysis of the C2A domain of human synaptotagmin 5 with an N-terminal His(6) tag. The crystals diffracted to 1.90 Å resolution and belonged to the hexagonal space group P6(5), with unit-cell parameters a = b = 93.97, c = 28.05 Å. A preliminary model of the protein structure has been built and refinement of the model is ongoing. © 2011 International Union of Crystallography. All rights reserved.

  14. Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional alpha-amylase/subtilisin inhibitor from Oryza sativa.

    PubMed

    Lin, Yi Hung; Peng, Wen Yan; Huang, Yen Chieh; Guan, Hong Hsiang; Hsieh, Ying Cheng; Liu, Ming Yih; Chang, Tschining; Chen, Chun Jung

    2006-08-01

    Rice bifunctional alpha-amylase/subtilisin inhibitor (RASI) can inhibit both alpha-amylase from larvae of the red flour beetle (Tribolium castaneum) and subtilisin from Bacillus subtilis. The synthesis of RASI is up-regulated during the late milky stage in developing seeds. The 8.9 kDa molecular-weight RASI from rice has been crystallized using the hanging-drop vapour-diffusion method. According to 1.81 angstroms resolution X-ray diffraction data from rice RASI crystals, the crystal belongs to space group P2(1)2(1)2, with unit-cell parameters a = 79.99, b = 62.95, c = 66.70 angstroms. Preliminary analysis indicates two RASI molecules in an asymmetric unit with a solvent content of 44%.

  15. Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional α-amylase/subtilisin inhibitor from Oryza sativa

    PubMed Central

    Lin, Yi-Hung; Peng, Wen-Yan; Huang, Yen-Chieh; Guan, Hong-Hsiang; Hsieh, Ying-Cheng; Liu, Ming-Yih; Chang, Tschining; Chen, Chun-Jung

    2006-01-01

    Rice bifunctional α-amylase/subtilisin inhibitor (RASI) can inhibit both α-­amylase from larvae of the red flour beetle (Tribolium castaneum) and subtilisin from Bacillus subtilis. The synthesis of RASI is up-regulated during the late milky stage in developing seeds. The 8.9 kDa molecular-weight RASI from rice has been crystallized using the hanging-drop vapour-diffusion method. According to 1.81 Å resolution X-ray diffraction data from rice RASI crystals, the crystal belongs to space group P21212, with unit-cell parameters a = 79.99, b = 62.95, c = 66.70 Å. Preliminary analysis indicates two RASI molecules in an asymmetric unit with a solvent content of 44%. PMID:16880545

  16. X-Ray Crystallographic Analysis, EPR Studies, and Computational Calculations of a Cu(II) Tetramic Acid Complex

    PubMed Central

    Matiadis, Dimitrios; Tsironis, Dimitrios; Stefanou, Valentina; Igglessi–Markopoulou, Olga; McKee, Vickie; Sanakis, Yiannis; Lazarou, Katerina N.

    2017-01-01

    In this work we present a structural and spectroscopic analysis of a copper(II) N-acetyl-5-arylidene tetramic acid by using both experimental and computational techniques. The crystal structure of the Cu(II) complex was determined by single crystal X-ray diffraction and shows that the copper ion lies on a centre of symmetry, with each ligand ion coordinated to two copper ions, forming a 2D sheet. Moreover, the EPR spectroscopic properties of the Cu(II) tetramic acid complex were also explored and discussed. Finally, a computational approach was performed in order to obtain a detailed and precise insight of product structures and properties. It is hoped that this study can enrich the field of functional supramolecular systems, giving place to the formation of coordination-driven self-assembly architectures. PMID:28316540

  17. X-ray crystallographic insights into post-synthetic metalation products in a metal-organic framework.

    PubMed

    Huxley, Michael T; Coghlan, Campbell J; Bloch, Witold M; Burgun, Alexandre; Doonan, Christian J; Sumby, Christopher J

    2017-01-13

    Post-synthetic modification of metal-organic frameworks (MOFs) facilitates a strategic transformation of potentially inert frameworks into functionalized materials, tailoring them for specific applications. In particular, the post-synthetic incorporation of transition-metal complexes within MOFs, a process known as 'metalation', is a particularly promising avenue towards functionalizing MOFs. Herein, we describe the post-synthetic metalation of a microporous MOF with various transition-metal nitrates. The parent framework, 1: , contains free-nitrogen donor chelation sites, which readily coordinate metal complexes in a single-crystal to single-crystal transformation which, remarkably, can be readily monitored by X-ray crystallography. The presence of an open void surrounding the chelation site in 1: prompted us to investigate the effect of the MOF pore environment on included metal complexes, particularly examining whether void space would induce changes in the coordination sphere of chelated complexes reminiscent of those found in the solution state. To test this hypothesis, we systematically metalated 1: with first-row transition-metal nitrates and elucidated the coordination environment of the respective transition-metal complexes using X-ray crystallography. Comparison of the coordination sphere parameters of coordinated transition-metal complexes in 1: against equivalent solid- and solution-state species suggests that the void space in 1: does not markedly influence the coordination sphere of chelated species but we show notably different post-synthetic metalation outcomes when different solvents are used.This article is part of the themed issue 'Coordination polymers and metal-organic frameworks: materials by design'.

  18. X-ray crystallographic studies on C-phycocyanins from cyanobacteria from different habitats: marine and freshwater

    SciTech Connect

    Satyanarayana, L.; Suresh, C. G.; Patel, Anamika; Mishra, Sandhya Ghosh, Pushpito Kumar

    2005-09-01

    The protein C-phycocyanin, involved in photosynthesis, has been purified from three cyanobacterial species: Spirulina, Phormidium and Lyngbya. These three proteins have been crystallized and characterized using X-ray crystallography. C-phycocyanins from three cyanobacterial cultures of freshwater and marine habitat, Spirulina, Phormidium and Lyngbya spp., were purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. Blue-coloured crystals in different crystal forms, monoclinic and hexagonal, were obtained for the three species. The crystals took 1–12 weeks to grow to full size using polyethylene glycols of different molecular weights as precipitants. The amino-acid sequences of these proteins show high similarity to other known C-phycocyanins from related organisms; however, the C-phycocyanins reported here showed different biochemical and biophysical properties, i.e. molecular weight, stability etc. The X-ray diffraction data were collected at resolutions of 3.0 Å for the monoclinic and 3.2 and 3.6 Å for the hexagonal forms. The unit-cell parameters corresponding to the monoclinic space group P2{sub 1} are a = 107.33, b = 115.64, c = 183.26 Å, β = 90.03° for Spirulina sp. C-phycocyanin and are similar for crystals of Phormidium and Lyngbya spp. C-phycocyanins. Crystals belonging to the hexagonal space group P6{sub 3}, with unit-cell parameters a = b = 154.97, c = 40.35 Å and a = b = 151.96, c = 39.06 Å, were also obtained for the C-phycocyanins from Spirulina and Lyngbya spp., respectively. The estimated solvent content is around 50% for the monoclinic crystals of all three species assuming the presence of two hexamers per asymmetric unit. The solvent content is 66.5 and 64.1% for the hexagonal crystals of C-phycocyanin from Spirulina and Lyngbya spp. assuming the presence of one αβ monomer per asymmetric unit.

  19. X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin.

    PubMed

    Larson, Steven B; Day, John S; McPherson, Alexander

    2010-04-13

    Further refinement of the model using maximum likelihood procedures and reevaluation of the native electron density map has shown that crystals of pig pancreatic alpha-amylase, whose structure we reported more than 15 years ago, in fact contain a substantial amount of carbohydrate. The carbohydrate fragments are the products of glycogen digestion carried out as an essential step of the protein's purification procedure. In particular, the substrate-binding cleft contains a limit dextrin of six glucose residues, one of which contains both alpha-(1,4) and alpha-(1,6) linkages to contiguous residues. The disaccharide in the original model, shared between two amylase molecules in the crystal lattice, but also occupying a portion of the substrate-binding cleft, is now seen to be a tetrasaccharide. There are, in addition, several other probable monosaccharide binding sites. Furthermore, we have further reviewed our X-ray diffraction analysis of alpha-amylase complexed with alpha-cyclodextrin. alpha-Amylase binds three cyclodextrin molecules. Glucose residues of two of the rings superimpose upon the limit dextrin and the tetrasaccharide. The limit dextrin superimposes in large part upon linear oligosaccharide inhibitors visualized by other investigators. By comprehensive integration of these complexes we have constructed a model for the binding of polysaccharides having the helical character known to be present in natural substrates such as starch and glycogen.

  20. X-ray crystallographic structure of a bacterial polysialyltransferase provides insight into the biosynthesis of capsular polysialic acid.

    PubMed

    Lizak, Christian; Worrall, Liam J; Baumann, Lars; Pfleiderer, Moritz M; Volkers, Gesa; Sun, Tianjun; Sim, Lyann; Wakarchuk, Warren; Withers, Stephen G; Strynadka, Natalie C J

    2017-07-19

    Polysialic acid (polySia) is a homopolymeric saccharide that is associated with some neuroinvasive pathogens and is found on selective cell types in their eukaryotic host. The presence of a polySia capsule on these bacterial pathogens helps with resistance to phagocytosis, cationic microbial peptides and bactericidal antibody production. The biosynthesis of bacterial polySia is catalysed by a single polysialyltransferase (PST) transferring sialic acid from a nucleotide-activated donor to a lipid-linked acceptor oligosaccharide. Here we present the X-ray structure of the bacterial PST from Mannheimia haemolytica serotype A2, thereby defining the architecture of this class of enzymes representing the GT38 family. The structure reveals a prominent electropositive groove between the two Rossmann-like domains forming the GT-B fold that is suitable for binding of polySia chain products. Complex structures of PST with a sugar donor analogue and an acceptor mimetic combined with kinetic studies of PST active site mutants provide insight into the principles of substrate binding and catalysis. Our results are the basis for a molecular understanding of polySia biosynthesis in bacteria and might assist the production of polysialylated therapeutic reagents and the development of novel antibiotics.

  1. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of d-lactate dehydrogenase from Lactobacillus jensenii

    PubMed Central

    Kim, Sangwoo; Kim, Yong Hwan; Kim, Kyung-Jin

    2014-01-01

    The thermostable d-lactate dehydrogenase from Lactobacillus jensenii (Lj d-LDH) is a key enzyme for the production of the d-form of lactic acid from pyruvate concomitant with the oxidation of NADH to NAD+. The polymers of lactic acid are used as biodegradable bioplastics. The Lj d-LDH protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 28%(w/v) polyethylene glycol 400, 100 mM Tris–HCl pH 9, 200 mM magnesium sulfate at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.1 Å. The crystal belonged to space group P3121, with unit-cell parameters a = b = 90.5, c = 157.8 Å. With two molecules per asymmetric unit, the crystal volume per unit protein weight (V M) is 2.58 Å3 Da−1, which corresponds to a solvent content of approximately 52.3%. The structure was solved by single-wavelength anomalous dispersion using a selenomethionine derivative. PMID:25084378

  2. Crystallization and preliminary X-ray crystallographic analysis of the Sulfolobus solfataricus nucleotide-exchange factor 1β

    SciTech Connect

    Ruggiero, Alessia; Masullo, Mariorosario; Arcari, Paolo; Raimo, Gennaro; Vitagliano, Luigi; Zagari, Adriana

    2005-11-01

    Nucleotide-exchange factor from S. solfataricus (SsEF-1β) has been successfully crystallized. X-ray diffraction data have been collected from the native enzyme and from the selenomethionine derivative of SsEF-1β to 1.97 and 1.83 Å resolution, respectively. The nucleotide-exchange factor isolated from the hyperthermophilic archaeon Sulfolobus solfataricus (SsEF-1β) consists of 90 residues and differs from eukaryal EF-1βs. The protein has been successfully crystallized using either microbatch-under-oil or vapour-diffusion methods. Crystals of native SsEF-1β diffract to 1.97 Å resolution and belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 106.46, b = 54.87, c = 44.03 Å. Diffraction data have also been collected from a selenomethionine derivative of SsEF-1β at 1.83 Å resolution. Model building using the phases derived from the MAD experiment is in progress.

  3. Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the human Rod–Zwilch–ZW10 (RZZ) complex

    SciTech Connect

    Altenfeld, Anika; Wohlgemuth, Sabine; Wehenkel, Annemarie; Musacchio, Andrea

    2015-03-20

    The 800 kDa complex of the human Rod, Zwilch and ZW10 proteins (the RZZ complex) was reconstituted in insect cells, purified, crystallized and subjected to preliminary X-ray diffraction analysis. The spindle-assembly checkpoint (SAC) monitors kinetochore–microtubule attachment during mitosis. In metazoans, the three-subunit Rod–Zwilch–ZW10 (RZZ) complex is a crucial SAC component that interacts with additional SAC-activating and SAC-silencing components, including the Mad1–Mad2 complex and cytoplasmic dynein. The RZZ complex contains two copies of each subunit and has a predicted molecular mass of ∼800 kDa. Given the low abundance of the RZZ complex in natural sources, its recombinant reconstitution was attempted by co-expression of its subunits in insect cells. The RZZ complex was purified to homogeneity and subjected to systematic crystallization attempts. Initial crystals containing the entire RZZ complex were obtained using the sitting-drop method and were subjected to optimization to improve the diffraction resolution limit. The crystals belonged to space group P3{sub 1} (No. 144) or P3{sub 2} (No. 145), with unit-cell parameters a = b = 215.45, c = 458.7 Å, α = β = 90.0, γ = 120.0°.

  4. X-ray Crystallographic Analyses of Pig Pancreatic α-Amylase with Limit Dextrin, Oligosaccharide and α-Cyclodextrin†‡

    PubMed Central

    Larson, Steven B.; Day, John S.; McPherson, Alexander

    2010-01-01

    Further refinement of the model using maximum likelihood procedures and re-evaluation of the native electron density map has shown that crystals of pig pancreatic α-amylase, whose structure we reported more than fifteen years ago, in fact contain a substantial amount of carbohydrate. The carbohydrate fragments are the products of glycogen digestion carried out as an essential step of the protein's purification procedure. In particular, the substrate-binding cleft contains a limit dextrin of six glucose residues, one of which contains both α-(1,4) and α-(1,6) linkages to contiguous residues. The disaccharide in the original model, shared between two amylase molecules in the crystal lattice, but also occupying a portion of the substrate binding cleft, is now seen to be a tetrasaccharide. There are, in addition, several other probable monosaccharide binding sites. To these results we have further reviewed our X-ray diffraction analysis of α-amylase complexed with α-cyclodextrin. α-Amylase binds three cyclodextrin molecules. Glucose residues of two of the rings superimpose upon the limit dextrin and the tetrasaccharide. The limit dextrin superimposes in large part upon linear oligosaccharide inhibitors visualized by other investigators. By comprehensive integration of these complexes we have constructed a model for the binding of polysaccharides having the helical character known to be present in natural substrates such as starch and glycogen. PMID:20222716

  5. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of SMU.961 protein from the caries pathogen Streptococcus mutans

    SciTech Connect

    Gao, Xiong-Zhuo; Li, Lan-Fen; Su, Xiao-Dong; Zhao, XiaoJun; Liang, Yu-He

    2007-10-01

    The SMU.961 protein from S. mutans was crystallized and preliminary characterization of the crystals, which diffracted to 2.9 Å resolution, shows them to belong to space group C2. The smu.961 gene encodes a putative protein of 183 residues in Streptococcus mutans, a major pathogen in human dental caries. The gene was cloned into expression vector pET28a and expressed in a substantial quantity in Escherichia coli strain BL21 (DE3) with a His tag at its N-terminus. The recombinant protein SMU.961 was purified to homogeneity in a two-step procedure consisting of Ni{sup 2+}-chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.9 Å resolution at beamline I911-3, MAX-II-lab, Sweden. The crystal belonged to space group C2, with unit-cell parameters a = 98.62, b = 73.73, c = 184.73 Å, β = 98.82°.

  6. Crystallization and preliminary X-ray crystallographic analysis of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

    SciTech Connect

    Ku, Min-Je; Lee, Won-Ho; Nam, Ki-hyun; Rhee, Kyeong-hee; Lee, Ki-Seog; Kim, Eunice EunKyung; Yu, Myung-Hee; Hwang, Kwang Yeon

    2005-04-01

    The tRNA-specific adenosine deaminase from the pathogenic bacteria S. pyogenes has been overexpressed and crystallized. The tRNA-specific adenosine deaminase from the pathogenic bacteria Streptococcus pyogenes (spTAD) has been overexpressed in Escherichia coli and crystallized in the presence of Zn{sup 2+} ion at 295 K using ammonium sulfate as a precipitant. Flash-cooled crystals of spTAD diffracted to 2.0 Å using 30%(v/v) glycerol as a cryoprotectant. X-ray diffraction data have been collected to 2.0 Å using synchrotron radiation. The crystal belongs to the tetragonal space group P4{sub 2}2{sub 1}2, with unit-cell parameters a = b = 81.042, c = 81.270 Å. The asymmetric unit contains one subunit of spTAD, with a corresponding crystal volume per protein weight (V{sub M}) of 3.3 Å{sup 3} Da{sup −1} and a solvent content of 62.7%.

  7. Crystallization and preliminary X-ray crystallographic studies of dehydroascorbate reductase (DHAR) from Oryza sativa L. japonica.

    PubMed

    Do, Hackwon; Kim, Il-Sup; Kim, Young-Saeng; Shin, Sun-Young; Kim, Jin-Ju; Mok, Ji-Eun; Park, Seong-Im; Wi, Ah Ram; Park, Hyun; Kim, Han-Woo; Yoon, Ho-Sung; Lee, Jun Hyuck

    2014-06-01

    Dehydroascorbate reductase from Oryza sativa L. japonica (OsDHAR), a key enzyme in the regeneration of vitamin C, maintains reduced pools of ascorbic acid to detoxify reactive oxygen species. In previous studies, the overexpression of OsDHAR in transgenic rice increased grain yield and biomass as well as the amount of ascorbate, suggesting that ascorbate levels are directly associated with crop production in rice. Hence, it has been speculated that the increased level of antioxidants generated by OsDHAR protects rice from oxidative damage and increases the yield of rice grains. However, the crystal structure and detailed mechanisms of this important enzyme need to be further elucidated. In this study, recombinant OsDHAR protein was purified and crystallized using the sitting-drop vapour-diffusion method at pH 8.0 and 298 K. Plate-shaped crystals were obtained using 0.15 M potassium bromide, 30%(w/v) PEG MME 2000 as a precipitant, and the crystals diffracted to a resolution of 1.9 Å on beamline 5C at the Pohang Accelerator Laboratory. The X-ray diffraction data indicated that the crystal contained one OsDHAR molecule in the asymmetric unit and belonged to space group P2₁ with unit-cell parameters a=47.03, b=48.38, c=51.83 Å, β=107.41°.

  8. Purification, crystallization and preliminary X-ray crystallographic analysis of 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1

    PubMed Central

    Rohman, Ali; van Oosterwijk, Niels; Dijkstra, Bauke W.

    2012-01-01

    3-Ketosteroid Δ1-dehydrogenase plays a crucial role in the early steps of steroid degradation by introducing a double bond between the C1 and C2 atoms of the A-ring of its 3-ketosteroid substrates. The 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1, a 56 kDa flavoprotein, was crystallized using the sitting-drop vapour-diffusion method at room temperature. The crystals grew in various buffers over a wide pH range (from pH 5.5 to 10.5), but the best crystallization condition consisted of 2%(v/v) PEG 400, 0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate. A native crystal diffracted X-rays to 2.0 Å resolution. It belonged to the primitive orthorhombic space group P212121, with unit-cell parameters a = 107.4, b = 131.6, c = 363.2 Å, and contained eight molecules in the asymmetric unit. The initial structure of the enzyme was solved using multi-wavelength anomalous dispersion (MAD) data collected from a Pt-derivatized crystal. PMID:22691786

  9. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of D-lactate dehydrogenase from Lactobacillus jensenii.

    PubMed

    Kim, Sangwoo; Kim, Yong Hwan; Kim, Kyung-Jin

    2014-08-01

    The thermostable D-lactate dehydrogenase from Lactobacillus jensenii (LjD-LDH) is a key enzyme for the production of the D-form of lactic acid from pyruvate concomitant with the oxidation of NADH to NAD(+). The polymers of lactic acid are used as biodegradable bioplastics. The LjD-LDH protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 28%(w/v) polyethylene glycol 400, 100 mM Tris-HCl pH 9, 200 mM magnesium sulfate at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.1 Å. The crystal belonged to space group P3121, with unit-cell parameters a = b = 90.5, c = 157.8 Å. With two molecules per asymmetric unit, the crystal volume per unit protein weight (VM) is 2.58 Å(3) Da(-1), which corresponds to a solvent content of approximately 52.3%. The structure was solved by single-wavelength anomalous dispersion using a selenomethionine derivative.

  10. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of β-ketothiolase B from Ralstonia eutropha H16.

    PubMed

    Kim, Eun-Jung; Son, Hyeoncheol Francis; Chang, Jeong Ho; Kim, Kyung-Jin

    2014-03-01

    Polyhydroxyalkanoates are linear polyesters that are produced by bacterial fermentation and are used as biodegradable bioplastics. β-Ketothiolase B (BktB) from Ralstonia eutropha (ReBktB) is a key enzyme for the production of various types of copolymers by catalyzing the condensation reactions of acetyl-CoA with propionyl-CoA and butyryl-CoA. The ReBktB protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 25% polyethylene glycol 3350, 0.1 M bis-tris pH 6.5, 0.2 M lithium sulfate at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.3 Å on a synchrotron beamline. The crystal belonged to space group C2221, with unit-cell parameters a = 106.95, b = 107.24, c = 144.14 Å. With two molecules per asymmetric unit, the crystal volume per unit protein weight (VM) is 2.54 Å(3) Da(-1), which corresponds to a solvent content of approximately 51.5%. The structure was solved by the molecular-replacement method and refinement of the structure is in progress.

  11. Crystallization and preliminary X-ray crystallographic analysis of a highly specific serpin from the beetle Tenebrio molitor

    PubMed Central

    Park, Sun Hee; Piao, Shunfu; Kwon, Hyun-Mi; Kim, Eun-Hye; Lee, Bok Luel; Ha, Nam-Chul

    2010-01-01

    The Toll signalling pathway, which is crucial for innate immunity, is transduced in insect haemolymph via a proteolytic cascade consisting of three serine proteases. The proteolytic cascade is downregulated by a specific serine protease inhibitor (serpin). Recently, the serpin SPN48 was found to show an unusual specific reactivity towards the terminal serine protease, Spätzle-processing enzyme, in the beetle Tenebrio molitor. In this study, the mature form of SPN48 was overexpressed in Escherichia coli and purified. The purified SPN48 protein was crystallized using 14% polyethylene glycol 8000 and 0.1 M 2-(N-morpho­lino)ethanesulfonic acid pH 6.0 as the precipitant. The crystals diffracted X-rays to 2.1 Å resolution and were suitable for structure determination. The crystals belonged to space group P21. The crystal structure will provide information regarding how SPN48 achieves its unusual specificity for its target protease. PMID:20124722

  12. Crystallization and preliminary X-ray crystallographic analysis of l-arabinose isomerase from thermophilic Geobacillus kaustophilus

    PubMed Central

    Cao, Thinh-Phat; Choi, Jin Myung; Lee, Sang-Jae; Lee, Yong-Jik; Lee, Sung-Keun; Jun, Youngsoo; Lee, Dong-Woo; Lee, Sung Haeng

    2014-01-01

    l-Arabinose isomerase (AI), which catalyzes the isomerization of l-arabinose to l-ribulose, can also convert d-galactose to d-tagatose, a natural sugar replacer, which is of commercial interest in the food and healthcare industries. Intriguingly, mesophilic and thermophilic AIs showed different substrate preferences and metal requirements in catalysis and different thermostabilities. However, the catalytic mechanism of thermophilic AIs still remains unclear. Therefore, thermophilic Geobacillus kaustophilus AI (GKAI) was overexpressed, purified and crystallized, and a preliminary X-ray diffraction data set was obtained. Diffraction data were collected from a GKAI crystal to 2.70 Å resolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 224.12, b = 152.95, c = 91.28 Å, β = 103.61°. The asymmetric unit contained six molecules, with a calculated Matthews coefficient of 2.25 Å3 Da−1 and a solvent content of 45.39%. The three-dimensional structure determination of GKAI is currently in progress by molecular replacement and model building. PMID:24419630

  13. Crystallization and preliminary X-ray crystallographic studies of Drep-3, a DFF-related protein from Drosophila melanogaster

    SciTech Connect

    Park, Hyun Ho; Tookes, Hansel Emory; Wu, Hao

    2006-06-01

    The D. melanogaster Drep-3 protein has been crystallized. Crystals were obtained at 293 K that diffracted to 2.8 Å resolution and belonged to space group P2{sub 1}2{sub 1}2{sub 1}. During apoptosis, DNA fragmentation is mainly mediated by the caspase-activated DFF40 nuclease. DFF40 exists as a heterodimeric complex with its inhibitor DFF45. Upon apoptosis induction, DFF45 is cleaved by caspases to allow DFF40 activation. Drep-3 is a recently identified regulator of the DFF40 system in Drosophila melanogaster. Here, Drep-3 was expressed with a C-terminal His tag in Escherichia coli and the protein was purified to homogeneity. Multi-angle light-scattering analysis showed that Drep-3 is a homotetramer in solution. Native and selenomethionine-substituted Drep-3 proteins were crystallized at 293 K and X-ray diffraction data were collected to 2.8 and 3.0 Å resolution, respectively. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 56.9, b = 125.4, c = 168.7 Å. The asymmetric unit is estimated to contain one homotetramer.

  14. Fluorescent sulfonamide carbonic anhydrase inhibitors incorporating 1,2,3-triazole moieties: Kinetic and X-ray crystallographic studies.

    PubMed

    Carta, Fabrizio; Ferraroni, Marta; Scozzafava, Andrea; Supuran, Claudiu T

    2016-01-15

    Fluorescent sulfonamide carbonic anhydrase (CA, EC 4.2.1.1) inhibitors (CAIs) were essential for demonstrating the role played by the tumor-associated isoform CA IX in acidification of tumors, cancer progression towards metastasis and for the development of imaging and therapeutic strategies for the management of hypoxic tumors which overexpress CA IX. However, the presently available such compounds are poorly water soluble which limits their use. Here we report new fluorescent sulfonamides 7, 8 and 10 with increased water solubility. The new derivatives showed poor hCA I inhibitory properties, but were effective inhibitors against the hCA II (KIs of 366-127 nM), CA IX (KIs of 8.1-36.9 nM), CA XII (KIs of 4.1-20.5 nM) and CA XIV (KIs of 12.8-53.6 nM). A high resolution X-ray crystal structure of one of these compounds bound to hCA II revealed the factors associated with the good inhibitory properties. Furthermore, this compound showed a three-fold increase of water solubility compared to a similar derivative devoid of the triazole moiety, making it an interesting candidate for ex vivo/in vivo studies.

  15. Crystallization and preliminary X-ray crystallographic analysis of BxlE, a xylobiose transporter from Streptomyces thermoviolaceus OPC-520

    SciTech Connect

    Seike, Kiho; Sato, Junji; Tomoo, Koji Ishida, Toshimasa; Yamano, Akihito; Ikenishi, Sadao; Miyamoto, Katsushiro; Tsujibo, Hiroshi

    2007-07-01

    To clarify the structural basis of sugar binding by BxlE at the atomic level, recombinant BxlE was crystallized using the hanging-drop vapour-diffusion method at 290 K. Together with the integral membrane proteins BxlF and BxlG, BxlE isolated from Streptomyces thermoviolaceus OPC-520 forms an ATP-binding cassette (ABC) transport system that mediates the uptake of xylan. To clarify the structural basis of sugar binding by BxlE at the atomic level, recombinant BxlE was crystallized using the hanging-drop vapour-diffusion method at 290 K. The crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 44.63, b = 63.27, c = 66.40 Å, β = 103.05°, and contained one 48 kDa molecule per asymmetric unit (V{sub M} = 1.96 Å{sup 3} Da{sup −1}). Diffraction data collected to a resolution of 1.65 Å using a rotating-anode X-ray source gave a data set with an overall R{sub merge} of 2.6% and a completeness of 91.3%. A data set from a platinum derivative is being used for phasing by the SAD method.

  16. Expression, purification, crystallization and preliminary X-ray crystallographic studies of a novel acetylcitrulline deacetylase from Xanthomonas campestris

    SciTech Connect

    Shi, Dashuang Yu, Xiaolin; Roth, Lauren; Morizono, Hiroki; Hathout, Yetrib; Allewell, Norma M.; Tuchman, Mendel

    2005-07-01

    The expression, purification and preliminary X-ray diffraction studies of a novel N-acetyl-l-citrulline deacetylase from X. campestris are reported. A novel N-acetyl-l-citrulline deacetylase that is able to catalyze the hydrolysis of N-acetyl-l-citrulline to acetate and citrulline was identified from Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the monoclinic space group C2 and diffract to 1.75 Å resolution, with unit-cell parameters a = 94.13, b = 95.23, c = 43.61 Å, β = 93.76°. Since attempts to use homologous structural models to solve the structure via molecular replacement were unsuccessful, the selenomethionine-substituted protein was prepared using an overnight auto-induction overexpression system. Selenomethionine incorporation into the protein was verified by MALDI–TOF/TOF mass-spectroscopic analysis after trypsin digestion. The crystals of the selenomethionine-substituted protein were prepared using crystallization conditions similar to those for the native protein. Multiple anomalous dispersion (MAD) data were collected at Brookhaven National Laboratory. Structure determination is under way using the MAD phasing method.

  17. Preparation, crystallization and preliminary X-ray crystallographic studies of diadenosine tetraphosphate hydrolase from Shigella flexneri 2a

    SciTech Connect

    Hu, Wenxin; Wang, Qihai; Bi, Ruchang

    2005-12-01

    The 31.3 kDa Ap{sub 4}A hydrolase from Shigella flexneri 2a has been cloned, expressed and purified using an Escherichia coli expression system. Crystals of Ap{sub 4}A hydrolase have been obtained by the hanging-drop technique at 291 K using PEG 550 MME as precipitant. Diadenosine tetraphosphate (Ap{sub 4}A) hydrolase (EC 3.6.1.41) hydrolyzes Ap{sub 4}A symmetrically in prokaryotes. It plays a potential role in organisms by regulating the concentration of Ap{sub 4}A in vivo. To date, no three-dimensional structures of proteins with significant sequence homology to this protein have been determined. The 31.3 kDa Ap{sub 4}A hydrolase from Shigella flexneri 2a has been cloned, expressed and purified using an Escherichia coli expression system. Crystals of Ap{sub 4}A hydrolase have been obtained by the hanging-drop technique at 291 K using PEG 550 MME as precipitant. Ap{sub 4}A hydrolase crystals diffract X-rays to 3.26 Å and belong to space group P2{sub 1}, with unit-cell parameters a = 118.9, b = 54.6, c = 128.5 Å, β = 95.7°.

  18. Crystallization and preliminary X-ray crystallographic studies of Pz peptidase A from Geobacillus collagenovorans MO-1.

    PubMed

    Kawasaki, Akio; Nakano, Hiroaki; Tsujimoto, Yoshiyuki; Matsui, Hiroshi; Shimizu, Tetsuya; Nakatsu, Toru; Kato, Hiroaki; Watanabe, Kunihiko

    2007-02-01

    Pz peptidase A is an intracellular M3 metallopeptidase found in the thermophile Geobacillus collagenovorans MO-1 that recognizes collagen-specific tripeptide units (Gly-Pro-Xaa). Pz peptidase A shares common reactions with mammalian thimet oligopeptidase (TOP) and neurolysin, but has extremely low primary sequence identity to these enzymes. In this work, Pz peptidase A was cocrystallized with a phosphine peptide inhibitor (PPI) that selectively inhibits TOP and neurolysin. The crystals belong to space group P2(1), with unit-cell parameters a = 56.38, b = 194.15, c = 59.93 A, beta = 106.22 degrees . This is the first crystallographic study of an M3 family peptidase-PPI complex.

  19. Crystallization and preliminary X-ray crystallographic studies of glutaredoxin 2 from Saccharomyces cerevisiae in different oxidation states

    SciTech Connect

    Discola, Karen Fulan; Oliveira, Marcos Antonio de; Monteiro Silva, Gustavo; Barcena, José Antonio; Porras, Pablo; Padilla, Alicia; Netto, Luis Eduardo Soares; Guimarães, Beatriz Gomes

    2005-04-01

    Glutaredoxin 2 (Grx2) from S. cerevisiae was expressed, purified and crystallized using the hanging-drop vapour-diffusion method. Crystals were obtained from protein treated with t-butyl hydroperoxide and from a sample not submitted to pre-treatment. Both crystals belong to the tetragonal space group P4{sub 1}2{sub 1}2, with very similar unit-cell parameters, and diffraction data were collected to 2.05 and 2.15 Å resolution, respectively. Glutaredoxins are small (9–12 kDa) heat-stable proteins that are highly conserved throughout evolution; the glutaredoxin active site (Cys-Pro-Tyr-Cys) is conserved in most species. Five glutaredoxin genes have been identified in Saccharomyces cerevisiae; however, Grx2 is responsible for the majority of oxidoreductase activity in the cell, suggesting that its primary function may be the detoxification of mixed disulfides generated by reactive oxygen species (ROS). Recombinant Grx2 was expressed in Escherichia coli as a 6×His-tagged fusion protein and purified by nickel-affinity chromatography. Prior to crystallization trials, the enzyme was submitted to various treatments with reducing agents and peroxides. Crystals suitable for X-ray diffraction experiments were obtained from untreated protein and protein oxidized with t-butyl hydroperoxide (10 mM). Complete data sets were collected to resolutions 2.15 and 2.05 Å for untreated and oxidized Grx2, respectively, using a synchrotron-radiation source. The crystals belong to space group P4{sub 1}2{sub 1}2, with similar unit-cell parameters.

  20. Crystallization and preliminary X-ray crystallographic analysis of biodegradative threonine deaminase (TdcB) from Salmonella typhimurium

    SciTech Connect

    Simanshu, Dhirendra K.; Chittori, Sagar; Savithri, H. S.; Murthy, M. R. N.

    2006-03-01

    S. typhimurium biodegradative threonine deaminase (TdcB), a member of the β-family of PLP-dependent enzymes, has been overexpressed, purified and crystallized in three different crystal forms using the hanging-drop vapour-diffusion method. Biodegradative threonine deaminase (TdcB) catalyzes the deamination of l-threonine to α-ketobutyrate, the first reaction in the anaerobic breakdown of l-threonine to propionate. Unlike the biosynthetic threonine deaminase, TdcB is insensitive to l-isoleucine and is activated by AMP. Here, the cloning of TdcB (molecular weight 36 kDa) from Salmonella typhimurium with an N-terminal hexahistidine affinity tag and its overexpression in Escherichia coli is reported. TdcB was purified to homogeneity using Ni–NTA affinity column chromatography and crystallized using the hanging-drop vapour-diffusion technique in three different crystal forms. Crystal forms I (unit-cell parameters a = 46.32, b = 55.30, c = 67.24 Å, α = 103.09, β = 94.70, γ = 112.94°) and II (a = 56.68, b = 76.83, c = 78.50 Å, α = 66.12, β = 89.16, γ = 77.08°) belong to space group P1 and contain two and four molecules of TdcB, respectively, in the asymmetric unit. Poorly diffracting form III crystals were obtained in space group C2 and based on the unit-cell volume are most likely to contain one molecule per asymmetric unit. Two complete data sets of resolutions 2.2 Å (crystal form I) and 1.7 Å (crystal form II) were collected at 100 K using an in-house X-ray source.

  1. An EXAFS Spectroscopic, Large-Angle X-Ray Scattering, And Crystallographic Study of Hexahydrated, Dimethyl Sulfoxide And Pyridine 1-Oxide Hexasolvated Mercury(II) Ions

    SciTech Connect

    Persson, I.; Eriksson, L.; Lindqvist-Reis, P.; Persson, P.; Sandstrom, M.

    2009-05-21

    The structure of the solvated mercury(II) ion in water and dimethyl sulfoxide has been studied by means of large-angle X-ray scattering (LAXS) and extended X-ray absorption fine structure (EXAFS) techniques. The distribution of the Hg-O distances is unusually wide and asymmetric in both solvents. In aqueous solution, hexahydrated [Hg(OH{sub 2}){sub 6}]{sup 2+} ions in a distorted octahedral configuration, with the centroid of the HgO distance at 2.38(1) {angstrom}, are surrounded by a diffuse second hydration sphere with HgOII distances of 4.20(2) {angstrom}. In dimethyl sulfoxide, the six HgO and HgS distances of the hexasolvated [Hg{l_brace}OS(CH{sub 3}){sub 2}{r_brace}{sub 6}]{sup 2+} complex are centered around 2.38(1) and 3.45(2) {angstrom}, respectively. The crystal structure of hexakis(pyridine 1-oxide)mercury(II) perchlorate has been redetermined. The space group R implies six equal HgO distances of 2.3416(7) {angstrom} for the [Hg(ONC{sub 5}H{sub 5}){sub 6}]{sup 2+} complex at 100 K. However, EXAFS studies of this compound, and of the solids hexaaquamercury(II) perchlorate and hexakis(dimethyl sulfoxide)mercury(II) trifluoromethanesulfonate, also with six equidistant HgO bonds according to crystallographic results, reveal in all cases strongly asymmetric HgO distance distributions. Vibronic coupling of valence states in a so-called pseudo-Jahn-Teller effect probably induces the distorted configurations.

  2. Characterization of Stress Relaxation, Dislocations and Crystallographic Tilt Via X-ray Microdiffraction in GaN (0001) Layers Grown by Maskless Pendeo-Epitaxy

    SciTech Connect

    Barabash, R.I.; Ice, G.E.; Liu, W.; Einfeldt, S.; Hommel, D.; Roskowski, A.M.; Davis, R.F.

    2010-06-25

    Intrinsic stresses due to lattice mismatch and high densities of threading dislocations and extrinsic stresses resulting from the mismatch in the coefficients of thermal expansion are present in almost all III-Nitride heterostructures. Stress relaxation in the GaN layers occurs in conventional and in pendeo-epitaxial films via the formation of additional misfit dislocations, domain boundaries, elastic strain and wing tilt. Polychromatic X-ray microdiffraction, high resolution monochromatic X-ray diffraction and finite element simulations have been used to determine the distribution of strain, dislocations, sub-boundaries and crystallographic wing tilt in uncoalesced and coalesced GaN layers grown by maskless pendeo-epitaxy. An important parameter was the width-to-height ratio of the etched columns of GaN from which the lateral growth of the wings occurred. The strain and tilt across the stripes increased with the width-to-height ratio. Tilt boundaries formed in the uncoalesced GaN layers at the column/wing interfaces for samples with a large ratio. Sharper tilt boundaries were observed at the interfaces formed by the coalescence of two laterally growing wings. The wings tilted upward during cooling to room temperature for both the uncoalesced and the coalesced GaN layers. It was determined that finite element simulations that account for extrinsic stress relaxation can explain the experimental results for uncoalesced GaN layers. Relaxation of both extrinsic and intrinsic stress components in the coalesced GaN layers contribute to the observed wing tilt and the formation of sub-boundaries.

  3. Characterization of Stress Relaxation, Dislocations and Crystallographic Tilt Via X-ray Microdiffraction in GaN (0001) Layers Grown by Maskless Pendeo-Epitaxy

    SciTech Connect

    Barabash, Rozaliya; Ice, Gene E; Liu, Wenjun; Einfeldt, S.; Hommel, D.; Roskowski, A. M.; Davis, R. F.

    2005-01-01

    Intrinsic stresses due to lattice mismatch and high densities of threading dislocations and extrinsic stresses resulting from the mismatch in the coefficients of thermal expansion are present in almost all III-Nitride heterostructures. Stress relaxation in the GaN layers occurs in conventional and in pendeo-epitaxial films via the formation of additional misfit dislocations, domain boundaries, elastic strain and wing tilt. Polychromatic X-ray microdiffraction, high resolution monochromatic X-ray diffraction and finite element simulations have been used to determine the distribution of strain, dislocations, sub-boundaries and crystallographic wing tilt in uncoalesced and coalesced GaN layers grown by maskless pendeo-epitaxy. An important parameter was the width-to-height ratio of the etched columns of GaN from which the lateral growth of the wings occurred. The strain and tilt across the stripes increased with the width-to-height ratio. Tilt boundaries formed in the uncoalesced GaN layers at the column/wing interfaces for samples with a large ratio. Sharper tilt boundaries were observed at the interfaces formed by the coalescence of two laterally growing wings. The wings tilted upward during cooling to room temperature for both the uncoalesced and the coalesced GaN layers. It was determined that finite element simulations that account for extrinsic stress relaxation can explain the experimental results for uncoalesced GaN layers. Relaxation of both extrinsic and intrinsic stress components in the coalesced GaN layers contribute to the observed wing tilt and the formation of sub-boundaries.

  4. An EXAFS spectroscopic, large-angle X-ray scattering, and crystallographic study of hexahydrated, dimethyl sulfoxide and pyridine 1-oxide hexasolvated mercury(II) ions.

    PubMed

    Persson, Ingmar; Eriksson, Lars; Lindqvist-Reis, Patric; Persson, Per; Sandström, Magnus

    2008-01-01

    The structure of the solvated mercury(II) ion in water and dimethyl sulfoxide has been studied by means of large-angle X-ray scattering (LAXS) and extended X-ray absorption fine structure (EXAFS) techniques. The distribution of the Hg-O distances is unusually wide and asymmetric in both solvents. In aqueous solution, hexahydrated [Hg(OH(2))(6)](2+) ions in a distorted octahedral configuration, with the centroid of the Hg-O distance at 2.38(1) A, are surrounded by a diffuse second hydration sphere with HgO(II) distances of 4.20(2) A. In dimethyl sulfoxide, the six Hg-O and HgS distances of the hexasolvated [Hg{OS(CH(3))(2)}(6)](2+) complex are centered around 2.38(1) and 3.45(2) A, respectively. The crystal structure of hexakis(pyridine 1-oxide)mercury(II) perchlorate has been redetermined. The space group R(-)3 implies six equal Hg-O distances of 2.3416(7) A for the [Hg(ONC(5)H(5))(6)](2+) complex at 100 K. However, EXAFS studies of this compound, and of the solids hexaaquamercury(II) perchlorate and hexakis(dimethyl sulfoxide)mercury(II) trifluoromethanesulfonate, also with six equidistant Hg-O bonds according to crystallographic results, reveal in all cases strongly asymmetric Hg-O distance distributions. Vibronic coupling of valence states in a so-called pseudo-Jahn-Teller effect probably induces the distorted configurations.

  5. Manganese binding properties of human calprotectin under conditions of high and low calcium: X-ray crystallographic and advanced electron paramagnetic resonance spectroscopic analysis.

    PubMed

    Gagnon, Derek M; Brophy, Megan Brunjes; Bowman, Sarah E J; Stich, Troy A; Drennan, Catherine L; Britt, R David; Nolan, Elizabeth M

    2015-03-04

    The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation. Herein, we investigate the remarkable Mn(II) coordination chemistry of human CP using X-ray crystallography as well as continuous-wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies. An X-ray crystallographic structure of Mn(II)-CP containing one Mn(II), two Ca(II), and two Na(I) ions per CP heterodimer is reported. The CW EPR spectrum of Ca(II)- and Mn(II)-bound CP prepared with a 10:0.9:1 Ca(II):Mn(II):CP ratio is characterized by an unusually low zero-field splitting of 485 MHz (E/D = 0.30) for the S = 5/2 Mn(II) ion, consistent with the high symmetry of the His6 binding site observed crystallographically. Results from electron spin-echo envelope modulation and electron-nuclear double resonance experiments reveal that the six Mn(II)-coordinating histidine residues of Ca(II)- and Mn(II)-bound CP are spectroscopically equivalent. The observed (15)N (I = 1/2) hyperfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating ε-nitrogen of the imidazole ring of each histidine ligand (A = [3.45, 3.71, 5.91] MHz) and the distal δ-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the binding affinity of CP for Mn(II) drops by two to three orders of magnitude and coincides with Mn(II) binding at the His6 site as well as other sites. This study demonstrates the role of Ca(II) in enabling high-affinity and specific binding of Mn(II) to the His6 site of human calprotectin.

  6. Manganese Binding Properties of Human Calprotectin under Conditions of High and Low Calcium: X-ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis

    SciTech Connect

    Gagnon, Derek M.; Brophy, Megan Brunjes; Bowman, Sarah E. J.; Stich, Troy A.; Drennan, Catherine L.; Britt, R. David; Nolan, Elizabeth M.

    2015-01-18

    The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation. Here in this paper, we investigate the remarkable Mn(II) coordination chemistry of human CP using X-ray crystallography as well as continuous-wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies. An X-ray crystallographic structure of Mn(II)-CP containing one Mn(II), two Ca(II), and two Na(I) ions per CP heterodimer is reported. The CW EPR spectrum of Ca(II)- and Mn(II)-bound CP prepared with a 10:0.9:1 Ca(II):Mn(II):CP ratio is characterized by an unusually low zero-field splitting of 485 MHz (E/D = 0.30) for the S = 5/2 Mn(II) ion, consistent with the high symmetry of the His6 binding site observed crystallographically. Results from electron spin–echo envelope modulation and electron–nuclear double resonance experiments reveal that the six Mn(II)-coordinating histidine residues of Ca(II)- and Mn(II)-bound CP are spectroscopically equivalent. The observed 15N (I = 1/2) hyperfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating ε-nitrogen of the imidazole ring of each histidine ligand (A = [3.45, 3.71, 5.91] MHz) and the distal δ-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the binding affinity of CP for Mn(II) drops by two to three orders of magnitude and coincides with Mn(II) binding at the His6 site as well as other sites. This study demonstrates the role of Ca(II) in enabling high-affinity and specific binding of Mn(II) to the His6 site of human calprotectin.

  7. Manganese Binding Properties of Human Calprotectin under Conditions of High and Low Calcium: X-ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis

    DOE PAGES

    Gagnon, Derek M.; Brophy, Megan Brunjes; Bowman, Sarah E. J.; ...

    2015-01-18

    The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation. Here in this paper, we investigate the remarkable Mn(II) coordination chemistry of human CP using X-ray crystallography as well as continuous-wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies. An X-ray crystallographic structure of Mn(II)-CP containing one Mn(II), two Ca(II), and two Na(I) ions per CP heterodimermore » is reported. The CW EPR spectrum of Ca(II)- and Mn(II)-bound CP prepared with a 10:0.9:1 Ca(II):Mn(II):CP ratio is characterized by an unusually low zero-field splitting of 485 MHz (E/D = 0.30) for the S = 5/2 Mn(II) ion, consistent with the high symmetry of the His6 binding site observed crystallographically. Results from electron spin–echo envelope modulation and electron–nuclear double resonance experiments reveal that the six Mn(II)-coordinating histidine residues of Ca(II)- and Mn(II)-bound CP are spectroscopically equivalent. The observed 15N (I = 1/2) hyperfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating ε-nitrogen of the imidazole ring of each histidine ligand (A = [3.45, 3.71, 5.91] MHz) and the distal δ-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the binding affinity of CP for Mn(II) drops by two to three orders of magnitude and coincides with Mn(II) binding at the His6 site as well as other sites. This study demonstrates the role of Ca(II) in enabling high-affinity and specific binding of Mn(II) to the His6 site of human calprotectin.« less

  8. Manganese Binding Properties of Human Calprotectin Under Conditions of High and Low Calcium: X-ray Crystallographic and Advanced EPR Spectroscopic Analysis

    PubMed Central

    Gagnon, Derek M.; Brophy, Megan Brunjes; Bowman, Sarah E. J.; Stich, Troy A.; Drennan, Catherine L.; Britt, R. David; Nolan, Elizabeth M.

    2015-01-01

    The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation. Herein, we investigate the remarkable Mn(II) coordination chemistry of human CP using X-ray crystallography as well as continuous wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies. An X-ray crystallographic structure of Mn(II)-CP containing one Mn(II), two Ca(II), and two Na(I) ions per CP heterodimer is reported. The CW EPR spectrum of Ca(II)- and Mn(II)-bound CP prepared with a 10:0.9:1 Ca(II):Mn(II):CP ratio is characterized by an unusually low zero-field splitting of 485 MHz (E/D = 0.30) for the S = 5/2 Mn(II) ion, consistent with the high symmetry of the His6 binding site observed crystallographically. Results from electron spin-echo envelope modulation and electron nuclear double resonance experiments reveal that the six Mn(II)-coordinating histidine residues of Ca(II)- and Mn(II)-bound CP are spectroscopically equivalent. The observed 15N (I = 1/2) hyperfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating ε-nitrogen of the imidazole ring of each histidine ligand (A = [3.45, 3.71, 5.91] MHz) and the distal δ-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the binding affinity of CP for Mn(II) drops by ca. two orders of magnitude and coincides with Mn(II) binding at the His6 site as well as other sites. This study demonstrates the role of Ca(II) in enabling high-affinity and specific binding of Mn(II) to the His6 site of human calprotectin. PMID:25597447

  9. X-ray Crystallographic Structure of Oligomers Formed by a Toxic β-Hairpin Derived from α-Synuclein: Trimers and Higher-Order Oligomers.

    PubMed

    Salveson, Patrick J; Spencer, Ryan K; Nowick, James S

    2016-04-06

    Oligomeric assemblies of the protein α-synuclein are thought to cause neurodegeneration in Parkinson's disease and related synucleinopathies. Characterization of α-synuclein oligomers at high resolution is an outstanding challenge in the field of structural biology. The absence of high-resolution structures of oligomers formed by α-synuclein impedes understanding the synucleinopathies at the molecular level. This paper reports the X-ray crystallographic structure of oligomers formed by a peptide derived from residues 36-55 of α-synuclein. The peptide 1a adopts a β-hairpin structure, which assembles in a hierarchical fashion. Three β-hairpins assemble to form a triangular trimer. Three copies of the triangular trimer assemble to form a basket-shaped nonamer. Two nonamers pack to form an octadecamer. Molecular modeling suggests that full-length α-synuclein may also be able to assemble in this fashion. Circular dichroism spectroscopy demonstrates that peptide 1a interacts with anionic lipid bilayer membranes, like oligomers of full-length α-synuclein. LDH and MTT assays demonstrate that peptide 1a is toxic toward SH-SY5Y cells. Comparison of peptide 1a to homologues suggests that this toxicity results from nonspecific interactions with the cell membrane. The oligomers formed by peptide 1a are fundamentally different than the proposed models of the fibrils formed by α-synuclein and suggest that α-Syn36-55, rather than the NAC, may nucleate oligomer formation.

  10. Synthesis and X-ray crystallographic investigation of N-(α-D-arabinopyranosyl)alkanamides as N-glycoprotein linkage region analogs.

    PubMed

    Srivastava, Amrita; Varghese, Babu; Loganathan, Duraikkannu

    2013-10-18

    N-Glycoprotein linkage region constituents namely 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all eukaryotes. Earlier crystallographic studies on the linkage region conformation revealed that among all the models and analogs of the N-glycoprotein linkage region, XylβNHAc showed maximum deviation in the ϕN value as compared to the value reported for the model compound, GlcNAcβNHAc. In order to understand the effect of another pentopyranose, viz., arabinose, on the N-glycosidic torsion angles and molecular assembly, three arabinopyranosyl alkanamides were synthesized and their X-ray crystal structures elucidated. A comparative analysis of the N-glycosidic torsion, ϕN of the three analogs revealed the greater rotational freedom around the C1-N1 bond as compared to the GlcNAc derivatives. Molecular assembly of propionamido and chloroacetamido derivatives is characterized by the presence of anti-parallel bilayers of the molecules. This unique molecular assembly is hitherto unknown in all other models and analogs of N-glycoprotein linkage region. This study reveals that N-glycosidic torsions are influenced by the glycan as well as molecular packing.

  11. X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative

    PubMed Central

    Hopcroft, Nicholas H.; Brogden, Anna L.; Searcey, Mark; Cardin, Christine J.

    2006-01-01

    Acridine-4-carboxamides form a class of known DNA mono-intercalating agents that exhibit cytotoxic activity against tumour cell lines due to their ability to inhibit topoisomerases. Previous studies of bis-acridine derivatives have yielded equivocal results regarding the minimum length of linker necessary between the two acridine chromophores to allow bis-intercalation of duplex DNA. We report here the 1.7 Å resolution X-ray crystal structure of a six-carbon-linked bis(acridine-4-carboxamide) ligand bound to d(CGTACG)2 molecules by non-covalent duplex cross-linking. The asymmetric unit consists of one DNA duplex containing an intercalated acridine-4-carboxamide chromophore at each of the two CG steps. The other half of each ligand is bound to another DNA molecule in a symmetry-related manner, with the alkyl linker threading through the minor grooves. The two crystallographically independent ligand molecules adopt distinct side chain interactions, forming hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast to the semi-disordered state of mono-intercalators bound to the same DNA molecule. The complex described here provides the first structural evidence for the non-covalent cross-linking of DNA by a small molecule ligand and suggests a possible explanation for the inconsistent behaviour of six-carbon linked bis-acridines in previous assays of DNA bis-intercalation. PMID:17145714

  12. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the TIR domain from the Brucella melitensis TIR-domain-containing protein TcpB.

    PubMed

    Alaidarous, Mohammed; Ve, Thomas; Ullah, M Obayed; Valkov, Eugene; Mansell, Ashley; Schembri, Mark A; Sweet, Matthew J; Kobe, Bostjan

    2013-10-01

    In mammals, Toll-like receptors (TLRs) recognize conserved microbial molecular signatures and induce an early innate immune response in the host. TLR signalling is mediated by interactions between the cytosolic TIR (Toll/interleukin-1 receptor) domains of the receptor and the adaptor proteins. Increasingly, it is apparent that pathogens target this interaction via pathogen-expressed TIR-domain-containing proteins to modulate immune responses. A TIR-domain-containing protein TcpB has been reported in the pathogenic bacterium Brucella melitensis. Studies have shown that TcpB interferes with the TLR2 and TLR4 signalling pathways to inhibit TLR-mediated inflammatory responses. Such interference may involve TIR-TIR-domain interactions between bacterial and mammalian proteins, but there is a lack of information about these interactions at the molecular level. In this study, the cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the protein construct corresponding to the TIR domain of TcpB (residues 120-250) are reported. The crystals diffracted to 2.6 Å resolution, have the symmetry of the monoclinic space group P2₁ and are most likely to contain four molecules in the asymmetric unit. The structure should help in understanding the molecular basis of how TcpB affects the innate immunity of the host.

  13. Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of the co-chaperonin XoGroES from Xanthomonas oryzae pv. oryzae.

    PubMed

    Doan, Thanh Thi Ngoc; Natarajan, Sampath; Song, Na-Hyun; Kim, Jisun; Kim, Jin-Kwang; Kim, Seung-hwan; Viet, Pham Tan; Kim, Jeong-Gu; Lee, Byoung-Moo; Ahn, Yeh-Jin; Kang, Lin-Woo

    2011-01-01

    Bacterial blight (BB), a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo), causes serious production losses of rice in Asian countries. Protein misfolding may interfere with the function of proteins in all living cells and must be prevented to avoid cellular disaster. All cells naturally contain molecular chaperones that assist the unfolded proteins in folding into the native structure. One of the well characterized chaperone complexes is GroEL-GroES. GroEL, which consists of two chambers, captures misfolded proteins and refolds them. GroES is a co-chaperonin protein that assists the GroEL protein as a lid that temporarily closes the chamber during the folding process. Xoo4289, the GroES gene from Xoo, was cloned and expressed for X-ray crystallographic study. The purified protein (XoGroES) was crystallized using the hanging-drop vapour-diffusion method and a crystal diffracted to 2.0 Å resolution. The crystal belonged to the hexagonal space group P6(1), with unit-cell parameters a=64.4, c=36.5 Å. The crystal contains a single molecule in the asymmetric unit, with a corresponding VM of 2.05 Å3 Da(-1) and a solvent content of 39.9%.

  14. 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.

  15. 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.

  16. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    SciTech Connect

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-10-01

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

  17. Probing mesitylborane and mesitylborate ligation within the coordination sphere of Cp*Ru(P(i)Pr3)+: a combined synthetic, X-ray crystallographic, and computational study.

    PubMed

    Hesp, Kevin D; Kannemann, Felix O; Rankin, Matthew A; McDonald, Robert; Ferguson, Michael J; Stradiotto, Mark

    2011-03-21

    The reaction of Cp*Ru(P(i)Pr(3))Cl (1) with MesBH(2) (Mes = 2,4,6-trimethylphenyl) afforded the mesitylborate complex Cp*Ru(P(i)Pr(3))(BH(2)MesCl) (2, 66%). Exposure of 2 to the chloride abstracting agent LiB(C(6)F(5))(4)·2.5OEt(2) provided [Cp*Ru(P(i)Pr(3))(BH(2)Mes)](+)B(C(6)F(5))(4)(-) (3, 54%), which features an unusual η(2)-B-H monoborane ligand. The related borate complex Cp*Ru(P(i)Pr(3))(BH(3)Mes) (5, 65%) was prepared from 1 and LiH(3)BMes. Attempts to effect the insertion of unsaturated organic substrates into the B-H bonds of 3 were unsuccessful, and efforts to dehydrohalogenate 2 using KO(t)Bu instead afforded the mesitylborate complex Cp*(P(i)Pr(3))Ru(BH(2)MesOH) (6, 48%). Treatment of 1 with benzyl potassium generated an intermediate hydridoruthenium complex (7) resulting from dehydrogenation of a P(i)Pr fragment, which in turn was observed to react with MesBH(2) to afford the mesitylborate complex Cp*(P((i)Pr)(2)(CH(3)CCH(2)))Ru(BH(3)Mes) (8, 47%). Crystallographic characterization data are provided for 2, 3, 5, 6, and 8. A combined X-ray crystallographic and density functional theory (DFT) investigation of 3 and 5, using Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) analysis, revealed that 3 and 5 are best described as donor-acceptor complexes between a Cp*(P(i)Pr(3))Ru(+) fragment and a bis(η(2)-B-H) coordinating mesitylborane(borate) ligand. Significant σ-donation from the B-H bonds into the Ru(II) center exists as evidenced by the NBO populations, bond orders, and AIM delocalization indices. In the case of 3, the vacant p orbital on boron is stabilized by Ru→B π back-donation as well as by resonance with the mesityl group.

  18. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data.

    PubMed

    Terwilliger, Thomas C; Bricogne, Gerard

    2014-10-01

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  19. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    SciTech Connect

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  20. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    DOE PAGES

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when itmore » was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.« less

  1. Expression, purification, crystallization and preliminary X-ray crystallographic studies of the trehalulose synthase MutB from Pseudomonas mesoacidophila MX-45.

    PubMed

    Ravaud, Stéphanie; Watzlawick, Hildegard; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2005-01-01

    The trehalulose synthase (MutB) from Pseudomonas mesoacidophila MX-45, belonging to glycoside hydrolase family 13, catalyses the isomerization of sucrose to trehalulose (alpha-D-glucosylpyranosyl-1,1-D-fructofuranose) and isomaltulose (alpha-D-glucosylpyranosyl-1,6-D-fructofuranose) as main products and glucose and fructose in residual amounts from the hydrolytic reaction. To date, a three-dimensional structure of a sucrose isomerase that produces mainly trehalulose, as is the case for MutB, has been lacking. Crystallographic studies of this 64 kDa enzyme have therefore been initiated in order to contribute to the understanding of the molecular basis of sucrose decomposition, isomerization and of the selectivity of this enzyme that leads to the formation of different products. The MutB protein has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms have been obtained: one diffracts X-rays to 1.6 A resolution using synchrotron radiation and belongs to space group P1, with unit-cell parameters a = 63.8, b = 72.0, c = 82.2 A, alpha = 67.5, beta = 73.1, gamma = 70.8 degrees, while the other form diffracts to 1.8 A resolution using synchrotron radiation and belongs to space group P2(1), with unit-cell parameters a = 63.7, b = 85.9, c = 119.7 A, beta = 97.7 degrees. A molecular-replacement solution has been found using the structure of the isomaltulose synthase (PalI) from Klebsiella sp. LX3 as a search model.

  2. Expression, purification, crystallization and preliminary X-ray crystallographic studies of the trehalulose synthase MutB from Pseudomonas mesoacidophila MX-45

    PubMed Central

    Ravaud, Stéphanie; Watzlawick, Hildegard; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2005-01-01

    The trehalulose synthase (MutB) from Pseudomonas mesoacidophila MX-45, belonging to glycoside hydrolase family 13, catalyses the isomerization of sucrose to trehalulose (α-d-glucosylpyranosyl-1,1-d-fructofuranose) and isomaltulose (α-­d-glucosylpyranosyl-1,6-d-fructofuranose) as main products and glucose and fructose in residual amounts from the hydrolytic reaction. To date, a three-dimensional structure of a sucrose isomerase that produces mainly trehalulose, as is the case for MutB, has been lacking. Crystallographic studies of this 64 kDa enzyme have therefore been initiated in order to contribute to the understanding of the molecular basis of sucrose decomposition, isomerization and of the selectivity of this enzyme that leads to the formation of different products. The MutB protein has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms have been obtained: one diffracts X-rays to 1.6 Å resolution using synchrotron radiation and belongs to space group P1, with unit-cell parameters a = 63.8, b = 72.0, c = 82.2 Å, α = 67.5, β = 73.1, γ = 70.8°, while the other form diffracts to 1.8 Å resolution using synchrotron radiation and belongs to space group P21, with unit-cell parameters a = 63.7, b = 85.9, c = 119.7 Å, β = 97.7°. A molecular-replacement solution has been found using the structure of the isomaltulose synthase (PalI) from Klebsiella sp. LX3 as a search model. PMID:16508103

  3. Expression, purification, crystallization and preliminary X-ray crystallographic studies of the trehalulose synthase MutB from Pseudomonas mesoacidophila MX-45

    SciTech Connect

    Ravaud, Stéphanie; Watzlawick, Hildegard; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2005-01-01

    The trehalulose synthase MutB from P. mesoacidophila MX-45 has been crystallized in two different crystal forms and diffraction data have been collected to 1.6 and 1.8 Å, respectively. The trehalulose synthase (MutB) from Pseudomonas mesoacidophila MX-45, belonging to glycoside hydrolase family 13, catalyses the isomerization of sucrose to trehalulose (α-d-glucosylpyranosyl-1,1-d-fructofuranose) and isomaltulose (α-d-glucosylpyranosyl-1,6-d-fructofuranose) as main products and glucose and fructose in residual amounts from the hydrolytic reaction. To date, a three-dimensional structure of a sucrose isomerase that produces mainly trehalulose, as is the case for MutB, has been lacking. Crystallographic studies of this 64 kDa enzyme have therefore been initiated in order to contribute to the understanding of the molecular basis of sucrose decomposition, isomerization and of the selectivity of this enzyme that leads to the formation of different products. The MutB protein has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms have been obtained: one diffracts X-rays to 1.6 Å resolution using synchrotron radiation and belongs to space group P1, with unit-cell parameters a = 63.8, b = 72.0, c = 82.2 Å, α = 67.5, β = 73.1, γ = 70.8°, while the other form diffracts to 1.8 Å resolution using synchrotron radiation and belongs to space group P2{sub 1}, with unit-cell parameters a = 63.7, b = 85.9, c = 119.7 Å, β = 97.7°. A molecular-replacement solution has been found using the structure of the isomaltulose synthase (PalI) from Klebsiella sp. LX3 as a search model.

  4. Expression, crystallization and preliminary X-ray crystallographic analysis of XometC, a cystathionine γ-lyase-like protein from Xanthomonas oryzae pv. oryzae

    SciTech Connect

    Ngo, Phuong-Thuy Ho; Kim, Jin-Kwang; Kim, Hyesoon; Jung, Junho; Ahn, Yeh-Jin; Kim, Jeong-Gu; Lee, Byoung-Moo; Kang, Hee-Wan; Kang, Lin-Woo

    2008-08-01

    XometC, a cystathionine γ-lyase-like protein from X. oryzae pv. oryzae and an antibacterial drug-target protein against bacterial blight, was cloned, purified and crystallized. Preliminary X-ray crystallographic analysis of XometC crystals was carried out. Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight of rice (Oryza sativa L.), one of the most devastating diseases of rice in most rice-growing countries. XometC, a cystathionine γ-lyase (CGL) like protein that is an antibacterial drug-target protein against Xoo, was cloned, expressed, purified and crystallized. CGL catalyzes the second step in the reverse-transsulfuration pathway, which is essential for the metabolic interconversion of the sulfur-containing amino acids cysteine and methionine. Crystals of two different shapes, plate-shaped and pyramid-shaped, diffracted to 2.9 and 3.2 Å resolution and belonged to the primitive orthogonal space group P2{sub 1}2{sub 1}2{sub 1} and the tetragonal space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = 73.0, b = 144.9, c = 152.3 Å and a = b = 78.2, c = 300.7 Å, respectively. For the P2{sub 1}2{sub 1}2{sub 1} crystals, three or four monomers exist in the asymmetric unit with a corresponding V{sub M} of 3.02 or 2.26 Å{sup 3} Da{sup −1} and a solvent content of 59.3 or 45.7%. For the P4{sub 1} (or P4{sub 3}) crystals, four or five monomers exist in the asymmetric unit with a corresponding V{sub M} of 2.59 or 2.09 Å{sup 3} Da{sup −1} and a solvent content of 52.5 or 40.6%.

  5. Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis.

    PubMed

    Smith, Clyde A; Toth, Marta; Weiss, Thomas M; Frase, Hilary; Vakulenko, Sergei B

    2014-10-01

    Broad-spectrum resistance to aminoglycoside antibiotics in clinically important Gram-positive staphylococcal and enterococcal pathogens is primarily conferred by the bifunctional enzyme AAC(6')-Ie-APH(2'')-Ia. This enzyme possesses an N-terminal coenzyme A-dependent acetyltransferase domain [AAC(6')-Ie] and a C-terminal GTP-dependent phosphotransferase domain [APH(2'')-Ia], and together they produce resistance to almost all known aminoglycosides in clinical use. Despite considerable effort over the last two or more decades, structural details of AAC(6')-Ie-APH(2'')-Ia have remained elusive. In a recent breakthrough, the structure of the isolated C-terminal APH(2'')-Ia enzyme was determined as the binary Mg2GDP complex. Here, the high-resolution structure of the N-terminal AAC(6')-Ie enzyme is reported as a ternary kanamycin/coenzyme A abortive complex. The structure of the full-length bifunctional enzyme has subsequently been elucidated based upon small-angle X-ray scattering data using the two crystallographic models. The AAC(6')-Ie enzyme is joined to APH(2'')-Ia by a short, predominantly rigid linker at the N-terminal end of a long α-helix. This α-helix is in turn intrinsically associated with the N-terminus of APH(2'')-Ia. This structural arrangement supports earlier observations that the presence of the intact α-helix is essential to the activity of both functionalities of the full-length AAC(6')-Ie-APH(2'')-Ia enzyme.

  6. Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP{sup +}

    SciTech Connect

    Wan, Qun Kovalevsky, Andrey Y.; Wilson, Mark A.; Bennett, Brad C.; Langan, Paul; Dealwis, Chris

    2014-05-25

    A 2.0 Å resolution neutron data set and a 1.6 Å resolution X-ray data set were collected for joint X-ray/neutron refinement of the ecDHFR–folate–NADP{sup +} complex in order to study the reaction mechanism of dihydrofolate reductase.

  7. (13)C and (19)F solid-state NMR and X-ray crystallographic study of halogen-bonded frameworks featuring nitrogen-containing heterocycles.

    PubMed

    Szell, Patrick M J; Gabriel, Shaina A; Gill, Russell D D; Wan, Shirley Y H; Gabidullin, Bulat; Bryce, David L

    2017-03-01

    Halogen bonding is a noncovalent interaction between the electrophilic region of a halogen (σ-hole) and an electron donor. We report a crystallographic and structural analysis of halogen-bonded compounds by applying a combined X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) approach. Single-crystal XRD was first used to characterize the halogen-bonded cocrystals formed between two fluorinated halogen-bond donors (1,4-diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene) and several nitrogen-containing heterocycles (acridine, 1,10-phenanthroline, 2,3,5,6-tetramethylpyrazine, and hexamethylenetetramine). New structures are reported for the following three cocrystals, all in the P21/c space group: acridine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C13H9N, 1,10-phenanthroline-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C12H8N2, and 2,3,5,6-tetramethylpyrazine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C8H12N2. (13)C and (19)F solid-state magic-angle spinning (MAS) NMR is shown to be a convenient method to characterize the structural features of the halogen-bond donor and acceptor, with chemical shifts attributable to cocrystal formation observed in the spectra of both nuclides. Cross polarization (CP) from (19)F to (13)C results in improved spectral sensitivity in characterizing the perfluorinated halogen-bond donor when compared to conventional (1)H CP. Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of magnetic shielding constants, along with optimization of the XRD structures, provide a final set of structures in best agreement with the experimental (13)C and (19)F chemical shifts. Data for carbons bonded to iodine remain outliers due to well-known relativistic effects.

  8. Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase

    PubMed Central

    Oksanen, E.; Blakeley, M. P.; Bonneté, F.; Dauvergne, M. T.; Dauvergne, F.; Budayova-Spano, M.

    2009-01-01

    Urate oxidase (Uox) catalyses the oxidation of urate to allantoin and is used to reduce toxic urate accumulation during chemotherapy. X-ray structures of Uox with various inhibitors have been determined and yet the detailed catalytic mechanism remains unclear. Neutron crystallography can provide complementary information to that from X-ray studies and allows direct determination of the protonation states of the active-site residues and substrate analogues, provided that large, well-ordered deuterated crystals can be grown. Here, we describe a method and apparatus used to grow large crystals of Uox (Aspergillus flavus) with its substrate analogues 8-azaxanthine and 9-methyl urate, and with the natural substrate urate, in the presence and absence of cyanide. High-resolution X-ray (1.05–1.20 Å) and neutron diffraction data (1.9–2.5 Å) have been collected for the Uox complexes at the European Synchrotron Radiation Facility and the Institut Laue-Langevin, respectively. In addition, room temperature X-ray data were also collected in preparation for joint X-ray and neutron refinement. Preliminary results indicate no major structural differences between crystals grown in H2O and D2O even though the crystallization process is affected. Moreover, initial nuclear scattering density maps reveal the proton positions clearly, eventually providing important information towards unravelling the mechanism of catalysis. PMID:19586953

  9. Structure-Guided Design and Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. Structure–Activity Relationships and Biochemical, X-ray Crystallographic, Cell-Based, and In Vivo Studies

    SciTech Connect

    Galasiti Kankanamalage, Anushka C.; Kim, Yunjeong; Weerawarna, Pathum M.; Uy, Roxanne Adeline Z.; Damalanka, Vishnu C.; Mandadapu, Sivakoteswara Rao; Alliston, Kevin R.; Mehzabeen, Nurjahan; Battaile, Kevin P.; Lovell, Scott; Chang, Kyeong-Ok; Groutas, William C.

    2015-04-09

    Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.

  10. Structure-Guided Design and Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. Structure–Activity Relationships and Biochemical, X-ray Crystallographic, Cell-Based, and In Vivo Studies

    DOE PAGES

    Galasiti Kankanamalage, Anushka C.; Kim, Yunjeong; Weerawarna, Pathum M.; ...

    2015-04-09

    Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.

  11. A crystallographic and spectroscopic study on the effect of X-ray radiation on the crystal structure of Melanocarpus albomyces laccase

    SciTech Connect

    Hakulinen, Nina . E-mail: nina.hakulinen@joensuu.fi; Kruus, Kristiina; Koivula, Anu; Rouvinen, Juha . E-mail: juha.rouvinen@joensuu.fi

    2006-12-01

    Laccases (p-diphenol dioxygen oxidoreductases) belong to the family of blue multicopper oxidases, which catalyse the four-electron reduction of dioxygen to water concomitantly through the oxidation of substrate molecules. Blue multicopper oxidases have four coppers, a copper (T1) forming a mononuclear site and a cluster of three coppers (T2, T3, and T3') forming a trinuclear site. Because X-rays are known to liberate electrons during data collection and may thus affect the oxidation state of metals, we have investigated the effect of X-ray radiation upon the crystal structure of a recombinant laccase from Melanocarpus albomyces through the use of crystallography and crystal absorption spectroscopy. Two data sets with different strategies, a low and a high-dose data set, were collected at synchrotron. We have observed earlier that the trinuclear site had an elongated electron density amidst coppers, suggesting dioxygen binding. The low-dose synchrotron structure showed similar elongated electron density, but the high-dose X-ray radiation removed the bulk of this density. Therefore, X-ray radiation could alter the active site of laccase from M. albomyces. Absorption spectra of the crystals (320, 420, and 590 nm) during X-ray radiation were measured at a home laboratory. Spectra clearly showed how that the band at 590 nm had vanished, resulting from the T1 copper being reduced, during the long X-ray measurements. The crystal colour changed from blue to colourless. Absorptions at 320 and 420 nm seemed to be rather permanent. The absorption at 320 nm is due to the T3 coppers and it is proposed that absorption at 420 nm is due to the T2 copper when dioxygen or a reaction intermediate is close to this copper.

  12. A crystallographic and spectroscopic study on the effect of X-ray radiation on the crystal structure of Melanocarpus albomyces laccase.

    PubMed

    Hakulinen, Nina; Kruus, Kristiina; Koivula, Anu; Rouvinen, Juha

    2006-12-01

    Laccases (p-diphenol dioxygen oxidoreductases) belong to the family of blue multicopper oxidases, which catalyse the four-electron reduction of dioxygen to water concomitantly through the oxidation of substrate molecules. Blue multicopper oxidases have four coppers, a copper (T1) forming a mononuclear site and a cluster of three coppers (T2, T3, and T3') forming a trinuclear site. Because X-rays are known to liberate electrons during data collection and may thus affect the oxidation state of metals, we have investigated the effect of X-ray radiation upon the crystal structure of a recombinant laccase from Melanocarpus albomyces through the use of crystallography and crystal absorption spectroscopy. Two data sets with different strategies, a low and a high-dose data set, were collected at synchrotron. We have observed earlier that the trinuclear site had an elongated electron density amidst coppers, suggesting dioxygen binding. The low-dose synchrotron structure showed similar elongated electron density, but the high-dose X-ray radiation removed the bulk of this density. Therefore, X-ray radiation could alter the active site of laccase from M. albomyces. Absorption spectra of the crystals (320, 420, and 590nm) during X-ray radiation were measured at a home laboratory. Spectra clearly showed how that the band at 590nm had vanished, resulting from the T1 copper being reduced, during the long X-ray measurements. The crystal colour changed from blue to colourless. Absorptions at 320 and 420nm seemed to be rather permanent. The absorption at 320nm is due to the T3 coppers and it is proposed that absorption at 420nm is due to the T2 copper when dioxygen or a reaction intermediate is close to this copper.

  13. Synthesis and x-ray crystallographic analysis of 4,6-di-O-acetyl-2,3-dideoxy-α-D-threo-hexopyranosyl cyanide.

    PubMed

    Rotella, Madeline; Giovine, Matthew; Dougherty, William; Boyko, Walter; Kassel, Scott; Giuliano, Robert

    2016-04-29

    The glycopyranosyl cyanide 4,6-di-O-acetyl-2,3-dideoxy-α-D-threo-hexopyranosyl cyanide has been synthesized from tri-O-acetyl-D-galactal by reaction with trimethylsilyl cyanide in the presence of boron trifluoride diethyl etherate followed by catalytic hydrogenation. The synthesis provides the α-anomer stereoselectively, the structure of which was assigned based on 2D NMR techniques and x-ray crystallography.

  14. Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy

    SciTech Connect

    Thomson, Stephen A.; Banker, Pierette; Bickett, D. Mark; Boucheron, Joyce A.; Carter, H. Luke; Clancy, Daphne C.; Cooper, Joel P.; Dickerson, Scott H.; Garrido, Dulce M.; Nolte, Robert T.; Peat, Andrew J.; Sheckler, Lauren R.; Sparks, Steven M.; Tavares, Francis X.; Wang, Liping; Wang, Tony Y.; Weiel, James E.

    2009-05-15

    Key binding interactions of the anthranilimide based glycogen phosphorylase a (GPa) inhibitor 2 from X-ray crystallography studies are described. This series of compounds bind to the AMP site of GP. Using the binding information the core and the phenyl urea moieties were optimized. This work culminated in the identification of compounds with single nanomolar potency as well as in vivo efficacy in a diabetic model.

  15. Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy.

    PubMed

    Thomson, Stephen A; Banker, Pierette; Bickett, D Mark; Boucheron, Joyce A; Carter, H Luke; Clancy, Daphne C; Cooper, Joel P; Dickerson, Scott H; Garrido, Dulce M; Nolte, Robert T; Peat, Andrew J; Sheckler, Lauren R; Sparks, Steven M; Tavares, Francis X; Wang, Liping; Wang, Tony Y; Weiel, James E

    2009-02-15

    Key binding interactions of the anthranilimide based glycogen phosphorylase a (GPa) inhibitor 2 from X-ray crystallography studies are described. This series of compounds bind to the AMP site of GP. Using the binding information the core and the phenyl urea moieties were optimized. This work culminated in the identification of compounds with single nanomolar potency as well as in vivo efficacy in a diabetic model.

  16. Crystallization and preliminary X-ray crystallographic study on a xyloglucan-specific exo-beta-glycosidase, oligoxyloglucan reducing-end specific cellobiohydrolase.

    PubMed

    Yaoi, Katsuro; Kondo, Hidemasa; Suzuki, Mamoru; Noro, Natsuko; Tsuda, Sakae; Mitsuishi, Yasushi

    2003-10-01

    A novel xyloglucan-specific exo-beta-glycosidase, oligoxyloglucan reducing-end specific cellobiohydrolase (OXG-RCBH), recognizes the reducing end of oligoxyloglucan and releases two glucosyl residue segments from the main chain. OXG-RCBH was crystallized by the hanging-drop vapour-diffusion method with polyethylene glycol 3000 and polyethylene glycol 400 as precipitants. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 61.0, b = 146.9, c = 211.9 A. The crystals diffract to a resolution of 2.2 A and are suitable for X-ray structure analysis.

  17. Structural confirmation, single X-ray crystallographic behavior, molecular docking and other physico-chemical properties of gerberinol, a natural dimethyl dicoumarol from Gerbera lanuginosa Benth. (Compositae)

    NASA Astrophysics Data System (ADS)

    Brahmachari, Goutam; Das, Saktipada; Kumar, Abhishek; Misra, Neeraj; Sharma, Sakshi; Gupta, Vivek K.

    2017-05-01

    The proposed structure of gerberinol (1), a naturally occurring dimethyl dicoumarol, has been conclusively established on the basis of its detailed spectral and single crystal X-ray analyses. The compound, C21H16O6, crystallizes in the monoclinic space group P21/c with the following unit-cell parameters: a = 14.0884(14), b = 15.1746(15), c = 7.6392(8)Å, α = 90.00°, β = 98.949(4)°, γ = 90.00° and Z = 4. The crystal structure was solved by direct methods using single-crystal X-ray diffraction data collected at room temperature and refined by full-matrix least-squares procedures to a final R-value of 11.43 for 2377 observed reflections. Exhaustive theoretical studies on the molecular structure, vibrational spectra, HOMO, LUMO, MESP surfaces, and molecular docking of this plant-derived natural molecule have also been performed. The equilibrium geometry of the title compound has been obtained and analyzed using DFT-B3LYP/6-311 + G(d,p) method. Molecular docking study of the molecule for predicting its possible biological activities revealed that the compound might be a potent antimicrobial, neurodegenerative and anticancer agent as evidenced from its excellent FF (full fitness) score for 1FUJ and 1ZX1 enzymes.

  18. Cloning, expression, purification, characterization, crystallization and X-ray crystallographic analysis of recombinant Der f 21 (rDer f 21) from Dermatophagoides farinae.

    PubMed

    Pang, Sze Lei; Ho, Kok Lian; Waterman, Jitka; Teh, Aik Hong; Chew, Fook Tim; Ng, Chyan Leong

    2015-11-01

    Dermatophagoides farinae is one of the major house dust mite (HDM) species that cause allergic diseases. N-terminally His-tagged recombinant Der f 21 (rDer f 21), a group 21 allergen, with the signal peptide truncated was successfully overexpressed in an Escherichia coli expression system. The purified rDer f 21 protein was initially crystallized using the sitting-drop vapour-diffusion method. Well diffracting protein crystals were obtained after optimization of the crystallization conditions using the hanging-drop vapour-diffusion method with a reservoir solution consisting of 0.19 M Tris-HCl pH 8.0, 32% PEG 400 at 293 K. X-ray diffraction data were collected to 1.49 Å resolution using an in-house X-ray source. The crystal belonged to the C-centered monoclinic space group C2, with unit-cell parameters a = 123.46, b = 27.71, c = 90.25 Å, β = 125.84°. The calculated Matthews coefficient (VM) of 2.06 Å(3) Da(-1) suggests that there are two molecules per asymmetric unit, with a solvent content of 40.3%. Despite sharing high sequence identity with Blo t 5 (45%) and Blo t 21 (41%), both of which were determined to be monomeric in solution, size-exclusion chromatography, static light scattering and self-rotation function analysis indicate that rDer f 21 is likely to be a dimeric protein.

  19. Preliminary X-ray crystallographic studies of BthTX-II, a myotoxic Asp49-phospholipase A{sub 2} with low catalytic activity from Bothrops jararacussu venom

    SciTech Connect

    Corrêa, L. C.; Marchi-Salvador, D. P.; Cintra, A. C. O.; Soares, A. M.

    2006-08-01

    A myotoxic Asp49-PLA{sub 2} with low catalytic activity from B. jararacussu (BthTX-II) was crystallized in the monoclinic crystal system; a complete X-ray diffraction data set was collected and a molecular-replacement solution was obtained. The oligomeric structure of BthTX-II resembles those of the Asp49-PLA{sub 2} PrTX-III and all bothropic Lys49-PLA{sub 2}s. For the first time, a complete X-ray diffraction data set has been collected from a myotoxic Asp49-phospholipase A{sub 2} (Asp49-PLA{sub 2}) with low catalytic activity (BthTX-II from Bothrops jararacussu venom) and a molecular-replacement solution has been obtained with a dimer in the asymmetric unit. The quaternary structure of BthTX-II resembles the myotoxin Asp49-PLA{sub 2} PrTX-III (piratoxin III from B. pirajai venom) and all non-catalytic and myotoxic dimeric Lys49-PLA{sub 2}s. In contrast, the oligomeric structure of BthTX-II is different from the highly catalytic and non-myotoxic BthA-I (acidic PLA{sub 2} from B. jararacussu). Thus, comparison between these structures should add insight into the catalytic and myotoxic activities of bothropic PLA{sub 2}s.

  20. X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa

    SciTech Connect

    Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou

    2016-10-26

    Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses inArabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein,Camelina sativalectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize the glycosylated recombinant atDORN1-ECD for crystallization. In addition, the glycosylated csI.9-ECD protein was crystallized at 291 K. X-ray diffraction data were collected at 4.6 Å resolution from a single crystal. The crystal belonged to space groupC222 orC2221, with unit-cell parametersa= 94.7,b= 191.5,c= 302.8 Å. These preliminary studies have laid the foundation for structural determination of the DORN1 and I.9 receptor proteins, which will lead to a better understanding of the perception and function of extracellular ATP in plants.

  1. H-bonded supramolecular assembly via proton transfer: Isolation, X-ray crystallographic characterization and SOD mimic activity of [Cu(dipic)2]2[PA-H]4·5H2O

    NASA Astrophysics Data System (ADS)

    Siddiqi, Zafar A.; Khalid, Mohd; Shahid, M.; Kumar, Sarvendra; Sharma, Prashant K.; Siddique, Armeen; Anjuli

    2013-02-01

    The title proton transfer complex was isolated from the reaction of CuCl2·2H2O with pyridine-2,6-dicarboxylic acid (dipic-H2) in presence of 3-amino-1-propanol (PA) under reflux condition. It was thoroughly characterized by FAB-mass, FT-IR, electronic (ligand field), EPR spectroscopic and X-ray crystallographic techniques. The complex crystallizes in the space group C1c1 of the monoclinic system. The unit cell parameters are, a = 17.247(5), b = 20.058(5) Å, c = 15.320(4) Å and β = 109.235(5)°. Extensive H-bonding between the complex anion [Cu(dipic)2]2- and the surrounding cations [PA-H]+ results in a 3D network, supported with additional π-π interactions of the ligand (dipic)2- neighboring units. The SOD mimic activity of the present complex was also examined using NBT assay.

  2. The exocyclic amino group of adenine in Pt(II) and Pd(II) complexes: a critical comparison of the X-ray crystallographic structural data and gas phase calculations.

    PubMed

    Silaghi-Dumitrescu, Radu; Mihály, Béla; Mihály, Timea; Attia, Amr A A; Sanz Miguel, Pablo J; Lippert, Bernhard

    2017-03-17

    A detailed computational (DFT level of theory) study regarding the nature of the exocyclic amino group, N6H2, of the model nucleobase 9-methyladenine (9MeA) and its protonated (9MeAH(+)) and deprotonated forms (9MeA-H), free and metal-complexed, has been conducted. The metals are Pt(II) and Pd(II), bonded to nitrogen-containing co-ligands (NH3, dien, bpy), with N1, N6, and N7 being the metal-binding sites, individually or in different combinations. The results obtained from gas phase calculations are critically compared with X-ray crystallography data, whenever possible. In the majority of cases, there is good qualitative agreement between calculated and experimentally determined C6-N6 bond lengths, but calculated values always show a trend to larger values, by 0.02-0.08 Å. Both methods indicate, with few exceptions, a high degree of double-bond character of C6-N6, consistent with an essentially sp(2)-hybridized N6 atom. The shortest values for C6-N6 distances in X-ray crystal structures are around 1.30 Å. Exceptions refer to cases in which DFT calculations suggest the existence of a hydrogen bond with N6H2 acting as a H bond acceptor, hence a situation with N6 having undergone a substantial hybridization shift toward sp(3). Nevertheless, even in these cases the C6-N6 bond (1.392 Å) is still halfway between a typical C-N single bond (1.48 Å) and a typical C=N double bond (1.28 Å). This scenario is, however, not borne out by X-ray crystallographic results, and is attributed to the absence of counter anions and solvent molecules in the calculated structures.

  3. Neutron and X-ray crystallographic analysis of the human α-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex.

    PubMed

    Yamada, Taro; Kurihara, Kazuo; Ohnishi, Yuki; Tamada, Taro; Tomoyori, Katsuaki; Masumi, Kenji; Tanaka, Ichiro; Kuroki, Ryota; Niimura, Nobuo

    2013-08-01

    The protonation states and hydration structures of the α-thrombin-bivalirudin complex were studied by joint XN refinement of the single crystal X-ray and neutron diffraction data at resolutions of 1.6 and 2.8Å, respectively. The atomic distances were estimated by carrying out X-ray crystallographic analysis at 1.25Å resolution. The complex represents a model of the enzyme-product (EP) complex of α-thrombin. The neutron scattering length maps around the active site suggest that the side chain of H57/H was deuterated. The joint XN refinement showed that occupancies for Dδ1 and Dε2 of H57/H were 1.0 and 0.7, respectively. However, no significant neutron scattering length density was observed around the hydroxyl oxygen Oγ of S195/H, which was close to the carboxylic carbon atom of dFPR-COOH. These observations suggest that the Oγ atom of S195/H is deprotonated and maintains its nucleophilicity in the EP complex. In addition to the active site, the hydration structures of the S1 subsite and the Exosite I, which are involved in the recognition of bivalirudin, are presented.

  4. Expression, purification, crystallization, and preliminary X-ray crystallographic analysis of OXA-17, an extended-spectrum {beta}-lactamase conferring severe antibiotic resistance

    SciTech Connect

    Lee, J. H. Sohn, S. G. Jung, H. I. An, Y. J. Lee, S. H.

    2013-07-15

    OXA-17, an extended-spectrum {beta}-lactamase (ESBL) conferring severe antibiotic resistance, hydrolytically inactivates {beta}-lactam antibiotics, inducing a lack of eradication of pathogenic bacteria by oxyimino {beta}-lactams and not helping hospital infection control. Thus, the enzyme is a potential target for developing antimicrobial agents against pathogens producing ESBLs. OXA-17 was purified and crystallized at 298 K. X-ray diffraction data from OXA-17 crystal have been collected to 1.85 A resolution using synchrotron radiation. The crystal of OXA-17 belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 48.37, b = 101.12, and c = 126.07 A. Analysis of the packing density shows that the asymmetric unit probably contains two molecules with a solvent content of 54.6%.

  5. Expression, purification, crystallization, and preliminary X-ray crystallographic analysis of OXA-17, an extended-spectrum β-lactamase conferring severe antibiotic resistance

    NASA Astrophysics Data System (ADS)

    Lee, J. H.; Sohn, S. G.; Jung, H. I.; An, Y. J.; Lee, S. H.

    2013-07-01

    OXA-17, an extended-spectrum β-lactamase (ESBL) conferring severe antibiotic resistance, hydrolytically inactivates β-lactam antibiotics, inducing a lack of eradication of pathogenic bacteria by oxyimino β-lactams and not helping hospital infection control. Thus, the enzyme is a potential target for developing antimicrobial agents against pathogens producing ESBLs. OXA-17 was purified and crystallized at 298 K. X-ray diffraction data from OXA-17 crystal have been collected to 1.85 Å resolution using synchrotron radiation. The crystal of OXA-17 belongs to space group P212121, with unit-cell parameters a = 48.37, b = 101.12, and c = 126.07 Å. Analysis of the packing density shows that the asymmetric unit probably contains two molecules with a solvent content of 54.6%.

  6. Synthesis of hydrolysis-resistant pyridoxal 5'-phosphate analogs and their biochemical and X-ray crystallographic characterization with the pyridoxal phosphatase chronophin.

    PubMed

    Knobloch, Gunnar; Jabari, Nauras; Stadlbauer, Sven; Schindelin, Hermann; Köhn, Maja; Gohla, Antje

    2015-06-15

    A set of phosphonic acid derivatives (1-4) of pyridoxal 5'-phosphate (PLP) was synthesized and characterized biochemically using purified murine pyridoxal phosphatase (PDXP), also known as chronophin. The most promising compound 1 displayed primarily competitive PDXP inhibitory activity with an IC50 value of 79μM, which was in the range of the Km of the physiological substrate PLP. We also report the X-ray crystal structure of PDXP bound to compound 3, which we solved to 2.75Å resolution (PDB code 5AES). The co-crystal structure proves that compound 3 binds in the same orientation as PLP, and confirms the mode of inhibition to be competitive. Thus, we identify compound 1 as a PDXP phosphatase inhibitor. Our results suggest a strategy to design new, potent and selective PDXP inhibitors, which may be useful to increase the sensitivity of tumor cells to treatment with cytotoxic agents.

  7. Spectroscopic and X-ray crystallographic evidence for electrostatic effects in 4-substituted cyclohexanone-derived hydrazones, imines, and corresponding salts.

    PubMed

    Dibble, David J; Ziller, Joseph W; Woerpel, K A

    2011-10-07

    The axial conformer of several 4-substituted cyclohexanone hydrazone salts was found to predominate in solution. Changes in the charge of the molecule and the polarity of the solvent led to changes in the conformational preference of each molecule that were consistent with electrostatic stabilization of the axial conformer. (1)H NMR spectroscopic analysis was utilized to determine the structure of cyclohexanone-derived substrates by comparison to conformationally restricted trans-decalone derivatives and computational models. X-ray crystallography demonstrated that the axial configuration of a pendant benzyloxy group is the preferred conformation of an iminium ion in the solid state. The structure of a neutral hydrazone was also determined to favor the axial configuration for a pendant benzyloxy group in the solid state.

  8. Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of leucine aminopeptidase (LAP) from the pepA gene of Xanthomonas oryzae pv. oryzae.

    PubMed

    Huynh, Kim-Hung; Natarajan, Sampath; Choi, Jeongyoon; Song, Na-Hyun; Kim, Jeong-Gu; Lee, Byoung-Moo; Ahn, Yeh-Jin; Kang, Lin-Woo

    2009-09-01

    Xanthomonas oryzae pv. oryzae (Xoo) causes the serious disease bacterial blight in rice. The pepA (Xoo0834) gene from Xoo is one of around 100 genes that have been selected for the design of antibacterial drugs. The pepA gene encodes leucine aminopeptidase (LAP), an exopeptidase that catalyzes the hydrolysis of leucine residues from the N-terminus of a protein or peptide. This enzyme was expressed in Escherichia coli, purified and crystallized, and preliminary X-ray structural studies have been carried out. The LAP crystal diffracted to 2.6 A resolution and belonged to the cubic space group P2(1)3. The unit-cell volume of the crystal was compatible with the presence of two monomers in the asymmetric unit.

  9. Effects of modifications of the linker in a series of phenylpropanoic acid derivatives: Synthesis, evaluation as PPARalpha/gamma dual agonists, and X-ray crystallographic studies.

    PubMed

    Casimiro-Garcia, Agustin; Bigge, Christopher F; Davis, Jo Ann; Padalino, Teresa; Pulaski, James; Ohren, Jeffrey F; McConnell, Patrick; Kane, Christopher D; Royer, Lori J; Stevens, Kimberly A; Auerbach, Bruce J; Collard, Wendy T; McGregor, Christine; Fakhoury, Stephen A; Schaum, Robert P; Zhou, Hairong

    2008-05-01

    A new series of alpha-aryl or alpha-heteroarylphenyl propanoic acid derivatives was synthesized that incorporate acetylene-, ethylene-, propyl-, or nitrogen-derived linkers as a replacement of the commonly used ether moiety that joins the central phenyl ring with the lipophilic tail. The effect of these modifications in the binding and activation of PPARalpha and PPARgamma was first evaluated in vitro. Compounds possessing suitable profiles were then evaluated in the ob/ob mouse model of type 2 diabetes. The propylene derivative 40 and the propyl derivative 53 demonstrated robust plasma glucose lowering activity in this model. Compound 53 was also evaluated in male Zucker diabetic fatty rats and was found to achieve normalization of glucose, triglycerides, and insulin levels. An X-ray crystal structure of the complex of 53 with the PPARgamma-ligand-binding domain was obtained and discussed in this report.

  10. Crystallization and X-ray crystallographic analysis of recombinant TylP, a putative γ-butyrolactone receptor protein from Streptomyces fradiae.

    PubMed

    Mohd-Sharif, Nurhikmah; Shaibullah, Sofiyah; Givajothi, Vasanthakumar; Tan, Cheng Seng; Ho, Kok Lian; Teh, Aik Hong; Baharum, Syarul Nataqain; Waterman, Jitka; Ng, Chyan Leong

    2017-02-01

    TylP is one of five regulatory proteins involved in the regulation of antibiotic (tylosin) production, morphological and physiological differentiation in Streptomyces fradiae. Its function is similar to those of various γ-butyrolactone receptor proteins. In this report, N-terminally His-tagged recombinant TylP protein (rTylP) was overproduced in Escherichia coli and purified to homogeneity. The rTylP protein was crystallized from a reservoir solution comprising 34%(v/v) ethylene glycol and 5%(v/v) glycerol. The protein crystals diffracted X-rays to 3.05 Å resolution and belonged to the trigonal space group P3121, with unit-cell parameters a = b = 126.62, c = 95.63 Å.

  11. X-ray crystallographic and mass spectrometric structure determination and functional characterization of succinylated porin from Rhodobacter capsulatus: implications for ion selectivity and single-channel conductance.

    PubMed Central

    Przybylski, M.; Glocker, M. O.; Nestel, U.; Schnaible, V.; Blüggel, M.; Diederichs, K.; Weckesser, J.; Schad, M.; Schmid, A.; Welte, W.; Benz, R.

    1996-01-01

    The role of charges near the pore mouth has been discussed in theoretical work about ion channels. To introduce new negative charges in a channel protein, amino groups of porin from Rhodobacter capsulatus 37b4 were succinylated with succinic anhydride, and the precise extent and sites of succinylations and structures of the succinylporins determined by mass spectrometry and X-ray crystallography. Molecular weight and peptide mapping analyses using matrix-assisted laser desorption-ionization mass spectrometry identified selective succinylation of three lysine-epsilon-amino groups (Lys-46, Lys-298, Lys-300) and the N-terminal alpha-amino group. The structure of a tetra-succinylated porin (TS-porin) was determined to 2.4 A and was generally found unchanged in comparison to native porin to form a trimeric complex. All succinylated amino groups found in a mono/di-succinylated porin (MS-porin) and a TS-porin are localized at the inner channel surface and are solvent-accessible: Lys-46 is located at the channel constriction site, whereas Lys-298, Lys-300, and the N-terminus are all near the periplasmic entrance of the channel. The Lys-46 residue at the central constriction loop was modeled as succinyl-lysine from the electron density data and shown to bend toward the periplasmic pore mouth. The electrical properties of the MS-and TS-porins were determined by reconstitution into black lipid membranes, and showed a negative charge effect on ion transport and an increased cation selectivity through the porin channel. The properties of a typical general diffusion porin changed to those of a channel that contains point charges near the pore mouth. The single-channel conductance was no longer a linear function of the bulk aqueous salt concentration. The substantially higher cation selectivity of the succinylated porins compared with the native protein is consistent with the increase of negatively charged groups introduced. These results show tertiary structure

  12. Crystallization and preliminary X-ray crystallographic studies of the biotin carboxyl carrier protein and biotin protein ligase complex from Pyrococcus horikoshii OT3

    SciTech Connect

    Bagautdinov, Bagautdin; Matsuura, Yoshinori; Bagautdinova, Svetlana; Kunishima, Naoki

    2007-04-01

    A truncated form of biotin carboxyl carrier protein containing the C-terminal half fragment (BCCPΔN76) and the biotin protein ligase (BPL) with the mutation R48A (BPL*) or the double mutation R48A K111A (BPL**) were successfully cocrystallized in the presence of ATP and biotin. The BPL*–BCCPΔN76 and BPL**–BCCPΔN76 crystals belong to space group P2{sub 1} and diffract X-rays to 2.7 and 2.0 Å resolution, respectively. Biotin protein ligase (BPL) catalyses the biotinylation of the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase. To elucidate the exact details of the protein–protein interactions in the biotinylation function, the C-terminal half fragment of BCCP (BCCPΔN76), the R48A mutant of BPL (BPL*) and the R48A K111A double mutant of BPL (BPL**), all of which are from Pyrococcus horikoshii OT3, have been expressed, purified and successfully cocrystallized. Cocrystals of the BPL*–BCCPΔN76 and BPL**–BCCPΔN76 complexes as well as crystals of BPL*, BPL** and BCCPΔN76 were obtained by the oil-microbatch method using PEG 20 000 as a precipitant at 295 K. Complete X-ray diffraction data sets for BPL*–BCCPΔN76 and BPL**–BCCPΔN76 crystals were collected at 100 K to 2.7 and 2.0 Å resolution, respectively, using synchrotron radiation. They belong to the monoclinic space group P2{sub 1}, with similar unit-cell parameters a = 69.85, b = 63.12, c = 75.64 Å, β = 95.9°. Assuming two subunits of the complex per asymmetric unit gives a V{sub M} value of 2.45 Å{sup 3} Da{sup −1} and a solvent content of 50%.

  13. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha H16

    PubMed Central

    Kim, Jieun; Kim, Kyung-Jin

    2014-01-01

    The (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha (RePaaH1) is an enzyme used in the biosynthesis of n-butanol from acetyl-CoA by the reduction of acetoacetyl-CoA to (S)-3-hydroxybutyryl-CoA. The RePaaH1 protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 1.4 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium chloride at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.6 Å on a synchrotron beamline. The crystal belonged to space group P3221, with unit-cell parameters a = b = 135.4, c = 97.2 Å. With three molecules per asymmetric unit, the crystal volume per unit protein weight (V M) is 2.68 Å3 Da−1, which corresponds to a solvent content of approximately 54.1%. The structure was solved by the single-wavelength anomalous dispersion method and refinement of the structure is in progress. PMID:25005097

  14. X-ray crystallographic, FT-IR and NMR studies as well as anticancer and antibacterial activity of the salt formed between ionophore antibiotic Lasalocid acid and amines

    NASA Astrophysics Data System (ADS)

    Huczyński, Adam; Rutkowski, Jacek; Wietrzyk, Joanna; Stefańska, Joanna; Maj, Ewa; Ratajczak-Sitarz, Małgorzata; Katrusiak, Andrzej; Brzezinski, Bogumil; Bartl, Franz

    2013-01-01

    Two new complexes of the ionophore antibiotic Lasalocid acid (LAS) with phenylamine (PhA) and butylamine (BuA) were synthesized and their molecular structures were studied using single crystal X-ray diffraction and spectroscopic methods. In the solid state both amines are protonated and all NH3+ protons are hydrogen bonded to etheric, hydroxyl and carboxylic oxygen atoms of the LAS anion. In chloroform solutions the structure observed in the crystal of LAS-BuA complex is preserved and an equilibrium between the LAS-PhA complex and dissociated Lasalocid acid and phenylamine is observed. In vitro antimicrobial tests of the complexes showed a significant activity towards some strains of Gram-positive bacteria. For the first time Lasalocid acid and its complexes with amines were tested in vitro for cytotoxic activity against human cancer cell lines: A-549 (lung), MCF-7 (breast), HT-29 (colon) and mouse cancer cell line P-388 (leukemia). We found that LAS and its complexes are strong cytotoxic agents towards all tested cell lines. The cytostatic activity of the compounds studied is greater than that of cisplatin, indicating that Lasalocid and its complexes are promising candidates for new anticancer drugs.

  15. Cloning, overexpression, crystallization and preliminary X-ray crystallographic analysis of a slow-processing mutant of penicillin G acylase from Kluyvera citrophila

    PubMed Central

    Varshney, Nishant Kumar; Ramasamy, Sureshkumar; Brannigan, James A.; Wilkinson, Anthony J.; Suresh, C. G.

    2013-01-01

    Kluyvera citrophila penicillin G acylase (KcPGA) has recently attracted increased attention relative to the well studied and commonly used Escherichia coli PGA (EcPGA) because KcPGA is more resilient to harsh conditions and is easier to immobilize for the industrial hydrolysis of natural penicillins to generate the 6-aminopenicillin (6-APA) nucleus, which is the starting material for semi-synthetic antibiotic production. Like other penicillin acylases, KcPGA is synthesized as a single-chain inactive pro-PGA, which upon autocatalytic processing becomes an active heterodimer of α and β chains. Here, the cloning of the pac gene encoding KcPGA and the preparation of a slow-processing mutant precursor are reported. The purification, crystallization and preliminary X-ray analysis of crystals of this precursor protein are described. The protein crystallized in two different space groups, P1, with unit-cell parameters a = 54.0, b = 124.6, c = 135.1 Å, α = 104.1, β = 101.4, γ = 96.5°, and C2, with unit-cell parameters a = 265.1, b = 54.0, c = 249.2 Å, β = 104.4°, using the sitting-drop vapour-diffusion method. Diffraction data were collected at 100 K and the phases were determined using the molecular-replacement method. The initial maps revealed electron density for the spacer peptide. PMID:23908045

  16. Complex assembly, crystallization and preliminary X-ray crystallographic studies of rhesus macaque MHC Mamu-A*01 complexed with an immunodominant SIV-Gag nonapeptide

    SciTech Connect

    Chu, Fuliang; Lou, Zhiyong; Gao, Bin; Bell, John I.; Rao, Zihe; Gao, George F.

    2005-06-01

    Crystallization of the first rhesus macaque MHC class I complex. Simian immunodeficiency virus (SIV) infection in rhesus macaques has been used as the best model for the study of human immunodeficiency virus (HIV) infection in humans, especially in the cytotoxic T-lymphocyte (CTL) response. However, the structure of rhesus macaque (or any other monkey model) major histocompatibility complex class I (MHC I) presenting a specific peptide (the ligand for CTL) has not yet been elucidated. Here, using in vitro refolding, the preparation of the complex of the rhesus macaque MHC I allele (Mamu-A*01) with human β{sub 2}m and an immunodominant peptide, CTPYDINQM (Gag-CM9), derived from SIV Gag protein is reported. The complex (45 kDa) was crystallized; the crystal belongs to space group I422, with unit-cell parameters a = b = 183.8, c = 155.2 Å. The crystal contains two molecules in the asymmetric unit and diffracts X-rays to 2.8 Å resolution. The structure is being solved by molecular replacement and this is the first attempt to determined the crystal structure of a peptide–nonhuman primate MHC complex.

  17. Crystallization and preliminary X-ray crystallographic investigations on a βγ-crystallin domain of absent in melanoma 1 (AIM1), a protein from Homo sapiens

    SciTech Connect

    Aravind, Penmatsa; Rajini, Bheemreddy; Sharma, Yogendra; Sankaranarayanan, Rajan

    2006-03-01

    The crystallization and preliminary X-ray diffraction analysis of AIM1g1, a βγ-crystallin domain of absent in melanoma (AIM1) protein from H. sapiens, is reported. AIM1g1 is a single βγ-crystallin domain from the protein absent in melanoma 1 (AIM1), which appears to play a role in the suppression of melanomas. This domain is known to bind calcium and its structure would help in identifying calcium-coordinating sites in vertebrate crystallins, which have hitherto been believed to have lost this ability during evolution. Crystallization of this domain was performed by the hanging-drop vapour-diffusion method. Crystals diffracted to a maximum resolution of 1.86 Å and were found to belong to space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 54.98, c = 59.73 Å. Solvent-content analysis indicated the presence of one monomer per asymmetric unit.

  18. Purification, crystallization and preliminary X-ray crystallographic analysis of the phosphatase domain (PA3346PD) of the response regulator PA3346 from Pseudomonas aeruginosa PAO1.

    PubMed

    Chen, Li Ying; Wu, Pei Hsun; Guan, Hong Hsiang; Fun, Hoong Kun; Chang, Hwan You; Chen, Chun Jung

    2015-04-01

    The phosphatase domain (PA3346PD) of the response regulator PA3346 modulates the downstream anti-anti-σ factor PA3347 to regulate swarming motility in Pseudomonas aeruginosa PAO1. PA3346PD, which comprises the protein phosphatase 2C domain (PP2C), is classified as a Ser/Thr phosphatase of the Mg(2+)- or Mn(2+)-dependent protein phosphatase (PPM) family. The recombinant PA3346PD, with molecular mass 26 kDa, was overexpressed in Escherichia coli, purified on an Ni(2+)-NTA agarose column and crystallized by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected from PA3346PD crystals to a resolution of 2.58 Å and the crystals belonged to space group I4₁32 or I4₃32, with unit-cell parameter a = 157.61 Å. Preliminary analysis indicates the presence of a monomer of PA3346PD in the asymmetric unit with a solvent content of 58.4%.

  19. Crystallization and preliminary X-ray crystallographic studies of the biotin carboxyl carrier protein and biotin protein ligase complex from Pyrococcus horikoshii OT3

    PubMed Central

    Bagautdinov, Bagautdin; Matsuura, Yoshinori; Bagautdinova, Svetlana; Kunishima, Naoki

    2007-01-01

    Biotin protein ligase (BPL) catalyses the biotinylation of the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase. To elucidate the exact details of the protein–protein interactions in the biotinylation function, the C-terminal half fragment of BCCP (BCCPΔN76), the R48A mutant of BPL (BPL*) and the R48A K111A double mutant of BPL (BPL**), all of which are from Pyrococcus horikoshii OT3, have been expressed, purified and successfully cocrystallized. Cocrystals of the BPL*–BCCPΔN76 and BPL**–BCCPΔN76 complexes as well as crystals of BPL*, BPL** and BCCPΔN76 were obtained by the oil-microbatch method using PEG 20 000 as a precipitant at 295 K. Complete X-ray diffraction data sets for BPL*–BCCPΔN76 and BPL**–BCCPΔN76 crystals were collected at 100 K to 2.7 and 2.0 Å resolution, respectively, using synchrotron radiation. They belong to the monoclinic space group P21, with similar unit-cell parameters a = 69.85, b = 63.12, c = 75.64 Å, β = 95.9°. Assuming two subunits of the complex per asymmetric unit gives a V M value of 2.45 Å3 Da−1 and a solvent content of 50%. PMID:17401210

  20. Crystallization and preliminary X-ray crystallographic studies of the biotin carboxyl carrier protein and biotin protein ligase complex from Pyrococcus horikoshii OT3.

    PubMed

    Bagautdinov, Bagautdin; Matsuura, Yoshinori; Bagautdinova, Svetlana; Kunishima, Naoki

    2007-04-01

    Biotin protein ligase (BPL) catalyses the biotinylation of the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase. To elucidate the exact details of the protein-protein interactions in the biotinylation function, the C-terminal half fragment of BCCP (BCCPDeltaN76), the R48A mutant of BPL (BPL*) and the R48A K111A double mutant of BPL (BPL**), all of which are from Pyrococcus horikoshii OT3, have been expressed, purified and successfully cocrystallized. Cocrystals of the BPL*-BCCPDeltaN76 and BPL**-BCCPDeltaN76 complexes as well as crystals of BPL*, BPL** and BCCPDeltaN76 were obtained by the oil-microbatch method using PEG 20 000 as a precipitant at 295 K. Complete X-ray diffraction data sets for BPL*-BCCPDeltaN76 and BPL**-BCCPDeltaN76 crystals were collected at 100 K to 2.7 and 2.0 A resolution, respectively, using synchrotron radiation. They belong to the monoclinic space group P2(1), with similar unit-cell parameters a = 69.85, b = 63.12, c = 75.64 A, beta = 95.9 degrees . Assuming two subunits of the complex per asymmetric unit gives a V(M) value of 2.45 A(3) Da(-1) and a solvent content of 50%.

  1. Crystallization and preliminary X-ray crystallographic study of the extracellular domain of the 4-1BB ligand, a member of the TNF family

    SciTech Connect

    Byun, Jung-Sue; Kim, Dong-Uk; Ahn, Byungchan; Kwon, Byoung Se; Cho, Hyun-Soo

    2006-01-01

    The extracellular domain of the 4-1BB ligand fused with glutathione-S-transferase was expressed in Escherichia coli (Origami) and purified by using affinity and ion-exchange column chromatographic methods. Crystals of the 4-1BB ligand were obtained at 290 K by the hanging-drop vapour-diffusion method. The 4-1BB ligand, a member of the tumour necrosis factor (TNF) family, is an important co-stimulatory molecule that plays a key role in the clonal expansion and survival of CD8+ T cells. Signalling through binding of the 4-1BB ligand and 4-1BB has been reported to enhance CD8+ T-cell expansion and protect activated CD8+ T cells from death. The 4-1BB ligand is an integral protein expressed on activated antigen-presenting cells. The extracellular domain of the 4-1BB ligand fused with glutathione-S-transferase was expressed in Escherichia coli (Origami) and purified by using affinity and ion-exchange column chromatographic methods. Crystals of the 4-1BB ligand were obtained at 290 K by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected from these crystals to 2.8 Å resolution and the crystals belong to space group C2, with unit-cell parameters a = 114.6, b = 73.8, c = 118.50 Å, β = 115.5°.

  2. Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of the biosynthetic N-acetylornithine aminotransferases from Salmonella typhimurium and Escherichia coli

    SciTech Connect

    Rajaram, V.; Prasad, K.; Ratna Prasuna, P.; Ramachandra, N.; Bharath, S. R.; Savithri, H. S.; Murthy, M. R. N.

    2006-10-01

    Acetylornithine aminotransferases, members of the type I subgroup II family of PLP-dependent enzymes, from S. typhimurium and E. coli have been cloned, overexpressed, purified and crystallized. Acetylornithine aminotransferase (AcOAT) is a type I pyridoxal 5′-phosphate-dependent enzyme catalyzing the conversion of N-acetylglutamic semialdehyde to N-acetylornithine in the presence of α-ketoglutarate, a step involved in arginine metabolism. In Escherichia coli, the biosynthetic AcOAT also catalyzes the conversion of N-succinyl-l-2-amino-6-oxopimelate to N-succinyl-l,l-diaminopimelate, one of the steps in lysine biosynthesis. It is closely related to ornithine aminotransferase. AcOAT was cloned from Salmonella typhimurium and E. coli, overexpressed in E. coli and purified using Ni–NTA affinity column chromatography. The enzymes crystallized in the presence of gabaculine. Crystals of E. coli AcOAT (eAcOAT) only diffracted X-rays to 3.5 Å and were twinned. The crystals of S. typhimurium AcOAT (sAcOAT) diffracted to 1.9 Å and had a dimer in the asymmetric unit. The structure of sAcOAT was solved by the molecular-replacement method.

  3. Complex assembly, crystallization and preliminary X-ray crystallographic studies of the swine major histocompatibility complex molecule SLA-1*1502.

    PubMed

    Pan, Xiaocheng; Qi, Jianxun; Zhang, Nianzhi; Li, Qirun; Yin, Chunsheng; Chen, Rong; Gao, Feng; Xia, Chun

    2011-05-01

    In order to illustrate the structure of the swine MHC class I (SLA-I) molecule and to evaluate the cytotoxic T lymphocyte (CTL) response against porcine reproductive and respiratory syndrome virus (PRRSV), the ternary complex of the SLA-I molecule termed SLA-1*1502 with β(2)-microglobulin and the CTL epitope TMPPGFELY (PRRSV-NSP9(TY9)) derived from PRRSV nonstructural protein 9 (residues 198-206) was assembled and crystallized. The crystal diffracted X-rays to 2.2 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 66.1, b = 74.1, c = 98.6 Å; it contained one molecule in the asymmetric unit. The Matthews coefficient and the solvent content were calculated to be 2.74 Å(3) Da(-1) and 55.17%, respectively. The results will be helpful in obtaining insight into the structural basis of the presentation of viral epitopes by SLA-I.

  4. Preliminary joint neutron time-of-flight and X-ray crystallographic study of human ABO(H) blood group A glycosyltransferase

    PubMed Central

    Schuman, B.; Fisher, S. Z.; Kovalevsky, A.; Borisova, S. N.; Palcic, M. M.; Coates, L.; Langan, P.; Evans, S. V.

    2011-01-01

    The biosyntheses of oligosaccharides and glycoconjugates are conducted by glycosyltransferases. These extraordinarily diverse and widespread enzymes catalyze the formation of glycosidic bonds through the transfer of a monosaccharide from a donor molecule to an acceptor molecule, with the stereochemistry about the anomeric carbon being either inverted or retained. Human ABO(H) blood group A α-1,3-N-acetylgalactosaminyltransferase (GTA) generates the corresponding antigen by the transfer of N-acetylgalactos­amine from UDP-GalNAc to the blood group H antigen. To understand better how specific active-site-residue protons and hydrogen-bonding patterns affect substrate recognition and catalysis, neutron diffraction studies were initiated at the Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center (LANSCE). A large single crystal was subjected to H/D exchange prior to data collection and time-of-flight neutron diffraction data were collected to 2.5 Å resolution at the PCS to ∼85% overall completeness, with complementary X-ray diffraction data collected from a crystal from the same drop and extending to 1.85 Å resolution. Here, the first successful neutron data collection from a glycosyltransferase is reported. PMID:21301100

  5. Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of XC847, a 3′-5′ oligoribonuclease from Xanthomonas campestris

    SciTech Connect

    Wu, Yan-You; Chin, Ko-Hsin; Chou, Chia-Cheng; Lee, Cheng-Chung; Shr, Hui-Lin; Gao, Fei Philip; Lyu, Ping-Chiang; Wang, Andrew H.-J.; Chou, Shan-Ho

    2005-10-01

    A DEDDh-type 3′-5′ oligoribonuclease from the plant pathogen X. campestris pv. campestris has been overexpressed in E. coli, purified and crystallized. The crystals diffracted to 2.1 Å with good quality. Oligoribonucleases are essential components of RNA and DNA metabolism and close homologues of genes encoding them are found not only in prokaryotes but also in a wide range of eukaryotes, including yeast and humans. Inactivation of the oligoribonuclease gene (orn) can result in cellular lethality. Despite their important biological function, they have been studied little from a structural point of view. In this report, the cloning, expression, crystallization and preliminary X-ray analysis of XC847, a DEDDh-type 3′-5′ oligoribonuclease from the plant pathogen Xanthomonas campestris pv. campestris, a Gram-negative bacterium causing major worldwide disease of cruciferous crops, is described. The XC847 crystals diffracted to a resolution of at least 2.1 Å. They are tetragonal and belong to space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 67.5, c = 89.8 Å. One molecule is present per asymmetric unit.

  6. High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D

    SciTech Connect

    Zhang, Y.; Robinson, H.; Gao, X.; Qin, L.; Buchko, G. W.; Varnum, S. M.

    2010-12-01

    Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8, b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.

  7. High-level Expression Purification Crystallization and Preliminary X-ray Crystallographic Studies of the Receptor Binding Domain of botulinum neurotoxin Serotype D

    SciTech Connect

    Y Zhang; X Gao; G Buchko; H Robinson; S Varnum

    2011-12-31

    Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8, b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.

  8. Expression, purification, crystallization and X-ray crystallographic studies of different redox states of the active site of thioredoxin 1 from the whiteleg shrimp Litopenaeus vannamei

    PubMed Central

    Campos-Acevedo, Adam A.; Garcia-Orozco, Karina D.; Sotelo-Mundo, Rogerio R.; Rudiño-Piñera, Enrique

    2013-01-01

    Thioredoxin (Trx) is a 12 kDa cellular redox protein that belongs to a family of small redox proteins which undergo reversible oxidation to produce a cystine disulfide bond through the transfer of reducing equivalents from the catalytic site cysteine residues (Cys32 and Cys35) to a disulfide substrate. In this study, crystals of thioredoxin 1 from the Pacific whiteleg shrimp Litopenaeus vannamei (LvTrx) were successfully obtained. One data set was collected from each of four crystals at 100 K and the three-dimensional structures of the catalytic cysteines in different redox states were determined: reduced and oxidized forms at 2.00 Å resolution using data collected at a synchrotron-radiation source and two partially reduced structures at 1.54 and 1.88 Å resolution using data collected using an in-house source. All of the crystals belonged to space group P3212, with unit-cell parameters a = 57.5 (4), b = 57.5 (4), c = 118.1 (8) Å. The asymmetric unit contains two subunits of LvTrx, with a Matthews coefficient (V M) of 2.31 Å3 Da−1 and a solvent content of 46%. Initial phases were determined by molecular replacement using the crystallographic model of Trx from Drosophila melanogaster as a template. In the present work, LvTrx was overexpressed in Escherichia coli, purified and crystallized. Structural analysis of the different redox states at the Trx active site highlights its reactivity and corroborates the existence of a dimer in the crystal. In the crystallographic structures the dimer is stabilized by several interactions, including a disulfide bridge between Cys73 of each LvTrx monomer, a hydrogen bond between the side chain of Asp60 of each monomer and several hydrophobic interactions, with a noncrystallographic twofold axis. PMID:23695560

  9. Expression, purification, crystallization and X-ray crystallographic studies of different redox states of the active site of thioredoxin 1 from the whiteleg shrimp Litopenaeus vannamei.

    PubMed

    Campos-Acevedo, Adam A; Garcia-Orozco, Karina D; Sotelo-Mundo, Rogerio R; Rudiño-Piñera, Enrique

    2013-05-01

    Thioredoxin (Trx) is a 12 kDa cellular redox protein that belongs to a family of small redox proteins which undergo reversible oxidation to produce a cystine disulfide bond through the transfer of reducing equivalents from the catalytic site cysteine residues (Cys32 and Cys35) to a disulfide substrate. In this study, crystals of thioredoxin 1 from the Pacific whiteleg shrimp Litopenaeus vannamei (LvTrx) were successfully obtained. One data set was collected from each of four crystals at 100 K and the three-dimensional structures of the catalytic cysteines in different redox states were determined: reduced and oxidized forms at 2.00 Å resolution using data collected at a synchrotron-radiation source and two partially reduced structures at 1.54 and 1.88 Å resolution using data collected using an in-house source. All of the crystals belonged to space group P3212, with unit-cell parameters a = 57.5 (4), b = 57.5 (4), c = 118.1 (8) Å. The asymmetric unit contains two subunits of LvTrx, with a Matthews coefficient (VM) of 2.31 Å(3) Da(-1) and a solvent content of 46%. Initial phases were determined by molecular replacement using the crystallographic model of Trx from Drosophila melanogaster as a template. In the present work, LvTrx was overexpressed in Escherichia coli, purified and crystallized. Structural analysis of the different redox states at the Trx active site highlights its reactivity and corroborates the existence of a dimer in the crystal. In the crystallographic structures the dimer is stabilized by several interactions, including a disulfide bridge between Cys73 of each LvTrx monomer, a hydrogen bond between the side chain of Asp60 of each monomer and several hydrophobic interactions, with a noncrystallographic twofold axis.

  10. Joint x-ray

    MedlinePlus

    X-ray - joint; Arthrography; Arthrogram ... x-ray technologist will help you position the joint to be x-rayed on the table. Once in place, pictures are taken. The joint may be moved into other positions for more ...

  11. Chest X Ray?

    MedlinePlus

    ... this page from the NHLBI on Twitter. Chest X Ray A chest x ray is a fast and painless imaging test that ... tissue scarring, called fibrosis. Doctors may use chest x rays to see how well certain treatments are working ...

  12. Cosmic x ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, Dan; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1990-01-01

    The annual progress report on Cosmic X Ray Physics is presented. Topics studied include: the soft x ray background, proportional counter and filter calibrations, the new sounding rocket payload: X Ray Calorimeter, and theoretical studies.

  13. Cosmic x ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, Dan; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1991-01-01

    The annual progress report on Cosmic X Ray Physics for the period 1 Jan. to 31 Dec. 1990 is presented. Topics studied include: soft x ray background, new sounding rocket payload: x ray calorimeter, and theoretical studies.

  14. Skull x-ray

    MedlinePlus

    X-ray - head; X-ray - skull; Skull radiography; Head x-ray ... Chernecky CC, Berger BJ. Radiography of skull, chest, and cervical spine - diagnostic. In: Chernecky CC, Berger BJ, eds. Laboratory Tests and Diagnostic Procedures . 6th ed. ...

  15. Chest X-Ray

    MedlinePlus

    ... by Image/Video Gallery Your radiologist explains chest x-ray. Transcript Welcome to Radiology Info dot org! Hello, ... you about chest radiography also known as chest x-rays. Chest x-rays are the most commonly performed ...

  16. X-ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure

    PubMed Central

    Stout, Jan; Van Driessche, Gonzalez; Savvides, Savvas N.; Van Beeumen, Jozef

    2007-01-01

    Dissimilatory oxidation of thiosulfate in the green sulfur bacterium Chlorobium limicola f. thiosulfatophilum is carried out by the ubiquitous sulfur-oxidizing (Sox) multi-enzyme system. In this system, SoxY plays a key role, functioning as the sulfur substrate-binding protein that offers its sulfur substrate, which is covalently bound to a conserved C-terminal cysteine, to another oxidizing Sox enzyme. Here, we report the crystal structures of a stand-alone SoxY protein of C. limicola f. thiosulfatophilum, solved at 2.15 Å and 2.40 Å resolution using X-ray diffraction data collected at 100 K and room temperature, respectively. The structure reveals a monomeric Ig-like protein, with an N-terminal α-helix, that oligomerizes into a tetramer via conserved contact regions between the monomers. The tetramer can be described as a dimer of dimers that exhibits one large hydrophobic contact region in each dimer and two small hydrophilic interface patches in the tetramer. At the tetramer interface patch, two conserved redox-active C-terminal cysteines form an intersubunit disulfide bridge. Intriguingly, SoxY exhibits a dimer/tetramer equilibrium that is dependent on the redox state of the cysteines and on the type of sulfur substrate component bound to them. Taken together, the dimer/tetramer equilibrium, the specific interactions between the subunits in the tetramer, and the significant conservation level of the interfaces strongly indicate that these SoxY oligomers are biologically relevant. PMID:17327392

  17. Crystallization and X-ray Crystallographic Analysis of the Adhesive SpaC Pilin Subunit in the SpaCBA Pilus of Gut-adapted Lactobacillus rhamnosus GG.

    PubMed

    Kant, Abhiruchi; von Ossowski, Ingemar; Palva, Airi; Krishnan, Vengadesan

    2016-01-01

    Gram-positive Lactobacillus rhamnosus GG, a gut-adapted commensalic (and probiotic) strain, is known to express sortase-assembled pili on its cell surface. These SpaCBA-called pili consist of three different types of building blocks; the SpaA backbone-pilin subunit and the SpaB and SpaC ancillary pilins. SpaC is a relatively large (~90kDa) multi-domain fimbrial adhesin, and while it is located primarily at the SpaCBA pilus tip, occasionally, it can also be detected throughout the length of pilus backbone. Functionally, SpaC mainly accounts for SpaCBA pilus-mediated interactions with intestinal mucus, collagen, and human gut epithelial cells. Moreover, SpaC adhesiveness is also perceived to have a causal relationship with SpaCBA pilus-induced host-cell immune responses. In order to improve the mechanistic understanding of SpaC and its adhesive properties by structural investigation, we purified and successfully crystallized a recombinant construct of the near full-length SpaC protein (residues 36-856) in the presence of magnesium ions. X-ray diffraction data were collected to 2.6 Å resolution. The SpaC crystal belongs to the space group P21212 with unit cell parameters a = 116.5, b = 128.3, c = 136.5 Å and contains two molecules in the asymmetric unit. Presence of conserved metal ion-dependent adhesion site containing von Willebrand factor type A domain suggests its likely role in the function of SpaC.

  18. Crystallization and preliminary X-ray crystallographic analysis of EstE1, a new and thermostable esterase cloned from a metagenomic library

    SciTech Connect

    Byun, Jung-Sue; Rhee, Jin-Kyu; Kim, Dong-Uk; Oh, Jong-Won; Cho, Hyun-Soo

    2006-02-01

    Recombinant EstE1 protein with a histidine tag at the C-terminus was overexpressed in Escherichia coli strain BL21(DE3) and then purified by affinity chromatography. The protein was then crystallized at 290 K by the hanging-drop vapour-diffusion method. EstE1, a new thermostable esterase, was isolated by functional screening of a metagenomic DNA library from thermal environment samples. This enzyme showed activity towards short-chain acyl derivatives of length C4–C6 at a temperature of 303–363 K and displayed a high thermostability above 353 K. EstE1 has 64 and 57% amino-acid sequence similarity to est{sub pc}-encoded carboxylesterase from Pyrobaculum calidifontis and AFEST from Archaeoglobus fulgidus, respectively. The recombinant protein with a histidine tag at the C-terminus was overexpressed in Escherichia coli strain BL21(DE3) and then purified by affinity chromatography. The protein was crystallized at 290 K by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.3 Å resolution from an EstE1 crystal; the crystal belongs to space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 73.71, c = 234.23 Å. Assuming the presence of four molecules in the asymmetric unit, the Matthews coefficient V{sub M} is calculated to be 2.2 Å{sup 3} Da{sup −1} and the solvent content is 44.1%.

  19. A search for blues brothers: X-ray crystallographic/spectroscopic characterization of the tetraarylbenzidine cation radical as a product of aging of solid magic blue.

    PubMed

    Talipov, Marat R; Hossain, Mohammad M; Boddeda, Anitha; Thakur, Khushabu; Rathore, Rajendra

    2016-03-14

    Magic blue (MB+˙ SbCl6− salt), i.e. tris-4-bromophenylamminium cation radical, is a routinely employed one-electron oxidant that slowly decomposes in the solid state upon storage to form so called ‘blues brothers’, which often complicate the quantitative analyses of the oxidation processes. Herein, we disclose the identity of the main ‘blues brother’ as the cation radical and dication of tetrakis-(4-bromophenyl)benzidine (TAB) by a combined DFT and experimental approach, including isolation of TAB+˙ SbCl6− and its X-ray crystallography characterization. The formation of TAB in aged magic blue samples occurs by a Scholl-type coupling of a pair of MB followed by a loss of molecular bromine. The recognition of this fact led us to the rational design and synthesis of tris(2-bromo-4-tert-butylphenyl)amine, referred to as ‘blues cousin’ (BC: Eox1 = 0.78 V vs. Fc/Fc+, λmax(BC+˙) = 805 nm, εmax = 9930 cm−1 M−1), whose oxidative dimerization is significantly hampered by positioning the sterically demanding tert-butyl groups at the para-positions of the aryl rings. A ready two-step synthesis of BC from triphenylamine and the high stability of its cation radical (BC+˙) promise that BC will serve as a ready replacement for MB and an oxidant of choice for mechanistic investigations of one-electron transfer processes in organic, inorganic, and organometallic transformations.

  20. X-ray and optical crystallographic parameters investigations of high frequency induction melted Al-(alpha-Al(2)O(3)) alloys.

    PubMed

    Bourbia, A; Draissia, M; Bedboudi, H; Boulkhessaim, S; Debili, M Y

    2010-01-01

    This article deals with the microstructural strengthening mechanisms of aluminium by means of hard alpha-Al(2)O(3) alumina fine particles. A broad of understanding views covering materials preparations, elaboration process, characterization techniques and associated microstructural characteristic parameters measurements is given. In order to investigate the microstructural characteristic parameters and the mechanical strengthening mechanisms of pure aluminium by hard fine particles, a set of Al-(alpha-Al(2)O(3)) alloys samples were made under vacuum by high fusion temperature melting, the high frequency (HF) process, and rapidly solidified under ambient temperature from a mixture of cold-compacted high-pure fine Al and alpha-Al(2)O(3) powders. The as-solidified Al-(alpha-Al(2)O(3)) alloys were characterized by means of X-ray diffraction (XRD) analyses, optical microscopy observations and Vickers microhardness tests in both brut and heat-treated states. It was found that the as-solidified HF Al-(alpha-Al(2)O(3)) alloys with compositions below 4 wt.% (alpha-Al(2)O(3)) are single-phase microstructures of the solid solution FCC Al phase and over two-phase microstructures of the solid solution FCC Al and the Rhombohedral alpha-Al(2)O(3) phases. The optical micrographs reveal the presence of a grain size refinement in these alloys. Vickers microhardness of the as-solidified Al-(alpha-Al(2)O(3)) is increased by means of pure fine alpha-Al(2)O(3) alumina particles. These combined effects of strengthening and grain size refinement observed in the as-solidified Al-(alpha-Al(2)O(3)) alloys are essentially due to a strengthening of Al by the alpha-Al(2)O(3) alumina particles insertion in the (HF) melted and rapidly solidified alloys.

  1. Crystallization and preliminary X-ray crystallographic analysis of an ice-binding protein (FfIBP) from Flavobacterium frigoris PS1.

    PubMed

    Do, Hackwon; Lee, Jun Hyuck; Lee, Sung Gu; Kim, Hak Jun

    2012-07-01

    Ice growth in a cold environment is fatal for polar organisms, not only because of the physical destruction of inner cell organelles but also because of the resulting chemical damage owing to processes such as osmotic shock. The properties of ice-binding proteins (IBPs), which include antifreeze proteins (AFPs), have been characterized and IBPs exhibit the ability to inhibit ice growth by binding to specific ice planes and lowering the freezing point. An ice-binding protein (FfIBP) from the Gram-negative bacterium Flavobacterium frigoris PS1, which was isolated from the Antarctic, has recently been overexpressed. Interestingly, the thermal hysteresis activity of FfIBP was approximately 2.5 K at 50 µM, which is ten times higher than that of the moderately active IBP from Arctic yeast (LeIBP). Although FfIBP closely resembles LeIBP in its amino-acid sequence, the antifreeze activity of FfIBP appears to be much greater than that of LeIBP. In an effort to understand the reason for this difference, an attempt was made to solve the crystal structure of FfIBP. Here, the crystallization and X-ray diffraction data of FfIBP are reported. FfIBP was crystallized using the hanging-drop vapour-diffusion method with 0.1 M sodium acetate pH 4.4 and 3 M sodium chloride as precipitant. A complete diffraction data set was collected to a resolution of 2.9 Å. The crystal belonged to space group P4(1)22, with unit-cell parameters a = b = 69.4, c = 178.2 Å. The asymmetric unit contained one monomer.

  2. An X-ray crystallographic and DFT study of the complementary hydrogen bonding of bidentate pyrrolide-imine Schiff base ligands

    NASA Astrophysics Data System (ADS)

    Akerman, Matthew P.; Chiazzari, Victoria A.

    2014-01-01

    Three pyrrolide-imine Schiff base compounds: 1-phenyl-N-[(E)-1H-pyrrol-2-ylmethylidene]methanamine (1), 2-phenyl-N-(1H-pyrrol-2-ylmethylidene)ethanamine (2) and 1-(naphthalen-1-yl)-N-[(E)-1H-pyrrol-2-ylmethylidene]methanamine (3) have been synthesized in this work. The compounds were all synthesized via solid-state reactions which proved to be a rapid and high yielding synthetic method. The solid state structures of compounds (1), (2) and (3) were elucidated by single crystal X-ray diffraction. The asymmetric unit of (1) comprises two symmetry independent molecules while the structures of (2) and (3) show a single molecule in the asymmetric unit. In the solid state the Schiff base ligands exist as discrete dimers supported by complementary hydrogen bonds between the pyrrole NH and imine nitrogen atom of an adjacent molecule. The hydrogen bond lengths (D⋯A) for compounds (1), (2) and (3) measure 3.074(1), 2.993(2) and 2.995(1) Å, respectively. In the solid state the dimeric structure of (1) exhibits C1 symmetry while the supramolecular structures of compounds (2) and (3) are inversion dimers (Ci symmetry). The compounds were studied by density functional theory at the B3LYP/6-311G(dp) level of theory, these simulations indicate that the self-recognition through hydrogen bonding is mainly dependant on favorable electrostatic interactions. The simulations show that the lowest energy conformation of (1) is of C2 symmetry, not the C1 symmetry of the solid-state structure. The solid state structure of (2) is of Ci symmetry; however, simulations in vacuo show that this conformation is a saddle point on the potential energy surface. The lowest energy conformation of the dimer is in fact of C2 symmetry and is 3.51 kJ mol-1 lower in energy than the inversion dimer.

  3. The X-ray Crystallographic Structure and Specificity profile of HAD Superfamily Phosphohydrolase BT1666: Comparison of Paralogous Functions in B. thetaiotaomicron†

    PubMed Central

    Lu, Zhibing; Dunaway-Mariano, Debra; Allen, Karen N.

    2012-01-01

    Analysis of the haloalkanoate dehalogenase superfamily (HADSF) has uncovered homologues occurring within the same organism that are found to possess broad, overlapping substrate specificities and low catalytic efficiencies. Here we compare the HADSF phosphatase BT1666 from Bacteroides thetaiotaomicron VPI-5482 to a homologue with high sequence identity (40%) from the same organism BT4131, a known hexose-phosphate phosphatase. The goal is to find if these enzymes represent duplicated versus paralogous activities. The X-ray crystal structure of BT1666 was determined to 1.82 Å resolution. Superposition of the BT1666 and BT4131 structures revealed a conserved fold and identical active sites suggestive of a common physiological substrate. The steady-state kinetic constants for BT1666 were determined for a diverse panel of phosphorylated metabolites to define its substrate specificity profile and overall level of catalytic efficiency. Whereas BT1666 and BT4131 are both promiscuous, their substrate specificity profiles are distinct. The catalytic efficiency of BT1666 (kcat/Km = 4.4 × 102 M-1 s-1 for the best substrate fructose 1,6-(bis)phosphate) is an order of magnitude less than that of BT4131 (kcat/Km = 6.7 × 103 M-1 s-1 for 2-deoxyglucose 6-phosphate). The seemingly identical active-site structures point to sequence variation outside the active site causing differences in conformational dynamics or subtle catalytic positioning effects that drive the divergence in catalytic efficiency and selectivity. The overlapping substrate profiles may be understood in terms of differential regulation of expression of the two enzymes or a conferred advantage in metabolic housekeeping functions by having a larger range of possible metabolites as substrates. PMID:21989931

  4. Structure and conformation of 2β,3β-epoxyestr-5(10)-en-1,4,17-trione, spectroscopic and X-ray crystallographic studies

    NASA Astrophysics Data System (ADS)

    Kapor, A.; Ribar, B.; Strümpel, M.; Gašić, M. J.; Milić, D.; Šolaja, B.

    2000-04-01

    Colourless single crystals were isolated as by-product during the synthesis of steroidal A-ring substituted 1,4-quinones (and epoxyquinols), as synthetic products with antibiotic and antitumor properties. Its structure was proposed by comparing IR, UV, 1H and 13C NMR spectra to the ones of quinone 2 and independently determined by an X-ray analysis, as 2β,3β-epoxyestr-5(10)-en-1,4,17-trione. Crystals belong to the monoclinic system with space group P21: a=6.767(3) Å, b=7.097(5) Å, c=15.748(5) Å, β=97.070(5)°, V=750.6(8) Å3, Z=2, D x=1.329 Mg m -3, μ( Mo K α)=0.093 mm-1. The structure was solved by direct methods and refined to a final R=0.064 for 1729 reflections with I>2 σ( I). The steroidal skeleton with chiral centre at C13 possesses the S configuration defining β-orientation of O2 atom bridging C2 and C3 atoms and β-oriented methyl group bonded to C13 atom. The best plane through the ring A and epoxy ring plane form an angle of 89.6(2)°. Conformational analysis of the steroid rings are performed by calculating the ring puckering parameters and asymmetry factors. The conformation of the A ring is screw-boat1S 6, ring B half-chair4H 3, ring C chair1C 4, and the five-membered D ring is half-chair2H 1 conformation. The crystal structure is stabilised by the weak C-H⋯O hydrogen bonds and van der Waals interaction.

  5. Crystallization and preliminary X-ray crystallographic analysis of α-glucosidase HaG from Halomonas sp. strain H11.

    PubMed

    Shen, Xing; Saburi, Wataru; Gai, Zuo-Qi; Komoda, Keisuke; Yu, Jian; Ojima-Kato, Teruyo; Kido, Yusuke; Matsui, Hirokazu; Mori, Haruhide; Yao, Min

    2014-04-01

    The α-glucosidase HaG from the halophilic bacterium Halomonas sp. strain H11 catalyzes the hydrolysis of the glucosidic linkage at the nonreducing end of α-glucosides, such as maltose and sucrose, to release α-glucose. Based on its amino-acid sequence, this enzyme is classified as a member of glycoside hydrolase family 13. HaG has three unique characteristics: (i) a very narrow substrate specificity, almost exclusively hydrolyzing disaccharides; (ii) activation by monovalent cations, such as K(+), Rb(+), Cs(+) and NH4(+); and (iii) high transfer activity of the glucose moiety to the OH group of low-molecular-weight compounds, including glycerol and 6-gingerol. Crystallographic studies have been performed in order to understand these special features. An expression vector was constructed and recombinant HaG protein was overexpressed, purified and crystallized. A data set to 2.15 Å resolution was collected and processed. The crystal belonged to space group P212121, with unit-cell parameters a = 60.2, b = 119.2, c = 177.2 Å. The structure has been determined by molecular replacement using the isomaltulose synthase PalI as the search model (PDB entry 1m53).

  6. Crystallization and preliminary X-ray crystallographic analysis of α-glucosidase HaG from Halomonas sp. strain H11

    PubMed Central

    Shen, Xing; Saburi, Wataru; Gai, Zuo-Qi; Komoda, Keisuke; Yu, Jian; Ojima-Kato, Teruyo; Kido, Yusuke; Matsui, Hirokazu; Mori, Haruhide; Yao, Min

    2014-01-01

    The α-glucosidase HaG from the halophilic bacterium Halomonas sp. strain H11 catalyzes the hydrolysis of the glucosidic linkage at the nonreducing end of α-­glucosides, such as maltose and sucrose, to release α-glucose. Based on its amino-acid sequence, this enzyme is classified as a member of glycoside hydrolase family 13. HaG has three unique characteristics: (i) a very narrow substrate specificity, almost exclusively hydrolyzing disaccharides; (ii) activation by monovalent cations, such as K+, Rb+, Cs+ and NH4 +; and (iii) high transfer activity of the glucose moiety to the OH group of low-molecular-weight compounds, including glycerol and 6-gingerol. Crystallographic studies have been performed in order to understand these special features. An expression vector was constructed and recombinant HaG protein was overexpressed, purified and crystallized. A data set to 2.15 Å resolution was collected and processed. The crystal belonged to space group P212121, with unit-cell parameters a = 60.2, b = 119.2, c = 177.2 Å. The structure has been determined by molecular replacement using the isomaltulose synthase PalI as the search model (PDB entry 1m53). PMID:24699739

  7. High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D

    SciTech Connect

    Zhang, Yanfeng; Gao, Xiaoli; Qin, Lin; Buchko, Garry W.; Robinson, Howard; Varnum, Susan M.

    2010-12-01

    Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and can cause neuroparalytic disease botulism. Due to the limitations of production and manipulation of holoenzymes, expressing non-toxic heavy chain receptor binding domains (HCR) has become a common strategy for vaccine and antibody development. Meanwhile, large quantities and highly purified soluble proteins are required for research areas such as antibody maturation and structural biology. We present high level expression and purification of the BoNT serotype D HCR in E. coli using a codon-optimized cDNA. By varying expression conditions, especially at low temperature, the protein was expressed at a high level with high solubility. About 150-200 mg protein was purified to >90% purity from 1 L cell culture. The recombinant D_HCR was crystallized and the crystals diffracted to 1.65 Å resolution. The crystals belong to space group P212121 with unit cell dimensions a = 60.8 Å, b = 89.7 Å, c = 93.9 Å. Preliminary crystallographic data analysis revealed one molecule in asymmetric unit.

  8. Crystallization and preliminary X-ray crystallographic analysis of β-ketoacyl-ACP synthase I (XoFabB) from Xanthomonas oryzae pv. oryzae.

    PubMed

    Doan, Thanh Thi Ngoc; Kim, Jin Kwang; Mac, Qui Khanh; Chung, Cheolwon; Sampath, Natarajan; Kim, Jeong Gu; Ahn, Yeh Jin; Kang, Lin Woo

    2011-12-01

    The proteins in the fatty-acid synthesis pathway in bacteria have significant potential as targets for the development of antibacterial agents. An essential elongation step in fatty-acid synthesis is performed by β-ketoacyl-acyl carrier protein synthase I (FabB). The organism Xanthomonas oryzae pv. oryzae (Xoo) causes a destructive bacterial blight disease of rice. The XoFabB protein from Xoo was expressed, purified and crystallized for the three-dimensional structure determination that is essential for the development of specific inhibitors of the enzyme. An XoFabB crystal diffracted to 3.0 Å resolution and belonged to the tetragonal space group P4(1), with unit-cell parameters a = b = 82.2, c = 233.2 Å. Assuming that the crystallographic structure contains four molecules in the asymmetric unit, the corresponding V(M) would be 2.18 Å(3) Da(-1) and the solvent content would be 43.5%. The initial structure was determined by the MOLREP program with an R factor of 44.0% and does contain four monomers in the asymmetric unit.

  9. Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of malonyl-CoA-acyl carrier protein transacylase (FabD) from Xanthomonas oryzae pv. oryzae.

    PubMed

    Jung, Jae-Wook; Natarajan, Sampath; Kim, Hyesoon; Ahn, Yeh-Jin; Kim, Seunghwan; Kim, Jeong-Gu; Lee, Byoung-Moo; Kang, Lin-Woo

    2008-12-01

    Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight in rice, which is one of the most devastating diseases in rice-cultivating countries. The Xoo0880 (fabD) gene coding for a malonyl-CoA-acyl carrier protein transacylase (MCAT) from Xoo was cloned and expressed in Escherichia coli. MCAT is an essential enzyme that catalyzes a key reaction of fatty-acid synthesis in bacteria and plants: the conversion of malonyl-CoA to malonyl-acyl carrier protein. The FabD enzyme was purified and crystallized in order to elucidate its three-dimensional structure and to determine its enzymatic reaction mechanism and biological importance. The crystal obtained diffracted to 1.9 A resolution and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 41.4, b = 74.6, c = 98.5 A. According to Matthews coefficient calculations, the crystallographic structure contains only one monomeric unit in the asymmetric unit with a V(M) of 2.21 A(3) Da(-1) and a solvent content of 44.3%.

  10. Photoluminescence, Dual-donor Energy Transfer and Single X-ray Crystallographic Studies of Eu3+ and Tb3+ complexes with pyridines and triazaphosphaadamantane oxide (TPAO) ligands

    NASA Astrophysics Data System (ADS)

    Forcha, Derick Akaju

    Coordination of several chromophoric ligands capable of sensitizing Tb 3+ and Eu3+ ions have been studied. Four new complexes of Eu3+ and Tb3+ ions were achieved by coordinating Eu with 4', 4''''- (1-4 phenylene) bis (2, 2':6', 2-terpyridine) , pyridino [2-3-b] pyrazines and 6,6‧‧-dibromo-2,2‧:6‧,2‧‧-terpyridine.The crystal structure of [Tb(TPAO)2(H2O) 4(Au(CN)2)3], was determined and shows a polymeric three-dimensional coordination with a monoclinic space group Cc, Z=4. The unit cell parameters are a = 17.4266(14) A, b = 10.8224(10) A, c = 18.0270(16) A, α = 90° beta = 109.309(3)° gamma = 90°. The structure exhibits an equilateral Au-Au-Au interaction bridged to a terbium core by the C-N groups. Three other complexes, viz [Eu(ppz) 2(H2O)n]Cl3, [Eu(ptpy)(H2O) n]Cl3 and [Eu(bbterp)(H2O)n]Cl 3, have also been synthesized and characterized using IR and luminescence spectroscopy, although no crystal was obtained suitable for X-ray diffraction analysis. The ligand tetra(2'-pyridyl)pyrazine (tppz) was also crystallized and its crystal structure solved. The results herein, elaborate the mode of dual donor sensitization from ligand groups to the lanthanide ions. The efficiency of energy transfer that occurs in the Ln3+ complexes has been calculated, taking into account the radiative and non radiative relaxation processes, and the limitation encountered. A broad excitation spectrum at 369, 366 and 380 nm were observed for [Eu(ppz)2(H2O) n]Cl3, [Eu(bbterp)(H2O)n]Cl3 and [Eu(ptpy)(H2O)n]Cl3 complexes, respectively upon monitoring the Eu3+ emission indicating the presence of ET in a donor-acceptor type interaction.

  11. How strong is hydrogen bonding in ionic liquids? Combined X-ray crystallographic, infrared/Raman spectroscopic, and density functional theory study.

    PubMed

    Katsyuba, Sergey A; Vener, Mikhail V; Zvereva, Elena E; Fei, Zhaofu; Scopelliti, Rosario; Laurenczy, Gabor; Yan, Ning; Paunescu, Emilia; Dyson, Paul J

    2013-08-01

    Hydrogen bonding in ionic liquids based on the 1-(2'-hydroxylethyl)-3-methylimidazolium cation ([C₂OHmim](+)) and various anions ([A](-)) of differing H-bond acceptor strength, viz. hexafluorophosphate [PF6](-), tetrafluoroborate [BF₄](-), bis(trifluoromethanesulfonimide) [Tf₂N](-), trifluoromethylsulfonate [OTf](-), and trifluoroacetate [TFA](-), was studied by a range of spectroscopic and computational techniques and, in the case of [C₂OHmim][PF6], by single crystal X-ray diffraction. The first quantitative estimates of the energy (E(HB)) and the enthalpy (-ΔH(HB)) of H-bonds in bulk ILs were obtained from a theoretical analysis of the solid-state electron-density map of crystalline [C₂OHmim][PF6] and an analysis of the IR spectra in crystal and liquid samples. E(HB) for OH···[PF6](-) H-bonds amounts to ~3.4-3.8 kcal·mol(-1), whereas weaker H-bonds (2.8-3.1 kcal·mol(-1)) are formed between aromatic C2H group of imidazolium ring and the [PF6](-) anion. The enthalpy of the OH···[A](-) H-bonds follows the order: [PF6] (2.4 kcal·mol(-1)) < [BF₄] (3.3 kcal·mol(-1)) < [Tf₂N] (3.4 kcal·mol(-1)) < [OTf] (4.7 kcal·mol(-1)l) < [TFA] (6.2 kcal·mol(-1)). The formation of aggregates of self-associated [C₂OHmim](+) cations is present in liquid [C₂OHmim][PF6], [C₂OHmim][BF₄], and [C₂OHmim][Tf₂N], with the energy of the OH···OH H-bonds amounting to ~6 kcal·mol(-1). Multiple secondary interactions in the bulk ILs influence their structure, vibrational spectra, and H-bond strength. In particular, these interactions can blue-shift the stretching frequencies of the CH groups of the imidazolium ring in spite of red-shifting CH···[A](-) H-bonds. They also weaken the H-bonding in the IL relative to the isolated ion pairs, with these anticooperative effects amounting to ca. 50% of the E(HB) value.

  12. Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde‡, ¶

    PubMed Central

    Toteva, Maria M.; Silvaggi, Nicholas R.; Allen, Karen N.; Richard, John P.

    2011-01-01

    for proton transfer. An ultra-high resolution (0.97 Å) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI•sugar complexes. PMID:21995300

  13. Chest x-ray

    MedlinePlus

    Chest radiography; Serial chest x-ray; X-ray - chest ... You stand in front of the x-ray machine. You will be told to hold your breath when the x-ray is taken. Two images are usually taken. You will ...

  14. A nifS-like gene, csdB, encodes an Escherichia coli counterpart of mammalian selenocysteine lyase. Gene cloning, purification, characterization and preliminary x-ray crystallographic studies.

    PubMed

    Mihara, H; Maeda, M; Fujii, T; Kurihara, T; Hata, Y; Esaki, N

    1999-05-21

    Selenocysteine lyase is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the exclusive decomposition of L-selenocysteine to L-alanine and elemental selenium. An open reading frame, named csdB, from Escherichia coli encodes a putative protein that is similar to selenocysteine lyase of pig liver and cysteine desulfurase (NifS) of Azotobacter vinelandii. In this study, the csdB gene was cloned and expressed in E. coli cells. The gene product was a homodimer with the subunit Mr of 44,439, contained 1 mol of PLP as a cofactor per mol of subunit, and catalyzed the release of Se, SO2, and S from L-selenocysteine, L-cysteine sulfinic acid, and L-cysteine, respectively, to yield L-alanine; the reactivity of the substrates decreased in this order. Although the enzyme was not specific for L-selenocysteine, the high specific activity for L-selenocysteine (5.5 units/mg compared with 0.019 units/mg for L-cysteine) supports the view that the enzyme can be regarded as an E. coli counterpart of mammalian selenocysteine lyase. We crystallized CsdB, the csdB gene product, by the hanging drop vapor diffusion method. The crystals were of suitable quality for x-ray crystallography and belonged to the tetragonal space group P43212 with unit cell dimensions of a = b = 128.1 A and c = 137.0 A. Consideration of the Matthews parameter Vm (3.19 A3/Da) accounts for the presence of a single dimer in the crystallographic asymmetric unit. A native diffraction dataset up to 2.8 A resolution was collected. This is the first crystallographic analysis of a protein of NifS/selenocysteine lyase family.

  15. X-Ray Crystallographic, Multifrequency EPR, and DFT Characterization of the Ni(PCy2NtBu2)2n+ Hydrogen Oxidation Catalyst in the Ni(I) Oxidation State

    PubMed Central

    Niklas, Jens; Westwood, Mark; Mardis, Kristy L.; Brown, Tiara L.; Pitts-McCoy, Anthony M.; Hopkins, Michael D.; Poluektov, Oleg G.

    2016-01-01

    The Ni(I) hydrogen oxidation catalyst [Ni(PCy2NtBu2)2]+ (1+; PCy2NtBu2= 1,5bis(tert-butyl)-3,7-dicyclo-hexyl-1,5-diaza-3,7-diphosphacychlooctane) has been studied using a combination of EPR techniques (X-, Q-, and D-band; electron-nuclear double resonance, hyperfine sublevel correlation spectroscopy), X-ray crystallography, and density functional theory (DFT) calculations. Crystallographic and DFT studies indicate that the molecular structure of 1+ is highly symmetrical. EPR spectroscopy has allowed determination of the electronic g-tensor and the spin density distribution on the ligands, and revealed that the Ni(I) center does not interact strongly with the potentially coordinating solvents acetonitrile and butyronitrile. The EPR spectra and magnetic parameters of 1+ are found to be distinctly different from those for the related compound [Ni(PPh2NPh2)2]+ (4+). One significant contributor to these differences is that the molecular structure of 4+ is unsymmetrical, unlike that of 1+. DFT calculations on derivatives in which the R and R′ groups are systematically varied have allowed elucidation of structure/substituent relationships and their corresponding influence on the magnetic resonance parameters. PMID:26098955

  16. Thoracic spine x-ray

    MedlinePlus

    Vertebral radiography; X-ray - spine; Thoracic x-ray; Spine x-ray; Thoracic spine films; Back films ... care provider's office. You will lie on the x-ray table in different positions. If the x-ray ...

  17. Bone x-ray

    MedlinePlus

    ... not being scanned. Alternative Names X-ray - bone Images Skeleton Skeletal spine Osteogenic sarcoma - x-ray References ... urac.org). URAC's accreditation program is an independent audit to verify that A.D.A.M. follows ...

  18. Dental x-rays

    MedlinePlus

    X-ray - teeth; Radiograph - dental; Bitewings; Periapical film; Panoramic film; Digital image ... dentist's office. There are many types of dental x-rays. Some of them are: Bitewing. Shows the crown ...

  19. X-ray (image)

    MedlinePlus

    X-rays are a form of ionizing radiation that can penetrate the body to form an image on ... will be shades of gray depending on density. X-rays can provide information about obstructions, tumors, and other ...

  20. 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)

  1. X-ray

    MedlinePlus

    ... image. For most x-rays, the risk of cancer or defects is very low. Most experts feel that the benefits of appropriate x-ray ... Geleijns J, Tack D. Medical physics: radiation risks. In: Adam A, Dixon AK, Gillard ...

  2. X-Ray Toolkit

    SciTech Connect

    2015-10-20

    Radiographic Image Acquisition & Processing Software for Security Markets. Used in operation of commercial x-ray scanners and manipulation of x-ray images for emergency responders including State, Local, Federal, and US Military bomb technicians and analysts.

  3. Sinus x-ray

    MedlinePlus

    Paranasal sinus radiography; X-ray - sinuses ... sinus x-ray is taken in a hospital radiology department. Or the x-ray may be taken ... Brown J, Rout J. ENT, neck, and dental radiology. In: Adam A, Dixon AK, Gillard JH Schaefer- ...

  4. Hand x-ray

    MedlinePlus

    X-ray - hand ... A hand x-ray is taken in a hospital radiology department or your health care provider's office by an ... technician. You will be asked to place your hand on the x-ray table, and keep it ...

  5. Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6′)-Ie-APH(2′′)-Ia revealed by crystallographic and small-angle X-ray scattering analysis

    PubMed Central

    Smith, Clyde A.; Toth, Marta; Weiss, Thomas M.; Frase, Hilary; Vakulenko, Sergei B.

    2014-01-01

    Broad-spectrum resistance to aminoglycoside antibiotics in clinically important Gram-positive staphylococcal and entero­coccal pathogens is primarily conferred by the bifunctional enzyme AAC(6′)-Ie-APH(2′′)-Ia. This enzyme possesses an N-terminal coenzyme A-dependent acetyltransferase domain [AAC(6′)-Ie] and a C-terminal GTP-dependent phosphotransferase domain [APH(2′′)-Ia], and together they produce resistance to almost all known aminoglycosides in clinical use. Despite considerable effort over the last two or more decades, structural details of AAC(6′)-Ie-APH(2′′)-Ia have remained elusive. In a recent breakthrough, the structure of the isolated C-terminal APH(2′′)-Ia enzyme was determined as the binary Mg2GDP complex. Here, the high-resolution structure of the N-terminal AAC(6′)-Ie enzyme is reported as a ternary kanamycin/coenzyme A abortive complex. The structure of the full-length bifunctional enzyme has subsequently been elucidated based upon small-angle X-ray scattering data using the two crystallographic models. The AAC(6′)-Ie enzyme is joined to APH(2′′)-Ia by a short, predominantly rigid linker at the N-terminal end of a long α-helix. This α-helix is in turn intrinsically associated with the N-terminus of APH(2′′)-Ia. This structural arrangement supports earlier observations that the presence of the intact α-helix is essential to the activity of both functionalities of the full-length AAC(6′)-Ie-APH(2′′)-Ia enzyme. PMID:25286858

  6. X-ray crystallography of viruses.

    PubMed

    Verdaguer, Nuria; Garriga, Damià; Fita, Ignacio

    2013-01-01

    For about 30 years X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography. Landmarks of new virus structures determinations, such as the ones from the first animal viruses or from the first membrane-containing viruses, have often been associated to methodological breakthroughs in X-ray crystallography. In this chapter we present the common ground of proteins and virus crystallography with an emphasis in the peculiarities of virus studies. For example, the solution of the phase problem, a central issue in X-ray diffraction, has benefited enormously from the presence of non-crystallographic symmetry in virus crystals.

  7. Crystallographic Instrumentation

    NASA Astrophysics Data System (ADS)

    Aslanov, L. A.; Fetisov, G. V.; Howard, J. A. K.

    1998-07-01

    Innovations in crystallographic instrumentation and the rapid development of methods of diffraction measurement have led to a vast improvement in our ability to determine crystal and molecular structure. This up-to-date resource will allow the reader to harness the potential of X-ray diffraction instruments. Different sources of X-radiation used in crystallography are introduced, including synchrotron radiation, as well as a systematic review of detectors for X-rays and basic instruments for single crystal and powder diffractometry. The principles of the diffraction experiment are discussed and related to their practical application with a comparative description of different scan procedures. Diffraction data collection and processing are also reviewed and methods for error correction are described. This book will provide a useful guide for researchers and students starting in this area of science, as well as skilled crystallographers.

  8. X-ray binaries

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Satellite X-ray experiments and ground-based programs aimed at observation of X-ray binaries are discussed. Experiments aboard OAO-3, OSO-8, Ariel 5, Uhuru, and Skylab are included along with rocket and ground-based observations. Major topics covered are: Her X-1, Cyg X-3, Cen X-3, Cyg X-1, the transient source A0620-00, other possible X-ray binaries, and plans and prospects for future observational programs.

  9. Anisotropic x ray magnetic linear dichroism - Its importance for the analysis of soft x ray spectra of magnetic oxides

    SciTech Connect

    van der Laan, G.; Arenholz, Elke

    2008-07-02

    Using spectroscopic information for x ray magnetometry and magnetic microscopy requires detailed theoretical understanding of spectral shape and magnitude of dichroism signals. We have shown unambiguously that--contrary to common belief--spectral shape and magnitude of x ray magnetic linear dichroism (XMLD) are not only determined by the relative orientation of magnetic moments and x ray polarization, but also their orientations relative to the crystallographic axes must be taken into account for accurate interpretation of XMLD data.

  10. Chest X-Ray

    MedlinePlus Videos and Cool Tools

    ... Site Index A-Z Spotlight Recently posted: Anal Cancer Facet Joint Block Video: Lung Cancer Screening Video: Upper GI Tract X-ray Video: ... of lung conditions such as pneumonia, emphysema and cancer. A chest x-ray requires no special preparation. ...

  11. X-ray Spectrometry.

    ERIC Educational Resources Information Center

    Markowicz, Andrzej A.; Van Grieken, Rene E.

    1984-01-01

    Provided is a selective literature survey of X-ray spectrometry from late 1981 to late 1983. Literature examined focuses on: excitation (photon and electron excitation and particle-induced X-ray emission; detection (wavelength-dispersive and energy-dispersive spectrometry); instrumentation and techniques; and on such quantitative analytical…

  12. X-ray beamsplitter

    DOEpatents

    Ceglio, N.M.; Stearns, D.G.; Hawryluk, A.M.; Barbee, T.W. Jr.

    1987-08-07

    An x-ray beamsplitter which splits an x-ray beam into two coherent parts by reflecting and transmitting some fraction of an incident beam has applications for x-ray interferometry, x-ray holography, x-ray beam manipulation, and x-ray laser cavity output couplers. The beamsplitter is formed of a wavelength selective multilayer thin film supported by a very thin x-ray transparent membrane. The beamsplitter resonantly transmits and reflects x-rays through thin film interference effects. A thin film is formed of 5--50 pairs of alternate Mo/Si layers with a period of 20--250 A. The support membrane is 10--200 nm of silicon nitride or boron nitride. The multilayer/support membrane structure is formed across a window in a substrate by first forming the structure on a solid substrate and then forming a window in the substrate to leave a free-standing structure over the window. 6 figs.

  13. X-Ray

    MedlinePlus

    ... of gray. For some types of X-ray tests, a contrast medium — such as iodine or barium — is introduced into your body to provide greater detail on the images. X-ray technology is used to examine many parts of the ...

  14. Abdominal x-ray

    MedlinePlus

    An abdominal x-ray is an imaging test to look at organs and structures in the abdomen. Organs include the spleen, stomach, and intestines. When the test is done to look at the bladder and kidney structures, it is called a KUB (kidneys, ureters, bladder) x-ray.

  15. X-ray beamsplitter

    DOEpatents

    Ceglio, Natale M.; Stearns, Daniel S.; Hawryluk, Andrew M.; Barbee, Jr., Troy W.

    1989-01-01

    An x-ray beamsplitter which splits an x-ray beam into two coherent parts by reflecting and transmitting some fraction of an incident beam has applications for x-ray interferometry, x-ray holography, x-ray beam manipulation, and x-ray laser cavity output couplers. The beamsplitter is formed of a wavelength selective multilayer thin film supported by a very thin x-ray transparent membrane. The beamsplitter resonantly transmits and reflects x-rays through thin film interference effects. A thin film is formed of 5-50 pairs of alternate Mo/Si layers with a period of 20-250 A. The support membrane is 10-200 nm of silicon nitride or boron nitride. The multilayer/support membrane structure is formed across a window in a substrate by first forming the structure on a solid substrate and then forming a window in the substrate to leave a free-standing structure over the window.

  16. X-ray lasers

    SciTech Connect

    Elton, R.C.

    1990-01-01

    This paper provides a source that surveys the fundamentals of x-ray lasers and summarizes recent advances. The author emphasizes x-ray lasers created using high temperature plasmas as the medium. Specific topics discussed included electron-collisional excitation pumping, plasma laser pumping, and gamma-ray lasers. Numerous literature references provided.

  17. X-ray lasers

    SciTech Connect

    Elton, R.C.

    1990-01-01

    This book is both an introduction to x-ray lasers and a how-to-guide for specialists. It provides comprehensive overview and describes useful examples of analysis and experiments as background and guidance for researchers undertaking new laser designs. The book collects the knowledge and experience gained in two decades of x-ray laser development.

  18. X-ray Spectrometry.

    ERIC Educational Resources Information Center

    Markowicz, Andrzej A.; Van Grieken, Rene E.

    1984-01-01

    Provided is a selective literature survey of X-ray spectrometry from late 1981 to late 1983. Literature examined focuses on: excitation (photon and electron excitation and particle-induced X-ray emission; detection (wavelength-dispersive and energy-dispersive spectrometry); instrumentation and techniques; and on such quantitative analytical…

  19. X-ray Polarimetry

    NASA Astrophysics Data System (ADS)

    Kallman, T.

    In spite of the recent advances in X-ray instrumentation, polarimetry remains an area which has been virtually unexplored in the last 20 years. The scientific motivation to study polarization has increased during this time: emission models designed to repro- duce X-ray spectra can be tested using polarization, and polarization detected in other wavelength bands makes clear predictions as to the X-ray polarization. Polarization remains the only way to infer geometrical properties of sources which are too small to be spatially resolved. At the same time, there has been recent progress in instrumen- tation which is likely to allow searches for X-ray polarization at levels significantly below what was possible for early detectors. In this talk I will review the history of X-ray polarimetry, discuss some experimental techniques and the scientific problems which can be addressed by future experiments.

  20. 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.

  1. X-ray laser

    DOEpatents

    Nilsen, Joseph

    1991-01-01

    An X-ray laser (10) that lases between the K edges of carbon and oxygen, i.e. between 44 and 23 Angstroms, is provided. The laser comprises a silicon (12) and dysprosium (14) foil combination (16) that is driven by two beams (18, 20) of intense line focused (22, 24) optical laser radiation. Ground state nickel-like dysprosium ions (34) are resonantly photo-pumped to their upper X-ray laser state by line emission from hydrogen-like silicon ions (32). The novel X-ray laser should prove especially useful for the microscopy of biological specimens.

  2. X-ray superbubbles

    NASA Technical Reports Server (NTRS)

    Cash, W.

    1983-01-01

    Four regions of the galaxy, the Cygnus Superbubble, the Eta Carina complex, the Orion/Eridanus complex, and the Gum Nebula, are discussed as examples of collective effects in the interstellar medium. All four regions share certain features, indicating a common structure. The selection effects which determine the observable X-ray properties of the superbubbles are discussed, and it is demonstrated that only a very few more in our Galaxy can be detected in X rays. X-ray observation of extragalactic superbubbles is shown to be possible but requires the capabilities of a large, high quality, AXAF class observatory.

  3. Abdomen X-Ray (Radiography)

    MedlinePlus

    ... News Physician Resources Professions Site Index A-Z X-ray (Radiography) - Abdomen Abdominal x-ray uses a very ... of an abdominal x-ray? What is abdominal x-ray? An x-ray (radiograph) is a noninvasive medical ...

  4. X-ray calorimeters

    NASA Astrophysics Data System (ADS)

    Porter, F. Scott

    X-ray calorimeter instruments for astrophysics have seen rapid development since they were invented in 1984. The prime instrument on all currently planned X-ray spectroscopic observatories is based on calorimeter technology. This relatively simple detection concept that senses the energy of an incident photon by measuring the temperature rise of an absorber material at very low temperatures can form the basis of a very high-performance, non-dispersive spectrometer. State-of-theart calorimeter instruments have resolving powers of over 3000, large simultaneous bandpasses, and near unit efficiency. This coupled with the intrinsic imaging capability of a pixilated X-ray calorimeter array, allows true spectral-spatial instruments to be constructed. This chapter briefly reviews the detection scheme, the state of the art in X-ray calorimeter instruments and the future outlook for this technology.

  5. X-ray - skeleton

    MedlinePlus

    ... medlineplus.gov/ency/article/003381.htm X-ray - skeleton To use the sharing features on this page, ... ray views may be uncomfortable. If the whole skeleton is being imaged, the test usually takes 1 ...

  6. X-Ray Diffraction.

    ERIC Educational Resources Information Center

    Smith, D. K.; Smith, K. L.

    1980-01-01

    Reviews applications in research and analytical characterization of compounds and materials in the field of X-ray diffraction, emphasizing new developments in applications and instrumentation in both single crystal and powder diffraction. Cites 414 references. (CS)

  7. Cosmic x ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, Dan; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1992-01-01

    This final report covers the period 1 January 1985 - 31 March 1992. It is divided into the following sections: the soft x-ray background; proportional counter and filter calibrations; sounding rocket flight preparations; new sounding rocket payload: x-ray calorimeter; and theoretical studies. Staff, publications, conference proceedings, invited talks, contributed talks, colloquia and seminars, public service lectures, and Ph. D. theses are listed.

  8. X-ray Binaries

    NASA Astrophysics Data System (ADS)

    Lewin, Walter H. G.; van Paradijs, Jan; van den Heuvel, Edward Peter Jacobus

    1997-01-01

    Preface; 1. The properties of X-ray binaries, N. E. White, F. Nagase and A. N. Parmar; 2. Optical and ultraviolet observations of X-ray binaries J. van Paradijs and J. E. McClintock; 3. Black-hole binaries Y. Tanaka and W. H. G. Lewin; 4. X-ray bursts Walter H. G. Lewin, Jan Van Paradijs and Ronald E. Taam; 5. Millisecond pulsars D. Bhattacharya; 6. Rapid aperiodic variability in binaries M. van der Klis; 7. Radio properties of X-ray binaries R. M. Hjellming and X. Han; 8. Cataclysmic variable stars France Anne-Dominic Córdova; 9. Normal galaxies and their X-ray binary populations G. Fabbiano; 10. Accretion in close binaries Andrew King; 11. Formation and evolution of neutron stars and black holes in binaries F. Verbunt and E. P. J. van den Heuvel; 12. The magnetic fields of neutron stars and their evolution D. Bhattacharya and G. Srinivasan; 13. Cosmic gamma-ray bursts K. Hurley; 14. A catalogue of X-ray binaries Jan van Paradijs; 15. A compilation of cataclysmic binaries with known or suspected orbital periods Hans Ritter and Ulrich Kolb; References; Index.

  9. Clocking femtosecond X rays.

    PubMed

    Cavalieri, A L; Fritz, D M; Lee, S H; Bucksbaum, P H; Reis, D A; Rudati, J; Mills, D M; Fuoss, P H; Stephenson, G B; Kao, C C; Siddons, D P; Lowney, D P; Macphee, A G; Weinstein, D; Falcone, R W; Pahl, R; Als-Nielsen, J; Blome, C; Düsterer, S; Ischebeck, R; Schlarb, H; Schulte-Schrepping, H; Tschentscher, Th; Schneider, J; Hignette, O; Sette, F; Sokolowski-Tinten, K; Chapman, H N; Lee, R W; Hansen, T N; Synnergren, O; Larsson, J; Techert, S; Sheppard, J; Wark, J S; Bergh, M; Caleman, C; Huldt, G; van der Spoel, D; Timneanu, N; Hajdu, J; Akre, R A; Bong, E; Emma, P; Krejcik, P; Arthur, J; Brennan, S; Gaffney, K J; Lindenberg, A M; Luening, K; Hastings, J B

    2005-03-25

    Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unprecedented brightness and short pulse duration. However, time-resolved studies at the resolution of the x-ray pulse duration are hampered by the inability to precisely synchronize an external laser to the accelerator. At the Sub-Picosecond Pulse Source at the Stanford Linear-Accelerator Center we solved this problem by measuring the arrival time of each high energy electron bunch with electro-optic sampling. This measurement indirectly determined the arrival time of each x-ray pulse relative to an external pump laser pulse with a time resolution of better than 60 fs rms.

  10. X-ray Reflection

    NASA Astrophysics Data System (ADS)

    Fabian, A. C.; Ross, R. R.

    2010-12-01

    Material irradiated by X-rays produces backscattered radiation which is commonly known as the Reflection Spectrum. It consists of a structured continuum, due at high energies to the competition between photoelectric absorption and electron scattering enhanced at low energies by emission from the material itself, together with a complex line spectrum. We briefly review the history of X-ray reflection in astronomy and discuss various methods for computing the reflection spectrum from cold and ionized gas, illustrated with results from our own work reflionx. We discuss how the reflection spectrum can be used to obtain the geometry of the accretion flow, particularly the inner regions around black holes and neutron stars.

  11. X-ray fluorescence experiment

    NASA Technical Reports Server (NTRS)

    Adler, I.; Trombka, J. I.; Gerard, J.; Schmadebeck, R.; Lowman, P.; Blodgett, H.; Yin, L.; Eller, E.; Lamothe, R.; Gorenstein, P.

    1972-01-01

    The preliminary results from the Sco X-1 and Cyg X-1 obtained from the Apollo 15 X-ray detector data are presented along with preliminary results of the X-ray fluorescence spectrometric data of the lunar surface composition. The production of the characteristic X-rays following the interaction of solar X-rays with the lunar surface is described along with the X-ray spectrometer. Preliminary analyses of the astronomical X-ray observation and the X-ray fluorescence data are presented.

  12. X-ray beam finder

    DOEpatents

    Gilbert, H.W.

    1983-06-16

    An X-ray beam finder for locating a focal spot of an X-ray tube includes a mass of X-ray opaque material having first and second axially-aligned, parallel-opposed faces connected by a plurality of substantially identical parallel holes perpendicular to the faces and a film holder for holding X-ray sensitive film tightly against one face while the other face is placed in contact with the window of an X-ray head.

  13. Neck x-ray

    MedlinePlus

    ... look at cervical vertebrae. These are the 7 bones of the spine in the neck. ... A neck x-ray can detect: Bone joint that is out of position (dislocation) Breathing in a foreign object Broken bone (fracture) Disk problems (disks ...

  14. Extremity x-ray

    MedlinePlus

    ... this test if you have signs of: A fracture Tumor Arthritis (inflammation of the joints) Normal Results The x-ray shows normal structures for the age of the person. What Abnormal Results Mean ... bone (fracture) Dislocated bone Osteomyelitis (infection) Arthritis Other conditions for ...

  15. Subgroup report on hard x-ray microprobes

    SciTech Connect

    Ice, G.E.; Barbee, T.; Bionta, R.; Howells, M.; Thompson, A.C.; Yun, W.

    1994-09-01

    The increasing availability of synchrotron x-ray sources has stimulated the development of advanced hard x-ray (E{>=}5 keV) microprobes. New x-ray optics have been demonstrated which show promise for achieving intense submicron hard x-ray probes. These probes will be used for extraordinary elemental detection by x-ray fluorescence/absorption and for microdiffraction to identify phase and strain. The inherent elemental and crystallographic sensitivity of an x-ray microprobe and its inherently nondestructive and penetrating nature makes the development of an advanced hard x-ray microprobe an important national goal. In this workshop state-of-the-art hard x-ray microprobe optics were described and future directions were discussed. Gene Ice, Oak Ridge National Laboratory (ORNL), presented an overview of the current status of hard x-ray microprobe optics and described the use of crystal spectrometers to improve minimum detectable limits in fluorescent microprobe experiments. Al Thompson, Lawrence Berkeley Laboratory (LBL), described work at the Center for X-ray Optics to develop a hard x-ray microprobe based on Kirkpatrick-Baez (KB) optics. Al Thompson also showed the results of some experimental measurements with their KB optics. Malcolm Howells presented a method for bending elliptical mirrors and Troy Barbee commented on the use of graded d spacings to achieve highest efficiency in KB multilayer microfocusing. Richard Bionta, Lawrence Livermore National Laboratory (LLNL), described the development of the first hard x-ray zone plates and future promise of so called {open_quotes}jelly roll{close_quotes} or sputter slice zone plates. Wenbing Yun, Argonne National Laboratory (ANL), described characterization of jelly roll and lithographically produced zone plates and described the application of zone plates to focus extremely narrow bandwidths by nuclear resonance. This report summarizes the presentations of the workshop subgroup on hard x-ray microprobes.

  16. X-ray crystallographic analysis of 3-(2'-phenyl-2,4'-bithiazole-4-carboxamido) propyldimethylsulphonium iodide, an analogue of the DNA-binding portion of bleomycin A2.

    PubMed

    Kuroda, R; Neidle, S; Riordan, J M; Sakai, T T

    1982-08-11

    The crystal and molecular structure of the title compound, an analogue of the DNA binding region of bleomycin A2, has been determined by X-ray crystallography. All the three independent molecules in an asymmetric unit are approximately planar with fully extended side chains. A computer graphics model-building study has shown that the phenyl group and the second thiazole ring can be intercalated between the base pairs of the double-stranded deoxydinucleoside phosphate d(CpG), and also that the sulphonium cation can interact with a backbone phosphate group. This model is in accord with NMR spectral data.

  17. X-ray crystallographic analysis of 3-(2'-phenyl-2,4'-bithiazole-4-carboxamido) propyldimethylsulphonium iodide, an analogue of the DNA-binding portion of bleomycin A2.

    PubMed Central

    Kuroda, R; Neidle, S; Riordan, J M; Sakai, T T

    1982-01-01

    The crystal and molecular structure of the title compound, an analogue of the DNA binding region of bleomycin A2, has been determined by X-ray crystallography. All the three independent molecules in an asymmetric unit are approximately planar with fully extended side chains. A computer graphics model-building study has shown that the phenyl group and the second thiazole ring can be intercalated between the base pairs of the double-stranded deoxydinucleoside phosphate d(CpG), and also that the sulphonium cation can interact with a backbone phosphate group. This model is in accord with NMR spectral data. PMID:6182526

  18. Resonant soft X-ray scattering on protein solutions

    NASA Astrophysics Data System (ADS)

    Ye, Dan; Le, Thinh; Wang, Cheng; Zwart, Peter; Gomez, Esther; Gomez, Enrique

    Protein structure is crucial for biological function, such that characterizing protein folding and packing is important for the design of therapeutics and enzymes. We propose resonant soft X-ray scattering (RSOXS) as an approach to study proteins and other biological assemblies in solution. Calculations of the scattering contrast suggest that soft X-ray scattering is more sensitive than hard X-ray scattering, because of contrast generated at the absorption edges of constituent elements such as carbon, nitrogen and oxygen. We have examined the structure of bovine serum albumin (BSA) in solution by RSOXS. We find that by varying incident X-ray energies, we are able to achieve higher scattering contrast near the absorption edge. From our RSOXS scattering result we are able to reconstruct the structure of BSA in 3D. These RSOXS results also agree with hard X-ray experiments, including crystallographic data. Our study demonstrates the potential of RSOXS for studying protein structure in solution.

  19. Time-Resolved X-Ray Crystallography of Heme Proteins

    SciTech Connect

    Srajer, Vukica; Royer, Jr., William E.

    2008-04-29

    Heme proteins, with their natural photosensitivity, are excellent systems for the application of time-resolved crystallographic methods. Ligand dissociation can be readily initiated by a short laser pulse with global structural changes probed at the atomic level by X-rays in real time. Third-generation synchrotrons provide 100-ps X-ray pulses of sufficient intensity for monitoring very fast processes. Successful application of such time-resolved crystallographic experiments requires that the structural changes being monitored are compatible with the crystal lattice. These techniques have recently permitted observing for the first time allosteric transitions in real time for a cooperative dimeric hemoglobin.

  20. Time-resolved x-ray crystallography of heme proteins

    PubMed Central

    Royer, William E.

    2012-01-01

    Heme proteins, with their natural photosensitivity, are excellent systems for the application of time-resolved crystallographic methods. Ligand dissociation can be readily initiated by a short laser pulse with global structural changes probed at the atomic level by X-rays in real time. Third generation synchrotrons provide 100ps X-ray pulses of sufficient intensity for monitoring very fast processes. Successful application of such time-resolved crystallographic experiments requires that the structural changes being monitored are compatible with the crystal lattice. These techniques have permitted observing allosteric transitions in real time for a cooperative dimeric hemoglobin. PMID:18433638

  1. Planetary X ray experiment

    NASA Technical Reports Server (NTRS)

    Anderson, K. A.

    1972-01-01

    Design studies for an X-ray experiment using solid state detectors and for an experiment using a proportional counter for investigating Jovian and Saturnian magnetospheres are reported. Background counting rates through the forward aperture and leakage fluxes are discussed for each design. It is concluded that the best choice of instrument appears to have following the characteristics: (1) two separate multiwire proportional counters for redundancy; (2) passive collimation to restrict the field to about 5 deg, wiregrid modulation collimation to about 0.1 deg angular resolution; (3) no active shielding system around the counter body; and (4) light passive shielding around any portion of the counter body exposed to space to absorb most of the cosmic X-ray background.

  2. Purification, crystallization and preliminary X-ray crystallographic analysis of ST1022, a putative member of the Lrp/AsnC family of transcriptional regulators isolated from Sulfolobus tokodaii strain 7

    SciTech Connect

    Nakano, Noboru; Kumarevel, Thirumananseri Matsunaga, Emiko; Shinkai, Akeo; Kuramitsu, Seiki; Yokoyama, Shigeyuki

    2007-11-01

    A putative member of the Lrp/AsnC family of transcriptional regulators, ST1022 from S. tokodaii strain 7, has been purified and crystallized in the absence and presence of the effector l-glutamine. A molecular-replacement solution was found using the FL11 transcriptional regulator from Pyrococcus sp. OT3 as a model and structural refinement is under way. The Lrp/AsnC family of transcriptional regulators, also known as feast/famine transcriptional regulators, are widely distributed among bacteria and archaea. This family of proteins are likely to be involved in cellular metabolism, with exogenous amino acids functioning as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of ST1022, a member of the Lrp/AsnC family of proteins, is reported with and without exogenous glutamine as the effector molecule. The crystals of native ST1022 and of the putative complex belong to the tetragonal space group I422, with unit-cell parameters a = b = 103.771, c = 73.297 Å and a = b = 103.846, c = 73.992 Å, respectively. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of one monomer per asymmetric unit.

  3. X-ray Spectrometer

    NASA Technical Reports Server (NTRS)

    Porter, F. Scott

    2004-01-01

    The X-ray Spectrometer (XRS) instrument is a revolutionary non-dispersive spectrometer that will form the basis for the Astro-E2 observatory to be launched in 2005. We have recently installed a flight spare X R S microcalorimeter spectrometer at the EBIT-I facility at LLNL replacing the XRS from the earlier Astro-E mission and providing twice the resolution. The X R S microcalorimeter is an x-ray detector that senses the heat deposited by the incident photon. It achieves a high energy resolution by operating at 0.06K and by carefully controlling the heat capacity and thermal conductance. The XRS/EBIT instrument has 32 pixels in a square geometry and achieves an energy resolution of 6 eV at 6 keV, with a bandpass from 0.1 to 12 keV (or more at higher operating temperature). The instrument allows detailed studies of the x-ray line emission of laboratory plasmas. The XRS/EBIT also provides an extensive calibration "library" for the Astro-E2 observatory.

  4. X-Ray Vision

    NASA Technical Reports Server (NTRS)

    Ramsey, B. D.; Elsner, R. F.; Engelhaupt, D.; Kolodziejczak, J. J.; ODell, S. L.; Speegle, C. O.; Weisskopf, M. C.

    2004-01-01

    We are fabricating optics for the hard-x-ray region using electroless nickel replication. The attraction of this process, which has been widely used elsewhere, is that the resulting full shell optics are inherently stable and thus can have very good angular resolution. The challenge with this process is to develop lightweight optics (nickel has a relatively high density of 8.9 g/cu cm), and to keep down the costs of mandrel fabrication. We accomplished the former through the development of high-strength nickel alloys that permit very thin shells without fabrication- and handling-induced deformations. For the latter, we have utilized inexpensive grinding and diamond turning to figure the mandrels and then purpose-built polishing machines to finish the surface. In-house plating tanks and a simple water-bath separation system complete the process. To date we have built shells ranging in size from 5 cm diameter to 50 cm, and with thickness down to 100 micron. For our HERO balloon program, we are fabricating over 200 iridium-coated shells, 250 microns thick, for hard-x-ray imaging up to 75 keV. Early test results on these have indicated half-power-diameters of 15 arcsec. The status of these and other hard-x-ray optics will be reviewed.

  5. X-Ray Vision

    NASA Technical Reports Server (NTRS)

    Ramsey, B. D.; Elsner, R. F.; Engelhaupt, D.; Kolodziejczak, J. J.; ODell, S. L.; Speegle, C. O.; Weisskopf, M. C.

    2004-01-01

    We are fabricating optics for the hard-x-ray region using electroless nickel replication. The attraction of this process, which has been widely used elsewhere, is that the resulting full shell optics are inherently stable and thus can have very good angular resolution. The challenge with this process is to develop lightweight optics (nickel has a relatively high density of 8.9 g/cu cm), and to keep down the costs of mandrel fabrication. We accomplished the former through the development of high-strength nickel alloys that permit very thin shells without fabrication- and handling-induced deformations. For the latter, we have utilized inexpensive grinding and diamond turning to figure the mandrels and then purpose-built polishing machines to finish the surface. In-house plating tanks and a simple water-bath separation system complete the process. To date we have built shells ranging in size from 5 cm diameter to 50 cm, and with thickness down to 100 micron. For our HERO balloon program, we are fabricating over 200 iridium-coated shells, 250 microns thick, for hard-x-ray imaging up to 75 keV. Early test results on these have indicated half-power-diameters of 15 arcsec. The status of these and other hard-x-ray optics will be reviewed.

  6. X-ray Spectrometer

    NASA Technical Reports Server (NTRS)

    Porter, F. Scott

    2004-01-01

    The X-ray Spectrometer (XRS) instrument is a revolutionary non-dispersive spectrometer that will form the basis for the Astro-E2 observatory to be launched in 2005. We have recently installed a flight spare X R S microcalorimeter spectrometer at the EBIT-I facility at LLNL replacing the XRS from the earlier Astro-E mission and providing twice the resolution. The X R S microcalorimeter is an x-ray detector that senses the heat deposited by the incident photon. It achieves a high energy resolution by operating at 0.06K and by carefully controlling the heat capacity and thermal conductance. The XRS/EBIT instrument has 32 pixels in a square geometry and achieves an energy resolution of 6 eV at 6 keV, with a bandpass from 0.1 to 12 keV (or more at higher operating temperature). The instrument allows detailed studies of the x-ray line emission of laboratory plasmas. The XRS/EBIT also provides an extensive calibration "library" for the Astro-E2 observatory.

  7. X-Ray Astronomy

    NASA Technical Reports Server (NTRS)

    Wu, S. T.

    2000-01-01

    Dr. S. N. Zhang has lead a seven member group (Dr. Yuxin Feng, Mr. XuejunSun, Mr. Yongzhong Chen, Mr. Jun Lin, Mr. Yangsen Yao, and Ms. Xiaoling Zhang). This group has carried out the following activities: continued data analysis from space astrophysical missions CGRO, RXTE, ASCA and Chandra. Significant scientific results have been produced as results of their work. They discovered the three-layered accretion disk structure around black holes in X-ray binaries; their paper on this discovery is to appear in the prestigious Science magazine. They have also developed a new method for energy spectral analysis of black hole X-ray binaries; four papers on this topics were presented at the most recent Atlanta AAS meeting. They have also carried Monte-Carlo simulations of X-ray detectors, in support to the hardware development efforts at Marshall Space Flight Center (MSFC). These computation-intensive simulations have been carried out entirely on the computers at UAH. They have also carried out extensive simulations for astrophysical applications, taking advantage of the Monte-Carlo simulation codes developed previously at MSFC and further improved at UAH for detector simulations. One refereed paper and one contribution to conference proceedings have been resulted from this effort.

  8. Structural changes that occur upon photolysis of the Fe(II)a3 - CO complex in the cytochrome ba3-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to CuB

    PubMed Central

    Liu, Bin; Zhang, Yang; Sage, J. Timothy; Soltis, S. Michael; Doukov, Tzanko; Chen, Ying; Stout, C. David; Fee, James A.

    2012-01-01

    The purpose of the work was to provide a crystallographic demonstration of the venerable idea that CO photolyzed from ferrous heme-a3 moves to the nearby cuprous ion in the cytochrome c oxidases. Crystal structures of CO-bound cytochrome ba3-oxidase from Thermus thermophilus, determined at ~ 2.8 – 3.2 Å resolution, reveal a Fe-C distance of ~2.0 Å, a Cu-O distance of 2.4 Å and a Fe-C-O angle of ~126°. Upon photodissociation at 100 K, X-ray structures indicate loss of Fea3-CO and appearance of CuB-CO having a Cu-C distance of ~1.9 Å and an O-Fe distance of ~2.3 Å. Absolute FTIR spectra recorded from single crystals of reduced ba3–CO that had not been exposed to X-ray radiation, showed several peaks around 1975 cm−1; after photolysis at 100 K, the absolute FTIR spectra also showed a significant peak at 2050 cm−1. Analysis of the “light’ minus ‘dark’ difference spectra showed four very sharp CO stretching bands at 1970 cm−1, 1977 cm−1, 1981 cm−1, and 1985 cm−1, previously assigned to the Fea3-CO complex, and a significantly broader CO stretching band centered at ~2050 cm−1, previously assigned to the CO stretching frequency of CuB bound CO. As expected for light propagating along the tetragonal axis of the P43212 space group, the single crystal spectra exhibit negligible dichroism. Absolute FTIR spectrometry of a CO-laden ba3 crystal, exposed to an amount of X-ray radiation required to obtain structural data sets before FTIR characterization, showed a significant signal due to photogenerated CO2 at 2337 cm−1 and one from traces of CO at 2133 cm−1; while bands associated with CO bound to either Fea3 or to CuB in “light” minus “dark” FTIR difference spectra shifted and broadened in response to X-ray exposure. In spite of considerable radiation damage to the crystals, both X-ray analysis at 2.8 and 3.2 Å and FTIR spectra support the long-held position that photolysis of Fea3-CO in cytochrome c oxidases leads to significant

  9. X-ray lithography masking

    NASA Technical Reports Server (NTRS)

    Smith, Henry I. (Inventor); Lim, Michael (Inventor); Carter, James (Inventor); Schattenburg, Mark (Inventor)

    1998-01-01

    X-ray masking apparatus includes a frame having a supporting rim surrounding an x-ray transparent region, a thin membrane of hard inorganic x-ray transparent material attached at its periphery to the supporting rim covering the x-ray transparent region and a layer of x-ray opaque material on the thin membrane inside the x-ray transparent region arranged in a pattern to selectively transmit x-ray energy entering the x-ray transparent region through the membrane to a predetermined image plane separated from the layer by the thin membrane. A method of making the masking apparatus includes depositing back and front layers of hard inorganic x-ray transparent material on front and back surfaces of a substrate, depositing back and front layers of reinforcing material on the back and front layers, respectively, of the hard inorganic x-ray transparent material, removing the material including at least a portion of the substrate and the back layers of an inside region adjacent to the front layer of hard inorganic x-ray transparent material, removing a portion of the front layer of reinforcing material opposite the inside region to expose the surface of the front layer of hard inorganic x-ray transparent material separated from the inside region by the latter front layer, and depositing a layer of x-ray opaque material on the surface of the latter front layer adjacent to the inside region.

  10. Monitoring X-Ray Emission from X-Ray Bursters

    NASA Technical Reports Server (NTRS)

    Kaaret, Philip

    1998-01-01

    The goal of this investigation was to use the All-Sky Monitor on the Rossi X-Ray Timing Explorer (RXTE) in combination with the Burst and Transient Source Experiment on the Compton Gamma-Ray Observatory to simultaneously measure the x-ray (2-12 keV) and hard x-ray (20-100 keV) emission from x-ray bursters. The investigation was successful. We made the first simultaneous measurement of hard and soft x-ray emission and found a strong anticorrelation of hard and soft x-ray emission from the X-Ray Burster 4U 0614+091. The monitoring performed under this investigation was also important in triggering target of opportunity observations of x-ray bursters made under the investigation hard x-ray emission of x-ray bursters approved for RXTE cycles 1 and 2. These observations lead to a number of papers on high-frequency quasi-periodic oscillations and on hard x-ray emission from the x-ray bursters 4U 0614+091 and 4U 1705-44.

  11. Panoramic Dental X-Ray

    MedlinePlus

    ... Physician Resources Professions Site Index A-Z Panoramic Dental X-ray Panoramic dental x-ray uses a ... Your e-mail address: Personal message (optional): Bees: Wax: Notice: RadiologyInfo respects your privacy. Information entered here ...

  12. Soft X-ray Imaging

    SciTech Connect

    Seely, John

    1999-05-20

    The contents of this report cover the following: (1) design of the soft x-ray telescope; (2) fabrication and characterization of the soft x-ray telescope; and (3) experimental implementation at the OMEGA laser facility.

  13. Fluctuation X-Ray Scattering

    SciTech Connect

    Saldin, PI: D. K.; Co-I's: J. C. H. Spence and P. Fromme

    2013-01-25

    The work supported by the grant was aimed at developing novel methods of finding the structures of biomolecules using x-rays from novel sources such as the x-ray free electron laser and modern synchrotrons

  14. Encapsulating X-Ray Detectors

    NASA Technical Reports Server (NTRS)

    Conley, Joseph M.; Bradley, James G.

    1987-01-01

    Vapor-deposited polymer shields crystals from environment while allowing X rays to pass. Polymer coating transparental to X rays applied to mercuric iodide detector in partial vacuum. Coating protects crystal from sublimation, chemical attack, and electrical degradation.

  15. Dual X-ray absorptiometry

    NASA Astrophysics Data System (ADS)

    Altman, Albert; Aaron, Ronald

    2012-07-01

    Dual X-ray absorptiometry is widely used in analyzing body composition and imaging. Both the method and its limitations are related to the Compton and photoelectric contributions to the X-ray attenuation coefficients of materials.

  16. X-Ray Exam: Foot

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Foot KidsHealth > For Parents > X-Ray Exam: Foot Print A A A What's in ... You Have Questions What It Is A foot X-ray is a safe and painless test that uses ...

  17. X-Ray Exam: Wrist

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Wrist KidsHealth > For Parents > X-Ray Exam: Wrist Print A A A What's in ... You Have Questions What It Is A wrist X-ray is a safe and painless test that uses ...

  18. X-Ray Exam: Ankle

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Ankle KidsHealth > For Parents > X-Ray Exam: Ankle Print A A A What's in ... You Have Questions What It Is An ankle X-ray is a safe and painless test that uses ...

  19. X-Ray Exam: Finger

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Finger KidsHealth > For Parents > X-Ray Exam: Finger Print A A A What's in ... You Have Questions What It Is A finger X-ray is a safe and painless test that uses ...

  20. X-Ray Exam: Pelvis

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Pelvis KidsHealth > For Parents > X-Ray Exam: Pelvis Print A A A What's in ... You Have Questions What It Is A pelvis X-ray is a safe and painless test that uses ...

  1. X-Ray Exam: Forearm

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Forearm KidsHealth > For Parents > X-Ray Exam: Forearm Print A A A What's in ... You Have Questions What It Is A forearm X-ray is a safe and painless test that uses ...

  2. Tunable X-ray source

    DOEpatents

    Boyce, James R [Williamsburg, VA

    2011-02-08

    A method for the production of X-ray bunches tunable in both time and energy level by generating multiple photon, X-ray, beams through the use of Thomson scattering. The method of the present invention simultaneously produces two X-ray pulses that are tunable in energy and/or time.

  3. X-Ray Exam: Hip

    MedlinePlus

    ... Old Feeding Your 1- to 2-Year-Old X-Ray Exam: Hip KidsHealth > For Parents > X-Ray Exam: Hip A A A What's in this ... español Radiografía: cadera What It Is A hip X-ray is a safe and painless test that uses ...

  4. X-Ray Exam: Wrist

    MedlinePlus

    ... Old Feeding Your 1- to 2-Year-Old X-Ray Exam: Wrist KidsHealth > For Parents > X-Ray Exam: Wrist A A A What's in this ... español Radiografía: muñeca What It Is A wrist X-ray is a safe and painless test that uses ...

  5. X-Ray Exam: Ankle

    MedlinePlus

    ... Old Feeding Your 1- to 2-Year-Old X-Ray Exam: Ankle KidsHealth > For Parents > X-Ray Exam: Ankle A A A What's in this ... español Radiografía: tobillo What It Is An ankle X-ray is a safe and painless test that uses ...

  6. X-Ray Exam: Foot

    MedlinePlus

    ... Old Feeding Your 1- to 2-Year-Old X-Ray Exam: Foot KidsHealth > For Parents > X-Ray Exam: Foot A A A What's in this ... español Radiografía: pie What It Is A foot X-ray is a safe and painless test that uses ...

  7. Insights into the phosphoryl transfer catalyzed by cAMP-dependent protein kinase: an X-ray crystallographic study of complexes with various metals and peptide substrate SP20.

    PubMed

    Gerlits, Oksana; Waltman, Mary Jo; Taylor, Susan; Langan, Paul; Kovalevsky, Andrey

    2013-05-28

    X-ray structures of several ternary substrate and product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with different bound metal ions. In the PKAc complexes, Mg(2+), Ca(2+), Sr(2+), and Ba(2+) metal ions could bind to the active site and facilitate the phosphoryl transfer reaction. ATP and a substrate peptide (SP20) were modified, and the reaction products ADP and the phosphorylated peptide were found trapped in the enzyme active site. Finally, we determined the structure of a pseudo-Michaelis complex containing Mg(2+), nonhydrolyzable AMP-PCP (β,γ-methyleneadenosine 5'-triphosphate) and SP20. The product structures together with the pseudo-Michaelis complex provide snapshots of different stages of the phosphorylation reaction. Comparison of these structures reveals conformational, coordination, and hydrogen bonding changes that might occur during the reaction and shed new light on its mechanism, roles of metals, and active site residues.

  8. X-ray crystallographic analysis of IMP-1 metallo-β-lactamase complexed with a 3-aminophthalic acid derivative, structure-based drug design, and synthesis of 3,6-disubstituted phthalic acid derivative inhibitors.

    PubMed

    Hiraiwa, Yukiko; Saito, Jun; Watanabe, Takashi; Yamada, Mototsugu; Morinaka, Akihiro; Fukushima, Takayoshi; Kudo, Toshiaki

    2014-10-15

    3-(4-Hydroxypiperidine-1-yl) phthalic acid 1 shows potent inhibitory activity against metallo-β-lactamase, which is known to inactivate β-lactam antibiotics such as carbapenems. Here, the structure of co-crystals of the metallo-β-lactamase IMP-1 and 1 was first analyzed by X-ray crystallography, and then used for structure-based drug design. Four novel compounds bearing substituents at the 6-position were synthesized to produce 3,6-disubstituted phthalic acid derivatives, and their IMP-1 inhibitory activity and synergistic effect with the carbapenem biapenem (BIPM) were evaluated. 3,6-Disubstituted phthalic acid derivatives showed potent IMP-1 inhibitory activity. In particular, compound 13 showed 10-fold higher IMP-1 inhibitory activity as compared with the parent derivative 1. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Fluoride-mediated capture of a noncovalent bound state of a reversible covalent enzyme inhibitor: X-ray crystallographic analysis of an exceptionally potent α-ketoheterocycle inhibitor of fatty acid amide hydrolase.

    PubMed

    Mileni, Mauro; Garfunkle, Joie; Ezzili, Cyrine; Cravatt, Benjamin F; Stevens, Raymond C; Boger, Dale L

    2011-03-23

    Two cocrystal X-ray structures of the exceptionally potent α-ketoheterocycle inhibitor 1 (K(i) = 290 pM) bound to a humanized variant of rat fatty acid amide hydrolase (FAAH) are disclosed, representing noncovalently and covalently bound states of the same inhibitor with the enzyme. Key to securing the structure of the noncovalently bound state of the inhibitor was the inclusion of fluoride ion in the crystallization conditions that is proposed to bind the oxyanion hole precluding inhibitor covalent adduct formation with stabilization of the tetrahedral hemiketal. This permitted the opportunity to detect important noncovalent interactions stabilizing the binding of the inhibitor within the FAAH active site independent of the covalent reaction. Remarkably, noncovalently bound 1 in the presence of fluoride appears to capture the active site in the same "in action" state with the three catalytic residues Ser241-Ser217-Lys142 occupying essentially identical positions observed in the covalently bound structure of 1, suggesting that this technique of introducing fluoride may have important applications in structural studies beyond inhibiting substrate or inhibitor oxyanion hole binding. Key insights to emerge from the studies include the observations that noncovalently bound 1 binds in its ketone (not gem diol) form, that the terminal phenyl group in the acyl side chain of the inhibitor serves as the key anchoring interaction overriding the intricate polar interactions in the cytosolic port, and that the role of the central activating heterocycle is dominated by its intrinsic electron-withdrawing properties. These two structures are also briefly compared with five X-ray structures of α-ketoheterocycle-based inhibitors bound to FAAH recently disclosed.

  10. Fluoride-Mediated Capture of a Noncovalent Bound State of a Reversible Covalent Enzyme Inhibitor: X-ray Crystallographic Analysis of an Exceptionally Potent [alpha]-Ketoheterocycle Inhibitor of Fatty Acid Amide Hydrolase

    SciTech Connect

    Mileni, Mauro; Garfunkle, Joie; Ezzili, Cyrine; Cravatt, Benjamin F.; Stevens, Raymond C.; Boger, Dale L.

    2011-11-02

    Two cocrystal X-ray structures of the exceptionally potent {alpha}-ketoheterocycle inhibitor 1 (K{sub i} = 290 pM) bound to a humanized variant of rat fatty acid amide hydrolase (FAAH) are disclosed, representing noncovalently and covalently bound states of the same inhibitor with the enzyme. Key to securing the structure of the noncovalently bound state of the inhibitor was the inclusion of fluoride ion in the crystallization conditions that is proposed to bind the oxyanion hole precluding inhibitor covalent adduct formation with stabilization of the tetrahedral hemiketal. This permitted the opportunity to detect important noncovalent interactions stabilizing the binding of the inhibitor within the FAAH active site independent of the covalent reaction. Remarkably, noncovalently bound 1 in the presence of fluoride appears to capture the active site in the same 'in action' state with the three catalytic residues Ser241-Ser217-Lys142 occupying essentially identical positions observed in the covalently bound structure of 1, suggesting that this technique of introducing fluoride may have important applications in structural studies beyond inhibiting substrate or inhibitor oxyanion hole binding. Key insights to emerge from the studies include the observations that noncovalently bound 1 binds in its ketone (not gem diol) form, that the terminal phenyl group in the acyl side chain of the inhibitor serves as the key anchoring interaction overriding the intricate polar interactions in the cytosolic port, and that the role of the central activating heterocycle is dominated by its intrinsic electron-withdrawing properties. These two structures are also briefly compared with five X-ray structures of {alpha}-ketoheterocycle-based inhibitors bound to FAAH recently disclosed.

  11. Fluoride-Mediated Capture of a Noncovalent Bound State of a Reversible Covalent Enzyme Inhibitor: X-ray Crystallographic Analysis of an Exceptionally Potent α-Ketoheterocycle Inhibitor of Fatty Acid Amide Hydrolase

    PubMed Central

    Mileni, Mauro; Garfunkle, Joie; Ezzili, Cyrine; Cravatt, Benjamin F.; Stevens, Raymond C.; Boger, Dale L.

    2011-01-01

    Two cocrystal X-ray structures of the exceptionally potent α-ketoheterocycle inhibitor 1 (Ki = 290 pM) bound to a humanized variant of rat fatty acid amide hydrolase (FAAH) are disclosed, representing noncovalently and covalently bound states of the same inhibitor with the enzyme. Key to securing the structure of the noncovalently bound state of the inhibitor was the inclusion of fluoride ion in the crystallization conditions that is proposed to bind the oxyanion hole precluding inhibitor covalent adduct formation with stabilization of the tetrahedral hemiketal. This permitted the opportunity to detect important noncovalent interactions stabilizing the binding of the inhibitor within the FAAH active site independent of the covalent reaction. Remarkably, noncovalently bound 1 in the presence of fluoride appears to capture the active site in the same “in action” state with the three catalytic residues Ser241–Ser217–Lys142 occupying essentially identical positions observed in the covalently bound structure of 1, suggesting that this technique of introducing fluoride may have important applications in structural studies beyond inhibiting substrate or inhibitor oxyanion hole binding. Key insights to emerge from the studies include the observations that noncovalently bound 1 binds in its ketone (not gem diol) form, that the terminal phenyl group in the acyl side chain of the inhibitor serves as the key anchoring interaction overriding the intricate polar interactions in the cytosolic port, and that the role of the central activating heterocycle is dominated by its intrinsic electron-withdrawing properties. These two structures are also briefly compared with five X-ray structures of α-ketoheterocycle-based inhibitors bound to FAAH recently disclosed. PMID:21355555

  12. SMM x ray polychromator

    NASA Technical Reports Server (NTRS)

    Saba, J. L. R.

    1993-01-01

    The objective of the X-ray Polychromator (XRP) experiment was to study the physical properties of solar flare plasma and its relation to the parent active region to understand better the flare mechanism and related solar activity. Observations were made to determine the temperature, density, and dynamic structure of the pre-flare and flare plasma as a function of wavelength, space and time, the extent to which the flare plasma departs from thermal equilibrium, and the variation of this departure with time. The experiment also determines the temperature and density structure of active regions and flare-induced changes in the regions.

  13. X-ray satellite

    NASA Technical Reports Server (NTRS)

    1985-01-01

    An overview of the second quarter 1985 development of the X-ray satellite project is presented. It is shown that the project is proceeding according to plan and that the projected launch date of September 9, 1987 is on schedule. An overview of the work completed and underway on the systems, subsystems, payload, assembly, ground equipment and interfaces is presented. Problem areas shown include cost increases in the area of focal instrumentation, the star sensor light scattering requirements, and postponements in the data transmission subsystems.

  14. X-ray lithography source

    DOEpatents

    Piestrup, Melvin A.; Boyers, David G.; Pincus, Cary

    1991-01-01

    A high-intensity, inexpensive X-ray source for X-ray lithography for the production of integrated circuits. Foil stacks are bombarded with a high-energy electron beam of 25 to 250 MeV to produce a flux of soft X-rays of 500 eV to 3 keV. Methods of increasing the total X-ray power and making the cross section of the X-ray beam uniform are described. Methods of obtaining the desired X-ray-beam field size, optimum frequency spectrum and elminating the neutron flux are all described. A method of obtaining a plurality of station operation is also described which makes the process more efficient and economical. The satisfying of these issues makes transition radiation an exellent moderate-priced X-ray source for lithography.

  15. X-ray lithography source

    DOEpatents

    Piestrup, M.A.; Boyers, D.G.; Pincus, C.

    1991-12-31

    A high-intensity, inexpensive X-ray source for X-ray lithography for the production of integrated circuits is disclosed. Foil stacks are bombarded with a high-energy electron beam of 25 to 250 MeV to produce a flux of soft X-rays of 500 eV to 3 keV. Methods of increasing the total X-ray power and making the cross section of the X-ray beam uniform are described. Methods of obtaining the desired X-ray-beam field size, optimum frequency spectrum and eliminating the neutron flux are all described. A method of obtaining a plurality of station operation is also described which makes the process more efficient and economical. The satisfying of these issues makes transition radiation an excellent moderate-priced X-ray source for lithography. 26 figures.

  16. Polycapillary X-ray optics for macromolecular crystallography

    NASA Astrophysics Data System (ADS)

    Hofmann, Frank Alexander

    Macromolecules, such as proteins, nucleic acids, and carbohydrates can be found in every living cell. Nearly every chemical reaction in a cell requires the presence of enzymes, which belong to the class of proteins. In order to understand these processes, it is vital to know the three-dimensional structure of enzymes and other macromolecules. One way to find the structure is X-ray crystallography. Macromolecules are very large compared to most inorganic molecules and they have a very weak diffracting power. Structure determination with X-ray crystallography requires single crystals. Single crystals of macromolecules are difficult to grow except to very small size. Thus, intense X-ray beams are required. In order to generate intense X-ray beams, many crystallographers use synchrotrons. Intense beams can also be generated using X-ray optics. The work described includes a systematic study of the application of both collimating and slightly focusing polycapillary optics to X-ray crystallographic structure determination of egg-white lysozyme using a standard rotating anode source and a low power tabletop microfocusing source. The results summarize a series of measurements comparing duplicate data sets obtained from an individual crystal on a rotating anode source. Intensity and data quality are discussed for measurements with a pinhole collimator, a collimating polycapillary optic, and a focusing polycapillary optic. The collected data were analyzed using conventional analysis software.

  17. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.

    PubMed

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I; Wilmanns, Matthias; Vértessy, Beáta G

    2013-12-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure.

  18. Crystallographic X-ray analyses of Yb@C(2v)(3)-C80 reveal a feasible rule that governs the location of a rare earth metal inside a medium-sized fullerene.

    PubMed

    Lu, Xing; Lian, Yongfu; Beavers, Christine M; Mizorogi, Naomi; Slanina, Zdenek; Nagase, Shigeru; Akasaka, Takeshi

    2011-07-20

    Single crystal X-ray diffraction studies of Yb@C(2v)(3)-C(80)·Ni(II)(OEP)·CS(2)·1.5C(6)H(6) (OEP = octaethylporphinate) reveal that a relatively flat region of the fullerene interacts with the Ni(II)(OEP) molecule, featuring shape-matching interactions. Surprisingly, it is found that the internal metal is located under a hexagonal carbon ring apart from the 2-fold axis of the C(2v)(3)-C(80) cage, presenting the first example of metallofullerenes with an asymmetrically positioned metal. Such an anomalous location of Yb(2+) is associated with its strong ability to pursue a large coordination number and the lack of hexagon along the C(2) axis of C(2v)(3)-C(80). It is accordingly assumed that a suitable cage hexagon is most likely to be preferred by the single rare earth metal to stay behind inside a medium-sized fullerene, such as C(80) and C(82).

  19. Noncovalent association phenomena of 2,5-dihydroxybenzoic acid with cyclic and linear oligosaccharides. A matrix-assisted laser desorption/ionization time-of-flight mass spectrometric and X-ray crystallographic study.

    PubMed

    Mele, A; Malpezzi, L

    2000-03-01

    D-Glucose and 19 glucose derivatives were investigated by positive and negative ion matrix assisted laser desorption/ionization time-of-flight mass spectrometry using 2,5-dihydroxybenzoic acid (DHB) as the matrix. The set of substrates includes oligomers of amylose and cellulose, native alpha-, beta-, and gamma-cyclodextrin, and chemically modified beta- and gamma-cyclodextrins. These analytes were chosen to modulate molecular weight, polarity, and capability of establishing noncovalent interactions with guest molecules. In the negative-ion mode, the DHB matrix gave rise to charged multicomponent adducts of type [M + DHB - H]- (M = oligosaccharide) selectively for those analytes matching the following conditions: (i) underivatized chemical structure and (ii) number of glucose units > or = 4. In the positive-ion polarity, only some amylose and cellulose derivatives and methylated beta-cyclodextrins provided small amount of cationized adducts with the matrix of type [M + DHB + X]+ (X = Na or K), along with ubiquitous [M + X]+ ions. The results are discussed by taking into account analyte-matrix association phenomena, such as hydrogen bond and inclusion phenomena, as a function of the molecular structure of the analyte. The conclusions derived by mass spectrometric data are compared with the X-ray diffraction data obtained on a single crystal of the 1:1 alpha-cyclodextrin - DHB noncovalent adduct.

  20. Insights into the Phosphoryl Transfer Catalyzed by cAMP-Dependent Protein Kinase: An X-ray Crystallographic Study of Complexes with Various Metals and Peptide Substrate SP20

    PubMed Central

    2013-01-01

    X-ray structures of several ternary substrate and product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with different bound metal ions. In the PKAc complexes, Mg2+, Ca2+, Sr2+, and Ba2+ metal ions could bind to the active site and facilitate the phosphoryl transfer reaction. ATP and a substrate peptide (SP20) were modified, and the reaction products ADP and the phosphorylated peptide were found trapped in the enzyme active site. Finally, we determined the structure of a pseudo-Michaelis complex containing Mg2+, nonhydrolyzable AMP-PCP (β,γ-methyleneadenosine 5′-triphosphate) and SP20. The product structures together with the pseudo-Michaelis complex provide snapshots of different stages of the phosphorylation reaction. Comparison of these structures reveals conformational, coordination, and hydrogen bonding changes that might occur during the reaction and shed new light on its mechanism, roles of metals, and active site residues. PMID:23672593

  1. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling

    PubMed Central

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I.; Wilmanns, Matthias; Vértessy, Beáta G.

    2013-01-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason–Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy (31P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme–product complex structure. PMID:23982515

  2. Crystallization and preliminary X-ray crystallographic study of the wild type and two mutants of the CP1 hydrolytic domain from Aquifex aeolicus leucyl-tRNA synthetase

    SciTech Connect

    Cura, Vincent; Olieric, Natacha; Guichard, Alexandre; Moras, Dino; Cavarelli, Jean

    2005-10-01

    The wild-type editing CP1 domain of A. aeolicus leucyl-tRNA synthetase and two mutant CP1 domains have been overexpressed, purified and crystallized. X-ray diffraction data have been collected to 1.8 Å, which has enabled determination of the structures by molecular replacement. The editing or hydrolytic CP1 domain of leucyl-tRNA synthetase (LeuRS) hydrolyses several misactivated amino acids. The CP1 domain of Aquifex aeolicus LeuRS was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. Crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 Å. Crystals diffract to beyond 1.8 Å resolution and contain two monomers in the asymmetric unit. Two CP1 mutants in which a conserved threonine residue essential for the fidelity of the hydrolytic pathway is mutated to alanine or glutamic acid have also been expressed and crystallized. Crystals of the two CP1 mutants are isomorphs of the wild type and diffract to beyond 1.9 Å resolution. All structures were solved by molecular-replacement techniques.

  3. Hard X-Ray Emission of X-Ray Bursters

    NASA Technical Reports Server (NTRS)

    Kaaret, P.

    1999-01-01

    The primary goal of this proposal was to perform an accurate measurement of the broadband x-ray spectrum of a neutron-star low-mass x-ray binary found in a hard x-ray state. This goal was accomplished using data obtained under another proposal, which has provided exciting new information on the hard x-ray emission of neutron-star low-mass x-ray binaries. In "BeppoSAX Observations of the Atoll X-Ray Binary 4U0614+091", we present our analysis of the spectrum of 4U0614+091 over the energy band from 0.3-150 keV. Our data confirm the presence of a hard x-ray tail that can be modeled as thermal Comptonization of low-energy photons on electrons having a very high temperature, greater than 220 keV, or as a non-thermal powerlaw. Such a very hard x-ray spectrum has not been previously seen from neutron-star low-mass x-ray binaries. We also detected a spectral feature that can be interpreted as reprocessing, via Compton reflection, of the direct emission by an optically-thick disk and found a correlation between the photon index of the power-law tail and the fraction of radiation reflected which is similar to the correlation found for black hole candidate x-ray binaries and Seyfert galaxies. A secondary goal was to measure the timing properties of the x-ray emission from neutronstar low-mass x-ray binaries in their low/hard states.

  4. X-ray crystallographic and tungsten-183 nuclear magnetic resonance structural studies of the [M4(H2O)2(XW9O34) 2]10- heteropolyanions (M = COII or Zn, X = P or As)

    USGS Publications Warehouse

    Evans, H.T.; Tourne, C.M.; Tourne, G.F.; Weakley, T.J.R.

    1986-01-01

    The crystal structures of K10[Co4(H2O)2(PW9O 34)2]??22H2O (1) and isomorphous K10[Zn4(H2O)2(AsW9O 34)2]??23H2O (2) have been determined {Mo-K?? radiation, space group P21/n, Z = 2; (1) a = 15.794(2), b = 21.360(2), c = 12.312(1) A??, ?? = 91.96??, R = 0.084 for 3 242 observed reflections [I ??? 3??(I)]; (2) a = 15.842(4), b = 21.327(5), c = 12.308(4) A??, ?? = 92.42(4)??, R = 0.066 for 4 675 observed reflections [F ??? 3??(F)]}. The anions have crystallographic symmetry 1 and non-crystallographic symmetry very close to 2/m (C2h). Each consists of two [XW9O34]9- moieties [??-B isomers; X = P (1) or As (2)] linked via four CoIIO6 or ZnO6 groups. Two Co or Zn atoms each carry a water ligand. The 183W n.m.r. spectra of the anions [Zn4(H2O)2(XW9O34) 2]10- (X = P or As) confirm that the anions retain 2/m symmetry in aqueous solution. Homonuclear coupling constants between 183W atoms are 5.8-9.0 Hz for adjacent WO6 octahedra sharing edges, and 19.6-25.0 Hz for octahedra sharing corners.

  5. Miniature x-ray source

    DOEpatents

    Trebes, James E.; Stone, Gary F.; Bell, Perry M.; Robinson, Ronald B.; Chornenky, Victor I.

    2002-01-01

    A miniature x-ray source capable of producing broad spectrum x-ray emission over a wide range of x-ray energies. The miniature x-ray source comprises a compact vacuum tube assembly containing a cathode, an anode, a high voltage feedthru for delivering high voltage to the anode, a getter for maintaining high vacuum, a connection for an initial vacuum pump down and crimp-off, and a high voltage connection for attaching a compact high voltage cable to the high voltage feedthru. At least a portion of the vacuum tube wall is highly x-ray transparent and made, for example, from boron nitride. The compact size and potential for remote operation allows the x-ray source, for example, to be placed adjacent to a material sample undergoing analysis or in proximity to the region to be treated for medical applications.

  6. British X-ray astronomy

    NASA Astrophysics Data System (ADS)

    Pounds, K. A.

    1986-09-01

    The development of solar and cosmic X-ray studies in the UK, in particular the Skylark and Ariel programs, is discussed. The characteristics and capabilities of the X-ray emulsion detector developed to monitor the solar X-radiation in the Skylark program, and of the proportional counter spectrometer developed for solar X-ray measurements on the Ariel I satellite are described. The designs and functions of the pin-hole camera, the Bragg crystal spectrometer, and the X-ray spectroheliograph are exmained. The Skylark observations of cosmic X-ray sources and high-resolution solar spectra, and the Ariel 5 data on cosmic X-ray sources are presented. Consideration is given to the Ariel 6, the U.S. Einstein Observatory, Exosat, and ASTRO-C.

  7. Solar X-ray physics

    SciTech Connect

    Bornmann, P.L. )

    1991-01-01

    Research on solar X-ray phenomena performed by American scientists during 1987-1990 is reviewed. Major topics discussed include solar images observed during quiescent times, the processes observed during solar flares, and the coronal, interplanetary, and terrestrial phenomena associated with solar X-ray flares. Particular attention is given to the hard X-ray emission observed at the start of the flare, the energy transfer to the soft X-ray emitting plasma, the late resolution of the flare as observed in soft X-ray, and the rate of occurrence of solar flares as a function of time and latitude. Pertinent aspects of nonflaring, coronal X-ray emission and stellar flares are also discussed. 175 refs.

  8. X-Ray Polarization Imaging

    DTIC Science & Technology

    2006-07-01

    anatomic structures. Johns and Yaffe (2), building on the work of Alvarez and Macovski (3) and that of Lehmann et al (4), discuss a method for...sources of contrast related to both the wave and par- ticulate nature of x rays. References 1. Johns PC, Yaffe MJ. X-ray characterization of normal and...application to mammography. Med Phys 1985; 12:289–296. 3. Alvarez RE, Macovski A. Energy-selective reconstructions in x-ray computerized tomography. Phys

  9. 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…

  10. 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…

  11. Soft-x-ray spectroscopy study of nanoscale materials

    SciTech Connect

    Guo, J.-H.

    2005-07-30

    The ability to control the particle size and morphology of nanoparticles is of crucial importance nowadays both from a fundamental and industrial point of view considering the tremendous amount of high-tech applications. Controlling the crystallographic structure and the arrangement of atoms along the surface of nanostructured material will determine most of its physical properties. In general, electronic structure ultimately determines the properties of matter. Soft X-ray spectroscopy has some basic features that are important to consider. X-ray is originating from an electronic transition between a localized core state and a valence state. As a core state is involved, elemental selectivity is obtained because the core levels of different elements are well separated in energy, meaning that the involvement of the inner level makes this probe localized to one specific atomic site around which the electronic structure is reflected as a partial density-of-states contribution. The participation of valence electrons gives the method chemical state sensitivity and further, the dipole nature of the transitions gives particular symmetry information. The new generation synchrotron radiation sources producing intensive tunable monochromatized soft X-ray beams have opened up new possibilities for soft X-ray spectroscopy. The introduction of selectively excited soft X-ray emission has opened a new field of study by disclosing many new possibilities of soft X-ray resonant inelastic scattering. In this paper, some recent findings regarding soft X-ray absorption and emission studies of various nanostructured systems are presented.

  12. X-ray Absorption Spectroscopy

    SciTech Connect

    Yano, Junko; Yachandra, Vittal K.

    2009-07-09

    This review gives a brief description of the theory and application of X-ray absorption spectroscopy, both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), especially, pertaining to photosynthesis. The advantages and limitations of the methods are discussed. Recent advances in extended EXAFS and polarized EXAFS using oriented membranes and single crystals are explained. Developments in theory in understanding the XANES spectra are described. The application of X-ray absorption spectroscopy to the study of the Mn4Ca cluster in Photosystem II is presented.

  13. X-ray photonics: Bending X-rays with nanochannels

    NASA Astrophysics Data System (ADS)

    Pelliccia, Daniele

    2016-02-01

    X-ray counterparts of visible light optical elements are notoriously difficult to realize because the refractive index of all materials is close to unity. It has now been demonstrated that curved waveguides fabricated on a silicon chip can channel and deflect X-ray beams by consecutive grazing reflections.

  14. Identification and H(D)-bond energies of C-H(D)Cl interactions in chloride-haloalkane clusters: a combined X-ray crystallographic, spectroscopic, and theoretical study.

    PubMed

    Serebryanskaya, Tatiyana V; Novikov, Alexander S; Gushchin, Pavel V; Haukka, Matti; Asfin, Ruslan E; Tolstoy, Peter M; Kukushkin, Vadim Yu

    2016-05-18

    The cationic (1,3,5-triazapentadiene)Pt(II) complex [Pt{NH[double bond, length as m-dash]C(N(CH2)5)N(Ph)C(NH2)[double bond, length as m-dash]NPh}2]Cl2 ([]Cl2) was crystallized from four haloalkane solvents giving [][Cl2(CDCl3)4], [][Cl2(CHBr3)4], [][Cl2(CH2Cl2)2], and [][Cl2(C2H4Cl2)2] solvates that were studied by X-ray diffraction. In the crystal structures of [][Cl2(CDCl3)4] and [][Cl2(CHBr3)4], the Cl(-) ion interacts with two haloform molecules via C-DCl(-) and C-HCl(-) contacts, thus forming the negatively charged isostructural clusters [Cl(CDCl3)2](-) and [Cl(CHBr3)2](-). In the structures of [][Cl2(CH2Cl2)2] and [][Cl2(C2H4Cl2)2], cations [](2+) are linked to a 3D-network by a system of H-bondings including one formed by each Cl(-) ion with CH2Cl2 or C2H4Cl2 molecules. The lengths and energies of these H-bonds in the chloride-haloalkane clusters were analyzed by DFT calculations (M06 functional) including AIM analysis. The crystal packing noticeably affected the geometry of the clusters, and energy of C-HCl(-) hydrogen bonds ranged from 1 to 6 kcal mol(-1). An exponential correlation (R(2) > 0.98) between the calculated Cl(-)H distances and the energies of the corresponding contacts was found and used to calculate hydrogen bond energies from the experimental Cl(-)H distances. Predicted energy values (3.3-3.9 kcal mol(-1) for the [Cl(CHCl3)2](-) cluster) are in a reasonable agreement with the energy of the Cl3C-HCl(-) bond estimated using ATRFTIR spectroscopy (2.7 kcal mol(-1)).

  15. Projection x-ray topography system at 1-BM x-ray optics test beamline at the advanced photon source

    SciTech Connect

    Stoupin, Stanislav Liu, Zunping; Trakhtenberg, Emil; Lang, Keenan; Goetze, Kurt; Sullivan, Joseph; Macrander, Albert; Raghothamachar, Balaji; Dudley, Michael

    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) in 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.

  16. X-ray based extensometry

    NASA Technical Reports Server (NTRS)

    Jordan, E. H.; Pease, D. M.

    1988-01-01

    A totally new method of extensometry using an X-ray beam was proposed. The intent of the method is to provide a non-contacting technique that is immune to problems associated with density variations in gaseous environments that plague optical methods. X-rays are virtually unrefractable even by solids. The new method utilizes X-ray induced X-ray fluorescence or X-ray induced optical fluorescence of targets that have melting temperatures of over 3000 F. Many different variations of the basic approaches are possible. In the year completed, preliminary experiments were completed which strongly suggest that the method is feasible. The X-ray induced optical fluorescence method appears to be limited to temperatures below roughly 1600 F because of the overwhelming thermal optical radiation. The X-ray induced X-ray fluorescence scheme appears feasible up to very high temperatures. In this system there will be an unknown tradeoff between frequency response, cost, and accuracy. The exact tradeoff can only be estimated. It appears that for thermomechanical tests with cycle times on the order of minutes a very reasonable system may be feasible. The intended applications involve very high temperatures in both materials testing and monitoring component testing. Gas turbine engines, rocket engines, and hypersonic vehicles (NASP) all involve measurement needs that could partially be met by the proposed technology.

  17. Astronomical X-Ray Optics

    NASA Technical Reports Server (NTRS)

    Joy, M. K.

    2000-01-01

    Over the past two decades, grazing incidence optics have transformed observational x-ray astronomy into a major scientific discipline at the cutting edge of research in astrophysics and cosmology. This review summarizes the fundamental design principles of grazing incidence optics for astronomical applications, describes the capabilities of the current generation of x-ray telescopes, and explores several avenues of future development.

  18. Dual x-ray absorptiometry

    NASA Astrophysics Data System (ADS)

    Altman, Albert; Aaron, Ronald

    2011-04-01

    Dual x-ray absorptiometry is widely used in analyzing body composition and imaging. We discuss the physics of the method and exhibit its limitations and show it is related to the Compton and photoelectric contributions to the x-ray absorption coefficients of materials.

  19. X-ray position detector

    NASA Technical Reports Server (NTRS)

    Garmire, G. (Inventor)

    1972-01-01

    An X-ray position detector for real time operation is described. A set of proportional counters is arranged into an array which can detect and indicate the position of an X-ray interaction within the array, in the X Y plane.

  20. X-ray shearing interferometer

    DOEpatents

    Koch, Jeffrey A [Livermore, CA

    2003-07-08

    An x-ray interferometer for analyzing high density plasmas and optically opaque materials includes a point-like x-ray source for providing a broadband x-ray source. The x-rays are directed through a target material and then are reflected by a high-quality ellipsoidally-bent imaging crystal to a diffraction grating disposed at 1.times. magnification. A spherically-bent imaging crystal is employed when the x-rays that are incident on the crystal surface are normal to that surface. The diffraction grating produces multiple beams which interfere with one another to produce an interference pattern which contains information about the target. A detector is disposed at the position of the image of the target produced by the interfering beams.

  1. X-Ray Tomographic Reconstruction

    SciTech Connect

    Bonnie Schmittberger

    2010-08-25

    Tomographic scans have revolutionized imaging techniques used in medical and biological research by resolving individual sample slices instead of several superimposed images that are obtained from regular x-ray scans. X-Ray fluorescence computed tomography, a more specific tomography technique, bombards the sample with synchrotron x-rays and detects the fluorescent photons emitted from the sample. However, since x-rays are attenuated as they pass through the sample, tomographic scans often produce images with erroneous low densities in areas where the x-rays have already passed through most of the sample. To correct for this and correctly reconstruct the data in order to obtain the most accurate images, a program employing iterative methods based on the inverse Radon transform was written. Applying this reconstruction method to a tomographic image recovered some of the lost densities, providing a more accurate image from which element concentrations and internal structure can be determined.

  2. X-Ray Diffraction Apparatus

    NASA Technical Reports Server (NTRS)

    Blake, David F. (Inventor); Bryson, Charles (Inventor); Freund, Friedmann (Inventor)

    1996-01-01

    An x-ray diffraction apparatus for use in analyzing the x-ray diffraction pattern of a sample is introduced. The apparatus includes a beam source for generating a collimated x-ray beam having one or more discrete x-ray energies, a holder for holding the sample to be analyzed in the path of the beam, and a charge-coupled device having an array of pixels for detecting, in one or more selected photon energy ranges, x-ray diffraction photons produced by irradiating such a sample with said beam. The CCD is coupled to an output unit which receives input information relating to the energies of photons striking each pixel in the CCD, and constructs the diffraction pattern of photons within a selected energy range striking the CCD.

  3. Focusing X-Ray Telescopes

    NASA Technical Reports Server (NTRS)

    O'Dell, Stephen; Brissenden, Roger; Davis, William; Elsner, Ronald; Elvis, Martin; Freeman, Mark; Gaetz, Terrance; Gorenstein, Paul; Gubarev, Mikhall; Jerlus, Diab; hide

    2010-01-01

    During the half-century history of x-ray astronomy, focusing x-ray telescopes, through increased effective area and finer angular resolution, have improved sensitivity by 8 orders of magnitude. Here, we review previous and current x-ray-telescope missions. Next, we describe the planned next-generation x-ray-astronomy facility, the International X-ray Observatory (IXO). We conclude with an overview of a concept for the next next-generation facility, Generation X. Its scientific objectives will require very large areas (about 10,000 sq m) of highly-nested, lightweight grazing-incidence mirrors, with exceptional (about 0.1-arcsec) resolution. Achieving this angular resolution with lightweight mirrors will likely require on-orbit adjustment of alignment and figure.

  4. X-ray monitoring optical elements

    DOEpatents

    Stoupin, Stanislav; Shvydko, Yury; Katsoudas, John; Blank, Vladimir D.; Terentyev, Sergey A.

    2016-12-27

    An X-ray article and method for analyzing hard X-rays which have interacted with a test system. The X-ray article is operative to diffract or otherwise process X-rays from an input X-ray beam which have interacted with the test system and at the same time provide an electrical circuit adapted to collect photoelectrons emitted from an X-ray optical element of the X-ray article to analyze features of the test system.

  5. X-ray diagnostics for TFTR

    SciTech Connect

    von Goeler, S.; Hill, K.W.; Bitter, M.

    1982-12-01

    A short description of the x-ray diagnostic preparation for the TFTR tokamak is given. The x-ray equipment consists of the limiter x-ray monitoring system, the soft x-ray pulse-height-analysis-system, the soft x-ray imaging system and the x-ray crystal spectrometer. Particular attention is given to the radiation protection of the x-ray systems from the neutron environment.

  6. The crystal and molecular structure of N{sub 2}H{sub 5}[M(N{sub 2}H{sub 3}COO){sub 3}].H{sub 2}O (M-bar {l_brace}Co, Zn{r_brace}) isomorphic compounds-an X-ray crystallographic, vibrational spectroscopic and quantum-chemical study

    SciTech Connect

    Jesih, Adolf; Rahten, Anka; Benkic, Primoz; Skapin, Tomaz; Pejov, Ljupco . E-mail: ljupcop@iunona.pmf.ukim.edu.mk; Petrusevski, Vladimir M.

    2004-12-01

    A systematic study of N{sub 2}H{sub 5}[M(N{sub 2}H{sub 3}COO){sub 3}].H{sub 2}O (M-bar {l_brace}Co, Zn{r_brace}) type of compounds, which are typical model systems for transition metal complexes with {alpha}-amino acids (the latter are not obtainable in crystalline form), was carried out. The crystal structures of these compounds were solved by X-ray crystallographic methods. FTIR spectra at room and low temperature ({approx}100K) as well as Raman spectra at room temperature were recorded, and analyzed in details. Also, the geometries of the Zn(N{sub 2}H{sub 3}COO){sub 3}{sup -} and N{sub 2}H{sub 5}{sup +} species were fully optimized at ab initio HF and B3LYP/6-31+G(d,p) level of theory, and subsequent vibrational analyses were performed on the basis of which several important reassignments of the IR and Raman bands were proposed. In order to study the binding energetics and the ligand-cation charge-transfer interactions within the Zn(N{sub 2}H{sub 3}COO){sub 3}{sup -} complex, NBO analysis was carried out, employing the second-order perturbation theory analysis of the Fock matrix (i.e., its Kohn-Sham analog) within the NBO basis.

  7. X-Ray Imaging System

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The FluoroScan Imaging System is a high resolution, low radiation device for viewing stationary or moving objects. It resulted from NASA technology developed for x-ray astronomy and Goddard application to a low intensity x-ray imaging scope. FlouroScan Imaging Systems, Inc, (formerly HealthMate, Inc.), a NASA licensee, further refined the FluoroScan System. It is used for examining fractures, placement of catheters, and in veterinary medicine. Its major components include an x-ray generator, scintillator, visible light image intensifier and video display. It is small, light and maneuverable.

  8. X-Ray Imaging System

    NASA Astrophysics Data System (ADS)

    1986-01-01

    The FluoroScan Imaging System is a high resolution, low radiation device for viewing stationary or moving objects. It resulted from NASA technology developed for x-ray astronomy and Goddard application to a low intensity x-ray imaging scope. FlouroScan Imaging Systems, Inc, (formerly HealthMate, Inc.), a NASA licensee, further refined the FluoroScan System. It is used for examining fractures, placement of catheters, and in veterinary medicine. Its major components include an x-ray generator, scintillator, visible light image intensifier and video display. It is small, light and maneuverable.

  9. Dissociative X-ray Lasing

    NASA Astrophysics Data System (ADS)

    Miao, Q.; Liu, J.-C.; Ågren, H.; Rubensson, J.-E.; Gel'mukhanov, F.

    2012-12-01

    X-ray lasing is predicted to ensue when molecules are pumped into dissociative core-excited states by a free-electron-laser pulse. The lasing is due to the population inversion created in the neutral dissociation product, and the process features self-trapping of the x-ray pulse at the gain ridge. Simulations performed for the HCl molecule pumped at the 2p1/2→6σ resonance demonstrate that the scheme can be used to create ultrashort coherent x-ray pulses.

  10. X-RAY MONITORING OF ULTRALUMINOUS X-RAY SOURCES

    SciTech Connect

    Kaaret, Philip; Feng Hua

    2009-09-10

    X-ray monitoring observations were performed with the Swift observatory of the ultraluminous X-ray sources Holmberg IX X-1, NGC 5408 X-1, and NGC 4395 X-2 and also of the nuclear X-ray source in NGC 4395. Holmberg IX X-1 remains in the hard X-ray spectral state as its flux varies by a factor of 7 up to a (isotropic) luminosity of 2.8 x 10{sup 40} erg s{sup -1}. This behavior may suggest an unusually massive compact object. We find excess power at periods near 60 days and 28 days in the X-ray emission from Holmberg IX X-1. Additional monitoring is required to test the significance of these signals. NGC 5408 X-1 and NGC 4395 X-2 appear to remain in the soft spectral state found by Chandra and XMM with little variation in spectral hardness even as the luminosity changes by a factor of 9. We found an outburst from the nuclear source in NGC 4395 reaching an X-ray luminosity of 9 x 10{sup 40} erg s{sup -1}, several times higher than any previously reported.

  11. Lumbosacral spine x-ray

    MedlinePlus

    ... should be taken before children receive x-rays. Considerations There are some back problems that an x- ... imaging for low back pain: advice for high-value health care from the American College of Physicians. ...

  12. Miniature x-ray source

    DOEpatents

    Trebes, James E.; Bell, Perry M.; Robinson, Ronald B.

    2000-01-01

    A miniature x-ray source utilizing a hot filament cathode. The source has a millimeter scale size and is capable of producing broad spectrum x-ray emission over a wide range of x-ray energies. The miniature source consists of a compact vacuum tube assembly containing the hot filament cathode, an anode, a high voltage feedthru for delivering high voltage to the cathode, a getter for maintaining high vacuum, a connector for initial vacuum pump down and crimp-off, and a high voltage connection for attaching a compact high voltage cable to the high voltage feedthru. At least a portion of the vacuum tube wall is fabricated from highly x-ray transparent materials, such as sapphire, diamond, or boron nitride.

  13. CELESTIAL X-RAY SOURCES.

    DTIC Science & Technology

    sources, (4) the physical conditions in the pulsating x-ray source in the Crab Nebula , and (5) miscellaneous related topics. A bibliography of all work performed under the contract is given. (Author)

  14. Nanoscale X-ray imaging

    NASA Astrophysics Data System (ADS)

    Sakdinawat, Anne; Attwood, David

    2010-12-01

    Recent years have seen significant progress in the field of soft- and hard-X-ray microscopy, both technically, through developments in source, optics and imaging methodologies, and also scientifically, through a wide range of applications. While an ever-growing community is pursuing the extensive applications of today's available X-ray tools, other groups are investigating improvements in techniques, including new optics, higher spatial resolutions, brighter compact sources and shorter-duration X-ray pulses. This Review covers recent work in the development of direct image-forming X-ray microscopy techniques and the relevant applications, including three-dimensional biological tomography, dynamical processes in magnetic nanostructures, chemical speciation studies, industrial applications related to solar cells and batteries, and studies of archaeological materials and historical works of art.

  15. Future x-ray missions

    NASA Astrophysics Data System (ADS)

    Mushotzky, Richard F.

    2002-11-01

    Recent results from XMM-Newton and Chandra show that sufficiently sensitive x_ray imaging and spectroscopic capabilities allow one to observe the evolution of active galaxies out to z ~ 6, the x-ray signature of luminous star forming galaxies at z~3, as well as the origin and evolution of cosmic structure. With the advent of new optical/UV/IR and radio capabilities in the next decade, it is appropriate to evaluate the future capabilities of planned x-ray missions (e.g., Constellation_X and Astro-E2) as well as other missions being developed (e.g., Gen-X, XEUS, and Astro-G) or under advance planning (MAXIM and EXIST). I will present a summary of the present status of the field and the capabilities of these missions for extragalactic x-ray astronomy.

  16. X-Ray Exam: Pelvis

    MedlinePlus

    ... KidsHealth in the Classroom What Other Parents Are Reading Your Child's Development (Birth to 3 Years) Feeding ... radiologist (a doctor who is specially trained in reading and interpreting X-ray images). The radiologist will ...

  17. X-Ray Exam: Forearm

    MedlinePlus

    ... KidsHealth in the Classroom What Other Parents Are Reading Your Child's Development (Birth to 3 Years) Feeding ... a radiologist (a doctor who's specially trained in reading and interpreting X-ray images). The radiologist will ...

  18. X-Ray Exam: Finger

    MedlinePlus

    ... KidsHealth in the Classroom What Other Parents Are Reading Your Child's Development (Birth to 3 Years) Feeding ... Results A radiologist, a doctor specially trained in reading and interpreting X-ray images, will look at ...

  19. Imaging X-ray spectrometer

    NASA Technical Reports Server (NTRS)

    Grant, P. A.; Jackson, J. W., Jr.; Alcorn, G. E.; Marshall, F. E. (Inventor)

    1984-01-01

    An X-ray spectrometer for providing imaging and energy resolution of an X-ray source is described. This spectrometer is comprised of a thick silicon wafer having an embedded matrix or grid of aluminum completely through the wafer fabricated, for example, by thermal migration. The aluminum matrix defines the walls of a rectangular array of silicon X-ray detector cells or pixels. A thermally diffused aluminum electrode is also formed centrally through each of the silicon cells with biasing means being connected to the aluminum cell walls and causes lateral charge carrier depletion between the cell walls so that incident X-ray energy causes a photoelectric reaction within the silicon producing collectible charge carriers in the form of electrons which are collected and used for imaging.

  20. X-ray microtomographic scanners

    SciTech Connect

    Syryamkin, V. I. Klestov, S. A.

    2015-11-17

    The article studies the operating procedures of an X-ray microtomographic scanner and the module of reconstruction and analysis 3D-image of a test sample in particular. An algorithm for 3D-image reconstruction based on image shadow projections and mathematical methods of the processing are described. Chapter 1 describes the basic principles of X-ray tomography and general procedures of the device developed. Chapters 2 and 3 are devoted to the problem of resources saving by the system during the X-ray tomography procedure, which is achieved by preprocessing of the initial shadow projections. Preprocessing includes background noise removing from the images, which reduces the amount of shadow projections in general and increases the efficiency of the group shadow projections compression. In conclusion, the main applications of X-ray tomography are presented.

  1. Bone X-Ray (Radiography)

    MedlinePlus

    ... have very controlled x-ray beams and dose control methods to minimize stray (scatter) radiation. This ensures that those parts of a patient's body not being imaged receive minimal radiation exposure. top ...

  2. Abdomen X-Ray (Radiography)

    MedlinePlus

    ... have very controlled x-ray beams and dose control methods to minimize stray (scatter) radiation. This ensures that those parts of a patient's body not being imaged receive minimal radiation exposure. top ...

  3. X-ray astronomical spectroscopy

    NASA Technical Reports Server (NTRS)

    Holt, S. S.

    1980-01-01

    The current status of the X-ray spectroscopy of celestial X-ray sources, ranging from nearby stars to distant quasars, is reviewed. Particular emphasis is placed on the role of such spectroscopy as a useful and unique tool in the elucidation of the physical parameters of the sources. The spectroscopic analysis of degenerate and nondegenerate stellar systems, galactic clusters and active galactic nuclei, and supernova remnants is discussed.

  4. X-ray computed tomography

    NASA Astrophysics Data System (ADS)

    1993-05-01

    The primary advantage of the X-ray computed tomography (XRCT) NDE method is that features are not superposed in the image, thereby rendering them easier to interpret than radiographic projection images. Industrial XRCT systems, unlike medical diagnostic systems, have no size and dosage constraints; they are accordingly used for systems from the scale of gas turbine blades, with hundreds-of-kV energies, to those of the scale of ICBMs, requiring MV-level X-ray energies.

  5. Electromechanical x-ray generator

    DOEpatents

    Watson, Scott A; Platts, David; Sorensen, Eric B

    2016-05-03

    An electro-mechanical x-ray generator configured to obtain high-energy operation with favorable energy-weight scaling. The electro-mechanical x-ray generator may include a pair of capacitor plates. The capacitor plates may be charged to a predefined voltage and may be separated to generate higher voltages on the order of hundreds of kV in the AK gap. The high voltage may be generated in a vacuum tube.

  6. X-ray Sensitive Material

    DTIC Science & Technology

    2015-12-01

    The research resulted in a composite material that holds a quasi-permanent electric charge and rapidly discharges the electric charge upon X-ray...temperature extremes encountered during processing and potential application. (U) The result of these efforts was a composite material that would hold a...quasi-permanent electric charge and rapidly discharge the electric charge upon X-ray exposure. The composite material combined the properties of an

  7. Tokamak x ray diagnostic instrumentation

    SciTech Connect

    Hill, K.W.; Beiersdorfer, P.; Bitter, M.; Fredrickson, E.; Von Goeler, S.; Hsuan, H.; Johnson, L.C.; Liew, S.L.; McGuire, K.; Pare, V.

    1987-01-01

    Three classes of x-ray diagnostic instruments enable measurement of a variety of tokamak physics parameters from different features of the x-ray emission spectrum. (1) The soft x-ray (1 to 50 keV) pulse-height-analysis (PHA) diagnostic measures impurity concentrations from characteristic line intensities and the continuum enhancement, and measures the electron temperature from the continuum slope. (2) The Bragg x-ray crystal spectrometer (XCS) measures the ion temperature and neutral-beam-induced toroidal rotation velocity from the Doppler broadening and wavelength shift, respectively, of spectral lines of medium-Z impurity ions. Impurity charge state distributions, precise wavelengths, and inner-shell excitation and recombination rates can also be studied. X rays are diffracted and focused by a bent crystal onto a position-sensitive detector. The spectral resolving power E/..delta..E is greater than 10/sup 4/ and time resolution is 10 ms. (3) The x-ray imaging system (XIS) measures the spatial structure of rapid fluctuations (0.1 to 100 kHZ) providing information on MHD phenomena, impurity transport rates, toroidal rotation velocity, plasma position, and the electron temperature profile. It uses an array of silicon surface-barrier diodes which view different chords of the plasma through a common slot aperture and operate in current (as opposed to counting) mode. The effectiveness of shields to protect detectors from fusion-neutron radiation effects has been studied both theoretically and experimentally.

  8. Cosmic X-ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, D.; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1985-01-01

    A progress report of research activities carried out in the area of cosmic X-ray physics is presented. The Diffuse X-ray Spectrometer DXS which has been flown twice as a rocket payload is described. The observation times proved to be too small for meaningful X-ray data to be obtained. Data collection and reduction activities from the Ultra-Soft X-ray background (UXT) instrument are described. UXT consists of three mechanically-collimated X-ray gas proportional counters with window/filter combinations which allow measurements in three energy bands, Be (80-110 eV), B (90-187 eV), and O (e84-532 eV). The Be band measurements provide an important constraint on local absorption of X-rays from the hot component of the local interstellar medium. Work has also continued on the development of a calorimetric detector for high-resolution spectroscopy in the 0.1 keV - 8keV energy range.

  9. X-Rays, Pregnancy and You

    MedlinePlus

    ... and Procedures Medical Imaging Medical X-ray Imaging X-Rays, Pregnancy and You Share Tweet Linkedin Pin it ... the decision with your doctor. What Kind of X-Rays Can Affect the Unborn Child? During most x- ...

  10. X-ray natural circular dichroism in copper metaborate

    SciTech Connect

    Ovchinnikova, E. N.; Rogalev, A.; Wilhelm, F.; Kozlovskaya, K. A.; Oreshko, A. P.; Dmitrienko, V. E.

    2016-07-15

    The local electronic structure of copper ions in a copper metaborate CuB{sub 2}O{sub 4} crystal is studied on the ESRF synchrotron using X-ray absorption polarization-dependent spectroscopy. The X-ray natural circular dichroism near the K absorption edge of copper is measured in the direction that is perpendicular to crystal axis c. The data obtained indicate the presence of hybridized p–d electronic states of copper. Theoretical calculations are used to separate the contributions of the two crystallographically nonequivalent positions of copper atoms in the unit cell of CuB{sub 2}O{sub 4} to the absorption and X-ray circular dichroism spectra of the crystal.

  11. X-ray microprobe: The next step in microcharacterization

    SciTech Connect

    Ice, G.E.

    1997-06-01

    The combination of high brilliance of third generation synchrotrons and advanced x-ray microfocusing optics will revolutionize microcharacterization. Kirkpatrick-Baez elliptical mirrors, zone plates, and condensing capillaries have all achieved intense submicron focused beams. Other focusing options are also under study including Bragg-Fresnel optics and compound refractive lenses. The intense micron-scale beams from advanced x-ray optics on third generation sources will provide unique information about the elemental and crystallographic distribution in samples and will enable a variety experiments previously unimaginable. X-ray microbeams can be used to map elemental distributions in two and three dimensions and can be used to study the phase, texture, and strain distributions of inhomogenous samples in two and three dimensions.

  12. Center for X-Ray Optics, 1992

    SciTech Connect

    Not Available

    1993-08-01

    This report discusses the following topics: Center for X-Ray Optics; Soft X-Ray Imaging wit Zone Plate Lenses; Biological X-Ray microscopy; Extreme Ultraviolet Lithography for Nanoelectronic Pattern Transfer; Multilayer Reflective Optics; EUV/Soft X-ray Reflectometer; Photoemission Microscopy with Reflective Optics; Spectroscopy with Soft X-Rays; Hard X-Ray Microprobe; Coronary Angiography; and Atomic Scattering Factors.

  13. Sequential x-ray diffraction topography at 1-BM x-ray optics testing beamline at the advanced photon source

    SciTech Connect

    Stoupin, Stanislav Shvyd’ko, Yuri; Trakhtenberg, Emil; Liu, Zunping; Lang, Keenan; Huang, Xianrong; Wieczorek, Michael; Kasman, Elina; Hammonds, John; Macrander, Albert; Assoufid, Lahsen

    2016-07-27

    We report progress on implementation and commissioning of sequential X-ray diffraction topography at 1-BM Optics Testing Beamline of the Advanced Photon Source to accommodate growing needs of strain characterization in diffractive crystal optics and other semiconductor single crystals. The setup enables evaluation of strain in single crystals in the nearly-nondispersive double-crystal geometry. Si asymmetric collimator crystals of different crystallographic orientations were designed, fabricated and characterized using in-house capabilities. Imaging the exit beam using digital area detectors permits rapid sequential acquisition of X-ray topographs at different angular positions on the rocking curve of a crystal under investigation. Results on sensitivity and spatial resolution are reported based on experiments with high-quality Si and diamond crystals. The new setup complements laboratory-based X-ray topography capabilities of the Optics group at the Advanced Photon Source.

  14. Ultrafast X-ray Sources

    SciTech Connect

    George Neil

    2010-04-19

    Since before the scattering of X-rays off of DNA led to the first understanding of the double helix structure, sources of X-rays have been an essential tool for scientists examining the structure and interactions of matter. The resolution of a microscope is proportional to the wavelength of light so x-rays can see much finer structures than visible light, down to single atoms. In addition, the energy of X-rays is resonant with the core atomic levels of atoms so with appropriate wavelengths the placement of specific atoms in a large molecule can be determined. Over 10,000 scientists use synchrotron sources, storage rings of high energy electrons, each year worldwide. As an example of such use, virtually every picture of a protein or drug molecule that one sees in the scientific press is a reconstruction based on X-ray scattering of synchrotron light from the crystallized form of that molecule. Unfortunately those pictures are static and proteins work through configuration (shape) changes in response to energy transfer. To understand how biological systems work requires following the energy flow to these molecules and tracking how shape changes drive their interaction with other molecules. We'd like to be able to freeze the action of these molecules at various steps along the way with an X-ray strobe light. How fast does it have to be? To actually get a picture of a molecule in a fixed configuration requires X-ray pulses as short as 30 femtoseconds (1/30 of a millionth of a millionth of a second). To capture the energy flow through changes in electronic levels requires a faster strobe, less than 1 femtosecond! And to acquire such information in smaller samples with higher accuracy demands brighter and brighter X-rays. Unfortunately modern synchrotrons (dubbed 3rd Generation Light Sources) cannot deliver such short bright pulses of X-rays. An entirely new approach is required, linear-accelerator (linac-)-based light sources termed 4th or Next Generation Light Sources

  15. Ultraluminous X-ray Sources.

    NASA Astrophysics Data System (ADS)

    Fabrika, S.; Sholukhova, O.; Abolmasov, P.

    2008-12-01

    We discuss a new type of X-ray sources discovered in galaxies -- ultraluminous X-ray sources (ULXs). They are of two order of magnitude brighter in X-rays than the brightest Galactic black holes. Two mod- els of ULXs are discussed: "intermediate mass" black holes, 100 - 10000 solar masses, with standard accretion disks, and "stellar mass" black holes with su- percritical accretion disks like that in the Galactic object SS 433. A study of gas nebulae surrounding these objects gives us a new important information on the central sources. The observed X-ray radiation of ULXs is not enough to power their nebulae. To understand both spectra and power of the nebulae one needs a powerful UV source. The ULXs must be such bright in UV range as they are in X-rays. Spectroscopy of gas filaments surrounding SS 433 proves that the intrinsic face-on luminosity of the supercritical accretion disk in the far UV region to be "sim; 10^40 erg/s. We expect that observations of ULXs with the WSO-UV Observatory, measurements their UV fluxes and spectral slopes solve the problem of ULXs between the two known models of these sources.

  16. X-rays surgical revolution.

    PubMed

    Toledo-Pereyra, Luis H

    2009-01-01

    Wilhelm Roentgen (1845-1923) created a surgical revolution with the discovery of the X-rays in late 1895 and the subsequent introduction of this technique for the management of surgical patients. No other physician or scientist had ever imagined such a powerful and worthwhile discovery. Other scientists paved the way for Roentgen to approach the use of these new X-rays for medical purposes. In this way, initially, and prior to Roentgen, Thompson, Hertz, and Lenard applied themselves to the early developments of this technology. They made good advances but never reached the clearly defined understanding brought about by Roentgen. The use of a Crookes tube, a barium platinocyanide screen, with fluorescent light and the generation of energy to propagate the cathode rays were the necessary elements for the conception of an X-ray picture. On November 8, 1895, Roentgen began his experiments on X-ray technology when he found that some kind of rays were being produced by the glass of the tube opposite to the cathode. The development of a photograph successfully completed this early imaging process. After six intense weeks of research, on December 22, he obtained a photograph of the hand of his wife, the first X-ray ever made. This would be a major contribution to the world of medicine and surgery.

  17. X-ray Echo Spectroscopy

    NASA Astrophysics Data System (ADS)

    Shvyd'ko, Yuri

    2016-02-01

    X-ray echo spectroscopy, a counterpart of neutron spin echo, is being introduced here to overcome limitations in spectral resolution and weak signals of the traditional inelastic x-ray scattering (IXS) probes. An image of a pointlike x-ray source is defocused by a dispersing system comprised of asymmetrically cut specially arranged Bragg diffracting crystals. The defocused image is refocused into a point (echo) in a time-reversal dispersing system. If the defocused beam is inelastically scattered from a sample, the echo signal acquires a spatial distribution, which is a map of the inelastic scattering spectrum. The spectral resolution of the echo spectroscopy does not rely on the monochromaticity of the x rays, ensuring strong signals along with a very high spectral resolution. Particular schemes of x-ray echo spectrometers for 0.1-0.02 meV ultrahigh-resolution IXS applications (resolving power >108 ) with broadband ≃5 - 13 meV dispersing systems are introduced featuring more than 103 signal enhancement. The technique is general, applicable in different photon frequency domains.

  18. Clocking Femtosecond X-Rays

    SciTech Connect

    Cavalieri, A L; Fritz, D M; Lee, S H; Bucksbaum, P H; Reis, D A; Mills, D M; Pahl, R; Rudati, J; Fuoss, P H; Stephenson, G B; Lowney, D P; MacPhee, A G; Weinstein, D; Falcone, R W; Als-Nielsen, J; Blome, C; Ischebeck, R; Schlarb, H; Tschentscher, T; Schneider, J; Sokolowski-Tinten, K; Chapman, H N; Lee, R W; Hansen, T N; Synnergren, O; Larsson, J; Techert, S; Sheppard, J; Wark, J S; Bergh, M; Calleman, C; Huldt, G; der Spoel, D v; Timneanu, N; Hajdu, J; Bong, E; Emma, P; Krejcik, P; Arthur, J; Brennan, S; Gaffney, K J; Lindenberg, A M; Hastings, J B

    2004-10-08

    The Sub-Picosecond Pulse Source (SPPS) at the Stanford Linear Accelerator Center (SLAC) produces the brightest ultrafast x-ray pulses in the world, and is the first to employ compressed femtosecond electron bunches for the x-ray source. Both SPPS and future X-ray Free Electron Lasers (XFEL's) will use precise measurements of individual electron bunches to time the arrival of x-ray pulses for time-resolved experiments. At SPPS we use electro-optic sampling (EOS) to perform these measurements. Here we present the first results using this method. An ultrafast laser pulse (135 fs) passes through an electro-optic crystal adjacent to the electron beam. The refractive index of the crystal is distorted by the strong electromagnetic fields of the ultra-relativistic electrons, and this transient birefringence is imprinted on the laser polarization. A polarizer decodes this signal, producing a time-dependent image of the compressed electron bunch. Our measurements yield the relative timing between an ultrafast optical laser and an ultrafast x-ray pulse to within 60 fs, making it possible to use the SPPS to observe atomic-scale ultrafast dynamics initiated by laser-matter interaction.

  19. AN X-RAY STUDY OF THE ETHYLENE GLYCOLMONTMORILLONITE COMPLEX.

    DTIC Science & Technology

    SOILS, * MONTMORILLONITE , *GLYCOLS, *X RAY SPECTROSCOPY, X RAY SPECTRA, X RAY SPECTRA, X RAY SPECTRA, CLAY MINERALS, COMPLEX COMPOUNDS, FOURIER ANALYSIS, CRYSTAL STRUCTURE, THERMAL PROPERTIES, MATHEMATICAL MODELS.

  20. Effect of distal sugars and interglycosidic linkage on the N-glycoprotein linkage region conformation: synthesis and X-ray crystallographic investigation of β-1-N-alkanamide derivatives of cellobiose and maltose as disaccharide analogs of the conserved chitobiosylasparagine linkage.

    PubMed

    Mathiselvam, Manoharan; Ramkumar, Venkatachalam; Loganathan, Duraikkannu; Pérez, Serge

    2014-01-01

    The linkage region constituents, 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and L-asparagine (Asn) are conserved in the N-glycoproteins of all eukaryotes. Elucidation of the structure and conformation of the linkage region of glycoproteins is important to understand the presentation and dynamics of the carbohydrate chain at the protein/cell surface. Earlier crystallographic studies using monosaccharide models and analogs of N-glycoprotein linkage region have shown that the N-glycosidic torsion, ϕN, is more influenced by the structural variation in the sugar part than that of the aglycon moiety. To access the influence of distal sugar as well as interglycosidic linkage (α or β) on the N-glycosidic torsion angles, cellobiosyl and maltosyl alkanamides have been synthesized and structural features of seven of these analogs have been characterized by X-ray crystallography. Comparative analysis of the seven disaccharide analogs with the reported monosaccharide analogs showed that the ϕN value of cellobiosyl analogs deviate ~9° with respect to GlcβNHAc. In the case of maltosyl analogs, deviation is more than 18°. These deviations indicate that the N-glycosidic torsion is influenced by addition of distal sugar as well as with respect to inter glycosidic linkage (α or β); it is less influenced by changes occurring at the aglycon. The χ₂ value of alkanamide derived from glucose, cellobiose and maltose exhibit a large range of variations (from 1.6° to -109.9°). This large span of χ₂ value suggests the greater degree of rotational freedom around C1'-C2' bond which is restricted in GlcNAc alkanamides. The present finding explicitly proved the importance of molecular architecture in the N-glycoproteins linkage region to maintain the linearity, planarity and rigidity. These factors are necessary for N-glycan to serve role in inter- as well as intramolecular carbohydrate-protein interactions.

  1. X-ray fluorescence holography.

    PubMed

    Hayashi, Kouichi; Happo, Naohisa; Hosokawa, Shinya; Hu, Wen; Matsushita, Tomohiro

    2012-03-07

    X-ray fluorescence holography (XFH) is a method of atomic resolution holography which utilizes fluorescing atoms as a wave source or a monitor of the interference field within a crystal sample. It provides three-dimensional atomic images around a specified element and has a range of up to a few nm in real space. Because of this feature, XFH is expected to be used for medium-range local structural analysis, which cannot be performed by x-ray diffraction or x-ray absorption fine structure analysis. In this article, we explain the theory of XFH including solutions to the twin-image problem, an advanced measuring system, and data processing for the reconstruction of atomic images. Then, we briefly introduce our recent applications of this technique to the analysis of local lattice distortions in mixed crystals and nanometer-size clusters appearing in the low-temperature phase of a shape-memory alloy.

  2. Ultraluminous X-Ray Sources

    NASA Astrophysics Data System (ADS)

    Kaaret, Philip; Feng, Hua; Roberts, Timothy P.

    2017-08-01

    We review observations of ultraluminous X-ray sources (ULXs). X-ray spectroscopic and timing studies of ULXs suggest a new accretion state distinct from those seen in Galactic stellar-mass black hole binaries. The detection of coherent pulsations indicates the presence of neutron-star accretors in three ULXs and therefore apparently super-Eddington luminosities. Optical and X-ray line profiles of ULXs and the properties of associated radio and optical nebulae suggest that ULXs produce powerful outflows, also indicative of super-Eddington accretion. We discuss models of super-Eddington accretion and their relation to the observed behaviors of ULXs. We review the evidence for intermediate mass black holes in ULXs. We consider the implications of ULXs for super-Eddington accretion in active galactic nuclei, heating of the early universe, and the origin of the black hole binary recently detected via gravitational waves.

  3. X-ray Timing Measurements

    NASA Technical Reports Server (NTRS)

    Strohmayer, T.

    2008-01-01

    We present new, extended X-ray timing measurements of the ultra-compact binary candidates V407 Vul and RX J0806.3+1527 (J0806), as well as a summary of the first high resolution X-ray spectra of 50806 obtained with the Chandra/LETG. The temporal baseline for both objects is approximately 12 years, and our measurements confirm the secular spin-up in their X-ray periods. The spin-up rate in 50806 is remarkably uniform at 3.55x10(exp -16)Hz/s, with a measurement precision of 0.2%. We place a limit (90% confidence) on 1 d dot nu < 4x10(exp -26)Hz/sq s. Interestingly, for V407 Vul we find the first evidence that the spin-up rate is slowing, with d dot\

  4. X-ray tensor tomography

    NASA Astrophysics Data System (ADS)

    Malecki, A.; Potdevin, G.; Biernath, T.; Eggl, E.; Willer, K.; Lasser, T.; Maisenbacher, J.; Gibmeier, J.; Wanner, A.; Pfeiffer, F.

    2014-02-01

    Here we introduce a new concept for x-ray computed tomography that yields information about the local micro-morphology and its orientation in each voxel of the reconstructed 3D tomogram. Contrary to conventional x-ray CT, which only reconstructs a single scalar value for each point in the 3D image, our approach provides a full scattering tensor with multiple independent structural parameters in each volume element. In the application example shown in this study, we highlight that our method can visualize sub-pixel fiber orientations in a carbon composite sample, hence demonstrating its value for non-destructive testing applications. Moreover, as the method is based on the use of a conventional x-ray tube, we believe that it will also have a great impact in the wider range of material science investigations and in future medical diagnostics. The authors declare no competing financial interests.

  5. Portable X-Ray Device

    NASA Technical Reports Server (NTRS)

    1983-01-01

    Portable x-ray instrument developed by NASA now being produced commercially as an industrial tool may soon find further utility as a medical system. The instrument is Lixiscope - Low Intensity X-Ray Imaging Scope -- a self-contained, battery-powered fluoroscope that produces an instant image through use of a small amount of radioactive isotope. Originally developed by Goddard Space Flight Center, Lixiscope is now being produced by Lixi, Inc. which has an exclusive NASA license for one version of the device.

  6. Coherent x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Pitney, John Allen

    Conventional x-ray diffraction has historically been done under conditions such that the measured signal consists of an incoherent addition of scattering which is coherent only on a length scale determined by the properties of the beam. The result of the incoherent summation is a statistical averaging over the whole illuminated volume of the sample, which yields certain kinds of information with a high degree of precision and has been key to the success of x-ray diffraction in a variety of applications. Coherent x-ray scattering techniques, such as coherent x-ray diffraction (CXD) and x-ray intensity fluctuation spectroscopy (XIFS), attempt to reduce or eliminate any incoherent averaging so that specific, local structures couple to the measurement without being averaged out. In the case of XIFS, the result is analogous to dynamical light scattering, but with sensitivity to length scales less than 200 nm and time scales from 10-3 s to 103 s. When combined with phase retrieval, CXD represents an imaging technique with the penetration, in situ capabilities, and contrast mechanisms associated with x-rays and with a spatial resolution ultimately limited by the x-ray wavelength. In practice, however, the spatial resolution of CXD imaging is limited by exposure to about 100 A. This thesis describes CXD measurements of the binary alloy Cu3Au and the adaptation of phase retrieval methods for the reconstruction of real-space images of Cu3Au antiphase domains. The theoretical foundations of CXD are described in Chapter 1 as derived from the kinematical formulation for x-ray diffraction and from the temporal and spatial coherence of radiation. The antiphase domain structure of Cu 3Au is described, along with the associated reciprocal-space structure which is measured by CXD. CXD measurements place relatively stringent requirements on the coherence properties of the beam and on the detection mechanism of the experiment; these requirements and the means by which they have been

  7. Cosmic X-ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, D.; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1986-01-01

    The analysis of the beryllium-filtered data from Flight 17.020 was completed. The data base provided by the Wisconsin diffuse X-ray sky survey is being analyzed by correlating the B and C band emission with individual velocity components of neutral hydrogen. Work on a solid state detector to be used in high resolution spectroscopy of diffuse or extend X-ray sources is continuing. A series of 21 cm observations was completed. A paper on the effects of process parameter variation on the reflectivity of sputter-deposited tungsten-carvon multilayers was published.

  8. X-ray emission spectroscopy.

    PubMed

    Bergmann, Uwe; Glatzel, Pieter

    2009-01-01

    We describe the chemical information that can be obtained by means of hard X-ray emission spectroscopy (XES). XES is presented as a technique that is complementary to X-ray absorption spectroscopy (XAS) and that provides valuable information with respect to the electronic structure (local charge- and spin-density) as well as the ligand environment of a 3d transition metal. We address non-resonant and resonant XES and present results that were recorded on Mn model systems and the Mn(4)Ca-cluster in the oxygen evolving complex of photosystem II. A brief description of the instrumentation is given with an outlook toward future developments.

  9. X-rays from stars.

    PubMed

    Güdel, Manuel

    2002-09-15

    More than two years of observation with Chandra and XMM-Newton has provided a rich harvest of new results on the physics of stellar coronae and winds. High-resolution X-ray spectroscopy in particular has opened new windows to the structure, the dynamics and the composition of stellar atmospheres. The present paper presents selected results from the areas of hot and cool stars and star formation, summarizing new views of the thermal structure and energy release in stellar coronae, observations of magnetically active brown dwarfs, the structure of winds in hot stars, the physics in colliding-wind binary systems, and X-rays from protostars and stellar jets.

  10. Chest X-Ray (Chest Radiography)

    MedlinePlus

    ... News Physician Resources Professions Site Index A-Z X-ray (Radiography) - Chest Chest x-ray uses a very ... limitations of Chest Radiography? What is a Chest X-ray (Chest Radiography)? The chest x-ray is the ...

  11. Compact Flash X-Ray Units

    DTIC Science & Technology

    1995-07-01

    Flash x-ray units are used to diagnose pulsed power driven experiments on the Pegasus machine at Los Alamos. Several unique designs of Marx powered...employing an x-ray tube configuration which allows closely spaced x-ray emitting anodes. These units all emit a 10 ns FWHM x-ray pulse. Their Marx banks

  12. SPINE-compatible ‘carboloops’: a new microshaped vitreous carbon sample mount for X-ray and neutron crystallography

    PubMed Central

    Romoli, Filippo; Mossou, Estelle; Cuypers, Maxime; van der Linden, Peter; Carpentier, Philippe; Mason, Sax A.; Forsyth, V. Trevor; McSweeney, Sean

    2014-01-01

    A novel vitreous carbon mount for macromolecular crystallography, suitable for neutron and X-ray crystallographic studies, has been developed. The technology described here is compatible both with X-ray and neutron cryo-crystallography. The mounts have low density and low background scattering for both neutrons and X-rays. They are prepared by laser cutting, allowing high standards of production quality, the ability to custom-design the mount to specific crystal sizes and large-scale production. PMID:24817737

  13. X-ray exposure sensor and controller

    NASA Technical Reports Server (NTRS)

    Berdahl, C. Martin (Inventor)

    1977-01-01

    An exposure controller for x-ray equipment is provided, which comprises a portable and accurate sensor which can be placed adjacent to and directly beneath the area of interest of an x-ray plate, and which measures the amount of exposure received by that area, and turns off the x-ray equipment when the exposure for the particular area of interest on the x-ray plate reaches the value which provides an optimal x-ray plate.

  14. X-ray backscatter imaging

    NASA Astrophysics Data System (ADS)

    Dinca, Dan-Cristian; Schubert, Jeffrey R.; Callerame, J.

    2008-04-01

    In contrast to transmission X-ray imaging systems where inspected objects must pass between source and detector, Compton backscatter imaging allows both the illuminating source as well as the X-ray detector to be on the same side of the target object, enabling the inspection to occur rapidly and in a wide variety of space-constrained situations. A Compton backscatter image is similar to a photograph of the contents of a closed container, taken through the container walls, and highlights low atomic number materials such as explosives, drugs, and alcohol, which appear as especially bright objects by virtue of their scattering characteristics. Techniques for producing X-ray images based on Compton scattering will be discussed, along with examples of how these systems are used for both novel security applications and for the detection of contraband materials at ports and borders. Differences between transmission and backscatter images will also be highlighted. In addition, tradeoffs between Compton backscatter image quality and scan speed, effective penetration, and X-ray source specifications will be discussed.

  15. Rontgen's Discovery of X Rays

    ERIC Educational Resources Information Center

    Thumm, Walter

    1975-01-01

    Relates the story of Wilhelm Conrad Rontgen and presents one view of the extent to which the discovery of the x-ray was an accident. Reconstructs the sequence of events that led to the discovery and includes photographs of the lab where he worked and replicas of apparatus used. (GS)

  16. Focused X-ray source

    DOEpatents

    Piestrup, M.A.; Boyers, D.G.; Pincus, C.I.; Maccagno, P.

    1990-08-21

    Disclosed is an intense, relatively inexpensive X-ray source (as compared to a synchrotron emitter) for technological, scientific, and spectroscopic purposes. A conical radiation pattern produced by a single foil or stack of foils is focused by optics to increase the intensity of the radiation at a distance from the conical radiator. 8 figs.

  17. 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.

  18. X-rays and magnetism.

    PubMed

    Fischer, Peter; Ohldag, Hendrik

    2015-09-01

    Magnetism is among the most active and attractive areas in modern solid state physics because of intriguing phenomena interesting to fundamental research and a manifold of technological applications. State-of-the-art synthesis of advanced magnetic materials, e.g. in hybrid structures paves the way to new functionalities. To characterize modern magnetic materials and the associated magnetic phenomena, polarized x-rays have emerged as unique probes due to their specific interaction with magnetic materials. A large variety of spectroscopic and microscopic techniques have been developed to quantify in an element, valence and site-sensitive way properties of ferro-, ferri-, and antiferromagnetic systems, such as spin and orbital moments, and to image nanoscale spin textures and their dynamics with sub-ns time and almost 10 nm spatial resolution. The enormous intensity of x-rays and their degree of coherence at next generation x-ray facilities will open the fsec time window to magnetic studies addressing fundamental time scales in magnetism with nanometer spatial resolution. This review will give an introduction into contemporary topics of nanoscale magnetic materials and provide an overview of analytical spectroscopy and microscopy tools based on x-ray dichroism effects. Selected examples of current research will demonstrate the potential and future directions of these techniques.

  19. Alpha proton x ray spectrometer

    NASA Technical Reports Server (NTRS)

    Rieder, Rudi; Waeke, H.; Economou, T.

    1994-01-01

    Mars Pathfinder will carry an alpha-proton x ray spectrometer (APX) for the determination of the elemental chemical composition of Martian rocks and soils. The instrument will measure the concentration of all major and some minor elements, including C, N, and O at levels above typically 1 percent.

  20. Stellar x-ray flares

    NASA Astrophysics Data System (ADS)

    Haisch, B.; Uchida, Y.; Kosugi, T.; Hudson, H. S.

    1995-01-01

    What is the importance of stellar X-ray flares to astrophysics, or even more, to the world at large? In the case of the Sun, changes in solar activity at the two temporal extremes can have quite significant consequences. Longterm changes in solar activity, such as the Maunder Minimum, can apparently lead to non-negligible alterations of the earth's climate. The extreme short term changes are solar flares, the most energetic of which can cause communications disruptions, power outages and ionizing radiation levels amounting to medical X-ray dosages on long commercial flights and even potentially lethal exposures for unshielded astronauts. Why does the Sun exhibit such behaviour? Even if we had a detailed knowledge of the relevant physical processes on the Sun - which we may be on the way to having in hand as evidenced by these Proceedings- our understanding would remain incomplete in regard to fundamental causation so long as we could not say whether the Sun is, in this respect, unique among the stars. This current paper discusses the stellar x-ray flare detections and astronomical models (quasi-static cooling model and two-ribbon model) that are used to observe the x-ray emission.

  1. Focused X-ray source

    DOEpatents

    Piestrup, Melvin A.; Boyers, David G.; Pincus, Cary I.; Maccagno, Pierre

    1990-01-01

    An intense, relatively inexpensive X-ray source (as compared to a synchrotron emitter) for technological, scientific, and spectroscopic purposes. A conical radiation pattern produced by a single foil or stack of foils is focused by optics to increase the intensity of the radiation at a distance from the conical radiator.

  2. X-Rays from Pluto

    NASA Image and Video Library

    2016-09-14

    The first detection of Pluto in X-rays has been made using NASA's Chandra X-ray Observatory in conjunction with observations from NASA's New Horizons spacecraft. As New Horizons approached Pluto in late 2014 and then flew by the planet during the summer of 2015, Chandra obtained data during four separate observations. During each observation, Chandra detected low-energy X-rays from the small planet. The main panel in this graphic is an optical image taken from New Horizons on its approach to Pluto, while the inset shows an image of Pluto in X-rays from Chandra. There is a significant difference in scale between the optical and X-ray images. New Horizons made a close flyby of Pluto but Chandra is located near the Earth, so the level of detail visible in the two images is very different. The Chandra image is 180,000 miles across at the distance of Pluto, but the planet is only 1,500 miles across. Pluto is detected in the X-ray image as a point source, showing the sharpest level of detail available for Chandra or any other X-ray observatory. This means that details over scales that are smaller than the X-ray source cannot be seen here. Detecting X-rays from Pluto is a somewhat surprising result given that Pluto - a cold, rocky world without a magnetic field - has no natural mechanism for emitting X-rays. However, scientists knew from previous observations of comets that the interaction between the gases surrounding such planetary bodies and the solar wind - the constant streams of charged particles from the sun that speed throughout the solar system -- can create X-rays. The researchers were particularly interested in learning more about the interaction between the gases in Pluto's atmosphere and the solar wind. The New Horizon spacecraft carries an instrument designed to measure that activity up-close -- Solar Wind Around Pluto (SWAP) -- and scientists examined that data and proposed that Pluto contains a very mild, close-in bowshock, where the solar wind first

  3. X-Ray Diffractive Optics

    NASA Technical Reports Server (NTRS)

    Dennis, Brian; Li, Mary; Skinner, Gerald

    2013-01-01

    X-ray optics were fabricated with the capability of imaging solar x-ray sources with better than 0.1 arcsecond angular resolution, over an order of magnitude finer than is currently possible. Such images would provide a new window into the little-understood energy release and particle acceleration regions in solar flares. They constitute one of the most promising ways to probe these regions in the solar atmosphere with the sensitivity and angular resolution needed to better understand the physical processes involved. A circular slit structure with widths as fine as 0.85 micron etched in a silicon wafer 8 microns thick forms a phase zone plate version of a Fresnel lens capable of focusing approx. =.6 keV x-rays. The focal length of the 3-cm diameter lenses is 100 microns, and the angular resolution capability is better than 0.1 arcsecond. Such phase zone plates were fabricated in Goddard fs Detector Development Lab. (DDL) and tested at the Goddard 600-microns x-ray test facility. The test data verified that the desired angular resolution and throughput efficiency were achieved.

  4. Compact x-ray source and panel

    SciTech Connect

    Sampayon, Stephen E.

    2008-02-12

    A compact, self-contained x-ray source, and a compact x-ray source panel having a plurality of such x-ray sources arranged in a preferably broad-area pixelized array. Each x-ray source includes an electron source for producing an electron beam, an x-ray conversion target, and a multilayer insulator separating the electron source and the x-ray conversion target from each other. The multi-layer insulator preferably has a cylindrical configuration with a plurality of alternating insulator and conductor layers surrounding an acceleration channel leading from the electron source to the x-ray conversion target. A power source is connected to each x-ray source of the array to produce an accelerating gradient between the electron source and x-ray conversion target in any one or more of the x-ray sources independent of other x-ray sources in the array, so as to accelerate an electron beam towards the x-ray conversion target. The multilayer insulator enables relatively short separation distances between the electron source and the x-ray conversion target so that a thin panel is possible for compactness. This is due to the ability of the plurality of alternating insulator and conductor layers of the multilayer insulators to resist surface flashover when sufficiently high acceleration energies necessary for x-ray generation are supplied by the power source to the x-ray sources.

  5. Thermal expansion in UO 2 determined by high-energy X-ray diffraction

    SciTech Connect

    Guthrie, M.; Benmore, C. J.; Skinner, L. B.; Alderman, O. L. G.; Weber, J. K. R.; Parise, J. B.; Williamson, M.

    2016-10-01

    Here we present crystallographic analyses of high-energy X-ray diffraction data on polycrystalline UO2 up to the melting temperature. The Rietveld refinements of our X-ray data are in agreement with previous measurements, but are systematically located around the upper bound of their uncertainty, indicating a slightly steeper trend of thermal expansion compared to established values. This observation is consistent with recent first principles calculations.

  6. Thermal expansion in UO2 determined by high-energy X-ray diffraction

    DOE PAGES

    Guthrie, M.; Benmore, C. J.; Skinner, L. B.; ...

    2016-06-24

    In this study, we present crystallographic analyses of high-energy X-ray diffraction data on polycrystalline UO2 up to the melting temperature. The Rietveld refinements of our X-ray data are in agreement with previous measurements, but are systematically located around the upper bound of their uncertainty, indicating a slightly steeper trend of thermal expansion compared to established values. This observation is consistent with recent first principles calculations.

  7. X-Ray Streak Camera.

    NASA Astrophysics Data System (ADS)

    Jaanimagi, Paul Ants

    Streak cameras are acknowledged as the only instruments capable of unambiguously diagnosing optical phenomena with a time resolution of the order of a picosecond on a single shot basis. As streak cameras become more extensively used for diagnostics in such fields as picosecond laser pulse generation, photo-chemistry, laser produced plasma studies, the instrument's capabilities are also being examined and limitations are becoming noticeable. One of the aims of this dissertation is to investigate the question of streak camera fidelity, especially with regard to linearity and dynamic range as a function of the time resolution. It is shown that the dynamic range is proportional to the product of the instrumental time resolution and the pulse width. The implications for femtosecond diagnostic capability are self-evident but a study of the sources of the limitations suggest distinct avenues for improving the systems. Since a streak camera employs an electron analog of the optical signal, clearly space charge will cause significant distortion at large current densities and consequently limit the dynamic range. Problems also result from nonlinear photocathode response, electron lens distortions, time of flight dispersion, phosphor reciprocity failure and nonlinear intensifier gain. The solution for some of these problems requires modifications to the basic tube designs. The National Research Council of Canada x-ray streak camera (based on a RCA C73435 image tube) was used as the starting point for testing electron optic designs and implementing the desired modifications. The objective of this work was to improve our x-ray diagnostic in sensitivity and in time resolution capability to < 10 ps. Ultimately this streak camera was to be used to time resolve the x -ray emission from plasmas produced by the COCO II and high pressure CO(,2) laser facilities at NRC. Features of the redesigned x-ray streak camera include: a large photocathode area (1.3 x 25 mm), a photoelectron

  8. X-ray reprocessing in binaries

    NASA Astrophysics Data System (ADS)

    Paul, Biswajit

    2016-07-01

    We will discuss several aspects of X-ray reprocessing into X-rays or longer wavelength radiation in different kinds of binary systems. In high mass X-ray binaries, reprocessing of hard X-rays into emission lines or lower temperature black body emission is a useful tool to investigate the reprocessing media like the stellar wind, clumpy structures in the wind, accretion disk or accretion stream. In low mass X-ray binaries, reprocessing from the surface of the companion star, the accretion disk, warps and other structures in the accretion disk produce signatures in longer wavelength radiation. X-ray sources with temporal structures like the X-ray pulsars and thermonuclear burst sources are key in such studies. We will discuss results from several new investigations of X-ray reprocessing phenomena in X-ray binaries.

  9. Identifications studies of Lauha Bhasma by X-ray diffraction and X-ray fluorescence.

    PubMed

    Bhargava, S C; Reddy, K R C; Sastry, G V S

    2012-01-01

    Procedures for preparation of Lauha Bhasma are described in ancient texts of Ayurveda. These procedures also begin with different source material for iron such as Teekshna Lauha and Kanta Lauha etc. In the present study, we have selected different source materials viz. magnetite iron ore for Kanta Lauha and pure (Armco grade) iron turnings for Teekshna Lauha. The standard procedures of preparation of Lauha Bhasma are carried out in identical conditions for these two raw materials. The final product from the Puta are characterized by using X-ray diffraction and X-ray fluorescence spectroscopy to understanding the crystallographic form or forms of iron oxides and their composition at the end of each Puta. The iron content at the end of repeated Putas (18 for Kanta Lauha and 20 for Teekshna Lauha) have shown a decrease in case of Teekshna Lauha since the starting material is pure iron while it showed only marginal decreases in the case of Kanta Lauha because the Fe(3)O(4) of magnetite is undergoing oxidation to Fe(2)O(3). The trace elements remain within the Bhasma in the form of various oxides of Si, Al, Ca, etc.

  10. Center for X-Ray Optics, 1986

    SciTech Connect

    Not Available

    1987-07-01

    The Center for X-Ray Optics has made substantial progress during the past year on the development of very high resolution x-ray technologies, the generation of coherent radiation at x-ray wavelengths, and, based on these new developments, had embarked on several scientific investigations that would not otherwise have been possible. The investigations covered in this report are topics on x-ray sources, x-ray imaging and applications, soft x-ray spectroscopy, synchrotron radiation, advanced light source and magnet structures for undulators and wigglers. (LSP)

  11. Effective X-ray beam size measurements of an X-ray tube and polycapillary X-ray lens system using a scanning X-ray fluorescence method

    NASA Astrophysics Data System (ADS)

    Gherase, Mihai R.; Vargas, Andres Felipe

    2017-03-01

    Size measurements of an X-ray beam produced by an integrated polycapillary X-ray lens (PXL) and X-ray tube system were performed by means of a scanning X-ray fluorescence (SXRF) method using three different metallic wires. The beam size was obtained by fitting the SXRF data with the analytical convolution between a Gaussian and a constant functions. For each chemical element in the wire an effective energy was calculated based on the incident X-ray spectrum and its photoelectric cross section. The proposed method can be used to measure the effective X-ray beam size in XRF microscopy studies.

  12. Ultraluminous X-ray Sources

    NASA Astrophysics Data System (ADS)

    Fabrika, S.

    2017-06-01

    The origin of Ultraluminous X-ray sources (ULXs) in external galaxies whose X-ray luminosities exceed those of the brightest black holes in our Galaxy by hundreds and thousands of times is mysterious. Here we report that all nearby persistent ULXs ever spectroscopically observed have the same optical spectra similar to that of SS 433, the only known supercritical accretor in our Galaxy. The spectra are apparently of WNL type (late nitrogen Wolf-Rayet stars) or LBV (luminous blue variables) in their hot state, which are very scarce stellar objects. We find that the spectra do not originate from WNL/LBV type donors and not in heated accretion disks, but from very hot winds from the accretion disks, which have similar physical conditions as the stellar winds from these stars. Our results suggest that bona-fide ULXs must constitute a homogeneous class of objects, which most likely have supercritical accretion disks.

  13. Microgap x-ray detector

    DOEpatents

    Wuest, Craig R.; Bionta, Richard M.; Ables, Elden

    1994-01-01

    An x-ray detector which provides for the conversion of x-ray photons into photoelectrons and subsequent amplification of these photoelectrons through the generation of electron avalanches in a thin gas-filled region subject to a high electric potential. The detector comprises a cathode (photocathode) and an anode separated by the thin, gas-filled region. The cathode may comprise a substrate, such a beryllium, coated with a layer of high atomic number material, such as gold, while the anode can be a single conducting plane of material, such as gold, or a plane of resistive material, such as chromium/silicon monoxide, or multiple areas of conductive or resistive material, mounted on a substrate composed of glass, plastic or ceramic. The charge collected from each electron avalanche by the anode is passed through processing electronics to a point of use, such as an oscilloscope.

  14. Microgap x-ray detector

    DOEpatents

    Wuest, C.R.; Bionta, R.M.; Ables, E.

    1994-05-03

    An x-ray detector is disclosed which provides for the conversion of x-ray photons into photoelectrons and subsequent amplification of these photoelectrons through the generation of electron avalanches in a thin gas-filled region subject to a high electric potential. The detector comprises a cathode (photocathode) and an anode separated by the thin, gas-filled region. The cathode may comprise a substrate, such a beryllium, coated with a layer of high atomic number material, such as gold, while the anode can be a single conducting plane of material, such as gold, or a plane of resistive material, such as chromium/silicon monoxide, or multiple areas of conductive or resistive material, mounted on a substrate composed of glass, plastic or ceramic. The charge collected from each electron avalanche by the anode is passed through processing electronics to a point of use, such as an oscilloscope. 3 figures.

  15. Tunable Coherent X-rays.

    PubMed

    Attwood, D; Halbach, K; Kim, K J

    1985-06-14

    A modern 1- to 2-billion-electron-volt synchrotron radiation facility (based on high-brightness electron beams and magnetic undulators) would generate coherent (laser-like) soft x-rays of wavelengths as short as 10 angstroms. The radiation would also be broadly tunable and subject to full polarization control. Radiation with these properties could be used for phase- and element-sensitive microprobing of biological assemblies and material interfaces as well as reserch on the production of electronic microstructures with features smaller than 1000 angstroms. These short wavelength capabilities, which extend to the K-absorption edges of carbon, nitrogen, and oxygen, are neither available nor projected for laboratory XUV lasers. Higher energy storage rings (5 to 6 billion electron volts) would generate significantly less coherent radiation and would be further compromised by additional x-ray thermal loading of optical components.

  16. Hard X-ray astrophysics

    NASA Technical Reports Server (NTRS)

    Rothschild, R. E.

    1981-01-01

    Past hard X-ray and lower energy satellite instruments are reviewed and it is shown that observation above 20 keV and up to hundreds of keV can provide much valuable information on the astrophysics of cosmic sources. To calculate possible sensitivities of future arrays, the efficiencies of a one-atmosphere inch gas counter (the HEAO-1 A-2 xenon filled HED3) and a 3 mm phoswich scintillator (the HEAO-1 A-4 Na1 LED1) were compared. Above 15 keV, the scintillator was more efficient. In a similar comparison, the sensitivity of germanium detectors did not differ much from that of the scintillators, except at high energies where the sensitivity would remain flat and not rise with loss of efficiency. Questions to be addressed concerning the physics of active galaxies and the diffuse radiation background, black holes, radio pulsars, X-ray pulsars, and galactic clusters are examined.

  17. 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.

  18. X-Ray-powered Macronovae

    NASA Astrophysics Data System (ADS)

    Kisaka, Shota; Ioka, Kunihito; Nakar, Ehud

    2016-02-01

    A macronova (or kilonova) was observed as an infrared excess several days after the short gamma-ray burst GRB 130603B. Although the r-process radioactivity is widely discussed as an energy source, it requires a huge mass of ejecta from a neutron star (NS) binary merger. We propose a new model in which the X-ray excess gives rise to the simultaneously observed infrared excess via thermal re-emission, and explore what constraints this would place on the mass and velocity of the ejecta. This X-ray-powered model explains both the X-ray and infrared excesses with a single energy source such as the central engine like a black hole, and allows for a broader parameter region than the previous models, in particular a smaller ejecta mass ˜ {10}-3{--}{10}-2{M}⊙ and higher iron abundance mixed as suggested by general relativistic simulations for typical NS-NS mergers. We also discuss the other macronova candidates in GRB 060614 and GRB 080503, and the implications for the search of electromagnetic counterparts to gravitational waves.

  19. X-ray imaging and x-ray source development at Lawrence Livermore National Laboratory

    SciTech Connect

    Trebes, J.; Balhorn, R.; Anderson, E.

    1993-12-01

    The Laser Program at Lawrence Livermore National Laboratory has a continuing effort to develop both x-ray sources and x-ray sources and x-ray microscopy. This effort includes the ongoing development of: (1) a wide range of x-ray lasers at the Nova Laser Facility, (2) a zone plate lens--multilayer mirror based x-ray microscope (3) three dimensional, high resolution x-ray microscopy (4) short wavelength, normal incidence multilayer x-ray mirrors, (5) compact, high average power lasers for producing x-ray lasers and laser plasma x-ray sources. We have constructed and operated an x-ray laser based transmission x-ray microscope. The advantage offered by the x-ray laser source is the extreme high brightness allows high resolution images to be made on a timescale faster than that for x-ray damage effects to appear. The microscope, consists of: the x-ray laser, a multilayer coated, near normal incidence spherical mirror used as a condenser, a silicon nitride specimen holder, an x-ray zone plate used as an objective lens, and a microchannel plate x-ray detector. The x-ray laser used is the Ni-like Ta x-ray laser operating with a wavelength of 4.48 nm, a pulselength of 200 spec, a divergence of 10 mrad, and an output energy of 10 microjoules.

  20. Producing X-rays at the APS

    ScienceCinema

    None

    2016-07-12

    An introduction and overview of the Advanced Photon Source at Argonne National Laboratory, the technology that produces the brightest X-ray beams in the Western Hemisphere, and the research carried out by scientists using those X-rays.

  1. Tuberculosis, advanced - chest x-rays (image)

    MedlinePlus

    ... tissue, and can cause tissue death. These chest x-rays show advanced pulmonary tuberculosis. There are multiple light ... location of cavities within these light areas. The x-ray on the left clearly shows that the opacities ...

  2. Aspergillosis - chest x-ray (image)

    MedlinePlus

    ... usually occurs in immunocompromised individuals. Here, a chest x-ray shows that the fungus has invaded the lung ... are usually seen as black areas on an x-ray. The cloudiness on the left side of this ...

  3. Advances in transmission x-ray optics

    SciTech Connect

    Ceglio, N.M.

    1983-01-01

    Recent developments in x-ray optics are reviewed. Specific advances in coded aperture imaging, zone plate lens fabrication, time and space resolved spectroscopy, and CCD x-ray detection are discussed.

  4. Extended X-ray absorption fine structure of bimetallic nanoparticles

    PubMed Central

    2011-01-01

    Summary Electronic and magnetic properties strongly depend on the structure of the material, especially on the crystal symmetry and chemical environment. In nanoparticles, the break of symmetry at the surface may yield different physical properties with respect to the corresponding bulk material. A useful tool to investigate the electronic structure, magnetic behaviour and local crystallographic structure is X-ray absorption spectroscopy. In this review, recent developments in the field of extended X-ray absorption fine structure measurements and in the analysis methods for structural investigations of bimetallic nanoparticles are highlighted. The standard analysis based on Fourier transforms is compared to the relatively new field of wavelet transforms that have the potential to outperform traditional analysis, especially in bimetallic alloys. As an example, the lattice expansion and inhomogeneous alloying found in FePt nanoparticles is presented, and this is discussed below in terms of the influence of employed density functional theory calculations on the magnetic properties. PMID:21977436

  5. Phase-sensitive X-ray imager

    DOEpatents

    Baker, Kevin Louis

    2013-01-08

    X-ray phase sensitive wave-front sensor techniques are detailed that are capable of measuring the entire two-dimensional x-ray electric field, both the amplitude and phase, with a single measurement. These Hartmann sensing and 2-D Shear interferometry wave-front sensors do not require a temporally coherent source and are therefore compatible with x-ray tubes and also with laser-produced or x-pinch x-ray sources.

  6. Advanced x-ray imaging spectrometer

    NASA Technical Reports Server (NTRS)

    Callas, John L. (Inventor); Soli, George A. (Inventor)

    1998-01-01

    An x-ray spectrometer that also provides images of an x-ray source. Coded aperture imaging techniques are used to provide high resolution images. Imaging position-sensitive x-ray sensors with good energy resolution are utilized to provide excellent spectroscopic performance. The system produces high resolution spectral images of the x-ray source which can be viewed in any one of a number of specific energy bands.

  7. Motorized Beam Alignment of a Commercial X-ray Diffractometer

    NASA Technical Reports Server (NTRS)

    Van Zandt, Noah R.; Myers, James F.; Rogers, Richard B

    2013-01-01

    X-ray diffraction (XRD) is a powerful analysis method that allows researchers to noninvasively probe the crystalline structure of a material. This includes the ability to determine the crystalline phases present, quantify surface residual stresses, and measure the distribution of crystallographic orientations. The Structures and Materials Division at the NASA Glenn Research Center (GRC) heavily uses the on-site XRD lab to characterize advanced metal alloys, ceramics, and polymers. One of the x-ray diffractometers in the XRD lab (Bruker D8 Discover) uses three different x-ray tubes (Cu, Cr, and Mn) for optimal performance over numerous material types and various experimental techniques. This requires that the tubes be switched out and aligned between experiments. This alignment maximizes the x-ray tube s output through an iterative process involving four set screws. However, the output of the x-ray tube cannot be monitored during the adjustment process due to standard radiation safety engineering controls that prevent exposure to the x-ray beam when the diffractometer doors are open. Therefore, the adjustment process is a very tedious series of blind adjustments, each followed by measurement of the output beam using a PIN diode after the enclosure doors are shut. This process can take up to 4 hr to perform. This technical memorandum documents an in-house project to motorize this alignment process. Unlike a human, motors are not harmed by x-ray radiation of the energy range used in this instrument. Therefore, using motors to adjust the set screws will allow the researcher to monitor the x-ray tube s output while making interactive adjustments from outside the diffractometer. The motorized alignment system consists of four motors, a motor controller, and a hand-held user interface module. Our goal was to reduce the alignment time to less than 30 min. The time available was the 10-week span of the Lewis' Educational and Research Collaborative Internship Project (LERCIP

  8. X-ray optics: Diamond brilliance

    NASA Astrophysics Data System (ADS)

    Durbin, Stephen M.; Colella, Roberto

    2010-03-01

    Most materials either absorb or transmit X-rays. This is useful for imaging but makes it notoriously difficult to build mirrors for reflective X-ray optics. A demonstration of the high X-ray reflectivity of diamond could provide a timely solution to make the most of the next generation of free-electron lasers.

  9. Student X-Ray Fluorescence Experiments

    ERIC Educational Resources Information Center

    Fetzer, Homer D.; And Others

    1975-01-01

    Describes the experimental arrangement for x-ray analysis of samples which involves the following: the radioisotopic x-ray disk source; a student-built fluorescence chamber; the energy dispersive x-ray detector, linear amplifier and bias supply; and a multichannel pulse height analyzer. (GS)

  10. Electron beam parallel X-ray generator

    NASA Technical Reports Server (NTRS)

    Payne, P.

    1967-01-01

    Broad X ray source produces a highly collimated beam of low energy X rays - a beam with 2 to 5 arc minutes of divergence at energies between 1 and 6 keV in less than 5 feet. The X ray beam is generated by electron bombardment of a target from a large area electron gun.

  11. Cryotomography x-ray microscopy state

    SciTech Connect

    Le Gros, Mark; Larabell, Carolyn A.

    2010-10-26

    An x-ray microscope stage enables alignment of a sample about a rotation axis to enable three dimensional tomographic imaging of the sample using an x-ray microscope. A heat exchanger assembly provides cooled gas to a sample during x-ray microscopic imaging.

  12. X-Ray Exam: Neck (For Parents)

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Neck KidsHealth > For Parents > X-Ray Exam: Neck Print A A A What's in ... español Radiografía: cuello What It Is A neck X-ray is a safe and painless test that uses ...

  13. Why Do I Need X-Rays?

    MedlinePlus

    ... to your desktop! more... Why Do I Need X-Rays? Article Chapters Why Do I Need X-Rays? print full article print this chapter email this article Radiographic, or X-ray, examinations provide your dentist with an important tool ...

  14. X-Ray Exam: Femur (Upper Leg)

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Femur (Upper Leg) KidsHealth > For Parents > X-Ray Exam: Femur (Upper Leg) Print A A A ... You Have Questions What It Is A femur X-ray is a safe and painless test that uses ...

  15. X-Ray Exam: Scoliosis (For Parents)

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet X-Ray Exam: Scoliosis KidsHealth > For Parents > X-Ray Exam: Scoliosis Print A A A What's in ... You Have Questions What It Is A scoliosis X-ray is a relatively safe and painless test that ...

  16. X-Ray Exam: Cervical Spine

    MedlinePlus

    ... to 2-Year-Old X-Ray Exam: Cervical Spine KidsHealth > For Parents > X-Ray Exam: Cervical Spine Print A A A What's in this article? ... Radiografía: columna cervical What It Is A cervical spine X-ray is a safe and painless test ...

  17. Supernova SN 2014C X-ray

    NASA Image and Video Library

    2017-01-24

    This image from NASA's Chandra X-ray Observatory shows spiral galaxy NGC 7331, center, in a three-color X-ray image. Red, green and blue colors are used for low, medium and high-energy X-rays, respectively. An unusual supernova called SN 2014C has been spotted in this galaxy. http://photojournal.jpl.nasa.gov/catalog/PIA21089

  18. Student X-Ray Fluorescence Experiments

    ERIC Educational Resources Information Center

    Fetzer, Homer D.; And Others

    1975-01-01

    Describes the experimental arrangement for x-ray analysis of samples which involves the following: the radioisotopic x-ray disk source; a student-built fluorescence chamber; the energy dispersive x-ray detector, linear amplifier and bias supply; and a multichannel pulse height analyzer. (GS)

  19. X-Ray Exam: Cervical Spine

    MedlinePlus

    ... to 2-Year-Old X-Ray Exam: Cervical Spine KidsHealth > For Parents > X-Ray Exam: Cervical Spine A A A What's in this article? What ... Radiografía: columna cervical What It Is A cervical spine X-ray is a safe and painless test ...

  20. Center for X-ray Optics, 1988

    SciTech Connect

    Not Available

    1989-04-01

    This report briefly reviews the following topics: soft-x-ray imaging; reflective optics for hard x-rays; coherent XUV sources; spectroscopy with x-rays; detectors for coronary artery imaging; synchrotron-radiation optics; and support for the advanced light source.

  1. Combined synchrotron X-ray tomography and X-ray powder diffraction using a fluorescing metal foil.

    PubMed

    Kappen, P; Arhatari, B D; Luu, M B; Balaur, E; Caradoc-Davies, T

    2013-06-01

    This study realizes the concept of simultaneous micro-X-ray computed tomography and X-ray powder diffraction using a synchrotron beamline. A thin zinc metal foil was placed in the primary, monochromatic synchrotron beam to generate a divergent wave to propagate through the samples of interest onto a CCD detector for tomographic imaging, thus removing the need for large beam illumination and high spatial resolution detection. Both low density materials (kapton tubing and a piece of plant) and higher density materials (Egyptian faience) were investigated, and elemental contrast was explored for the example of Cu and Ni meshes. The viability of parallel powder diffraction using the direct beam transmitted through the foil was demonstrated. The outcomes of this study enable further development of the technique towards in situ tomography∕diffraction studies combining micrometer and crystallographic length scales, and towards elemental contrast imaging and reconstruction methods using well defined fluorescence outputs from combinations of known fluorescence targets (elements).

  2. Combined synchrotron X-ray tomography and X-ray powder diffraction using a fluorescing metal foil

    NASA Astrophysics Data System (ADS)

    Kappen, P.; Arhatari, B. D.; Luu, M. B.; Balaur, E.; Caradoc-Davies, T.

    2013-06-01

    This study realizes the concept of simultaneous micro-X-ray computed tomography and X-ray powder diffraction using a synchrotron beamline. A thin zinc metal foil was placed in the primary, monochromatic synchrotron beam to generate a divergent wave to propagate through the samples of interest onto a CCD detector for tomographic imaging, thus removing the need for large beam illumination and high spatial resolution detection. Both low density materials (kapton tubing and a piece of plant) and higher density materials (Egyptian faience) were investigated, and elemental contrast was explored for the example of Cu and Ni meshes. The viability of parallel powder diffraction using the direct beam transmitted through the foil was demonstrated. The outcomes of this study enable further development of the technique towards in situ tomography/diffraction studies combining micrometer and crystallographic length scales, and towards elemental contrast imaging and reconstruction methods using well defined fluorescence outputs from combinations of known fluorescence targets (elements).

  3. A Compact X-Ray System for Support of High Throughput Crystallography

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Gubarev, Mikhail; Gibson, Walter M.; Joy, Marshall K.; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Standard x-ray systems for crystallography rely on massive generators coupled with optics that guide X-ray beams onto the crystal sample. Optics for single-crystal diffractometry include total reflection mirrors, polycapillary optics or graded multilayer monochromators. The benefit of using polycapillary optic is that it can collect x-rays over tile greatest solid angle, and thus most efficiently, utilize the greatest portion of X-rays emitted from the Source, The x-ray generator has to have a small anode spot, and thus its size and power requirements can be substantially reduced We present the design and results from the first high flux x-ray system for crystallography that combine's a microfocus X-ray generator (40microns FWHM Spot size at a power of 45 W) and a collimating, polycapillary optic. Diffraction data collected from small test crystals with cell dimensions up to 160A (lysozyme and thaumatin) are of high quality. For example, diffraction data collected from a lysozyme crystal at RT yielded R=5.0% for data extending to 1.70A. We compare these results with measurements taken from standard crystallographic systems. Our current microfocus X-ray diffraction system is attractive for supporting crystal growth research in the standard crystallography laboratory as well as in remote, automated crystal growth laboratory. Its small volume, light-weight, and low power requirements are sufficient to have it installed in unique environments, i.e.. on-board International Space Station.

  4. Mobile X-Ray Unit.

    DTIC Science & Technology

    1996-10-28

    anode 8 surrounded by a coaxial annulus of stainless steel mesh which 9 serves as the cathode, control electronics, and a plurality of 10 spark gap...34Siemens-tube" configuration. More 7 particularly, the X-ray tube 16 has a conical copper/tungsten 8 anode 28, and a stainless steel mesh punched to...160 and 162 each having a typical diameter of 14 2.75 inches. The conflat flanges 160 and 162 are mated to a 15 stainless steel tube 164 having a

  5. X-ray Spectroscopy of Cooling Cluster

    SciTech Connect

    Peterson, J.R.; Fabian, A.C.; /Cambridge U., Inst. of Astron.

    2006-01-17

    We review the X-ray spectra of the cores of clusters of galaxies. Recent high resolution X-ray spectroscopic observations have demonstrated a severe deficit of emission at the lowest X-ray temperatures as compared to that expected from simple radiative cooling models. The same observations have provided compelling evidence that the gas in the cores is cooling below half the maximum temperature. We review these results, discuss physical models of cooling clusters, and describe the X-ray instrumentation and analysis techniques used to make these observations. We discuss several viable mechanisms designed to cancel or distort the expected process of X-ray cluster cooling.

  6. Atmospheric electron x-ray spectrometer

    NASA Technical Reports Server (NTRS)

    Feldman, Jason E. (Inventor); George, Thomas (Inventor); Wilcox, Jaroslava Z. (Inventor)

    2002-01-01

    The present invention comprises an apparatus for performing in-situ elemental analyses of surfaces. The invention comprises an atmospheric electron x-ray spectrometer with an electron column which generates, accelerates, and focuses electrons in a column which is isolated from ambient pressure by a:thin, electron transparent membrane. After passing through the membrane, the electrons impinge on the sample in atmosphere to generate characteristic x-rays. An x-ray detector, shaping amplifier, and multi-channel analyzer are used for x-ray detection and signal analysis. By comparing the resultant data to known x-ray spectral signatures, the elemental composition of the surface can be determined.

  7. X-ray imaging for palaeontology.

    PubMed

    Hohenstein, P

    2004-05-01

    Few may be aware that X-ray imaging is used in palaeontology and has been used since as early as 1896. The X-raying, preparation and exposure of Hunsrück slate fossils are described. Hospital X-ray machines are used by the author in his work. An X-ray is vital to provide evidence that preparation of a slate is worthwhile as well as to facilitate preparation even if there is little external sign of what lies within. The beauty of the X-ray exposure is an added bonus.

  8. X-ray transmissive debris shield

    DOEpatents

    Spielman, Rick B.

    1996-01-01

    An X-ray debris shield for use in X-ray lithography that is comprised of an X-ray window having a layer of low density foam exhibits increased longevity without a substantial increase in exposure time. The low density foam layer serves to absorb the debris emitted from the X-ray source and attenuate the shock to the window so as to reduce the chance of breakage. Because the foam is low density, the X-rays are hardly attenuated by the foam and thus the exposure time is not substantially increased.

  9. X-ray transmissive debris shield

    DOEpatents

    Spielman, R.B.

    1996-05-21

    An X-ray debris shield for use in X-ray lithography that is comprised of an X-ray window having a layer of low density foam exhibits increased longevity without a substantial increase in exposure time. The low density foam layer serves to absorb the debris emitted from the X-ray source and attenuate the shock to the window so as to reduce the chance of breakage. Because the foam is low density, the X-rays are hardly attenuated by the foam and thus the exposure time is not substantially increased.

  10. Method for spatially modulating X-ray pulses using MEMS-based X-ray optics

    DOEpatents

    Lopez, Daniel; Shenoy, Gopal; Wang, Jin; Walko, Donald A.; Jung, Il-Woong; Mukhopadhyay, Deepkishore

    2015-03-10

    A method and apparatus are provided for spatially modulating X-rays or X-ray pulses using microelectromechanical systems (MEMS) based X-ray optics. A torsionally-oscillating MEMS micromirror and a method of leveraging the grazing-angle reflection property are provided to modulate X-ray pulses with a high-degree of controllability.

  11. X-ray transparent Microfluidics for Protein Crystallization and Biomineralization

    NASA Astrophysics Data System (ADS)

    Opathalage, Achini

    Protein crystallization demands the fundamental understanding of nucleation and applying techniques to find the optimal conditions to achieve the kinetic pathway for a large and defect free crystal. Classical nucleation theory predicts that the nucleation occurs at high supersaturation conditions. In this dissertation we sought out to develop techniques to attain optimal supersaturation profile to a large defect free crystal and subject it to in-situ X-ray diffraction using microfluidics. We have developed an emulsion-based serial crystallographic technology in nanolitre-sized droplets of protein solution encapsulated in to nucleate 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 un-oriented crystals. As proof of concept, the structure of Glucose Isomerase was solved to 2.1 A. We have developed a suite of X-ray semi-transparent micrfluidic devices which enables; controlled evaporation as a method of increasing supersaturation and manipulating the phase space of proteins and small molecules. We exploited the inherently high water permeability of the thin X-ray semi-transparent devices as a mean of increasing the supersaturation by controlling the evaporation. We fabricated the X-ray semi-transparent version of the PhaseChip with a thin PDMS membrane by which the storage and the reservoir layers are separated, and studies the phase transition of amorphous CaCO3.

  12. X-ray lithography using holographic images

    DOEpatents

    Howells, Malcolm R.; Jacobsen, Chris

    1995-01-01

    A non-contact X-ray projection lithography method for producing a desired X-ray image on a selected surface of an X-ray-sensitive material, such as photoresist material on a wafer, the desired X-ray image having image minimum linewidths as small as 0.063 .mu.m, or even smaller. A hologram and its position are determined that will produce the desired image on the selected surface when the hologram is irradiated with X-rays from a suitably monochromatic X-ray source of a selected wavelength .lambda.. On-axis X-ray transmission through, or off-axis X-ray reflection from, a hologram may be used here, with very different requirements for monochromaticity, flux and brightness of the X-ray source. For reasonable penetration of photoresist materials by X-rays produced by the X-ray source, the wavelength X, is preferably chosen to be no more than 13.5 nm in one embodiment and more preferably is chosen in the range 1-5 nm in the other embodiment. A lower limit on linewidth is set by the linewidth of available microstructure writing devices, such as an electron beam.

  13. X ray imaging microscope for cancer research

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.; Shealy, David L.; Brinkley, B. R.; Baker, Phillip C.; Barbee, Troy W., Jr.; Walker, Arthur B. C., Jr.

    1991-01-01

    The NASA technology employed during the Stanford MSFC LLNL Rocket X Ray Spectroheliograph flight established that doubly reflecting, normal incidence multilayer optics can be designed, fabricated, and used for high resolution x ray imaging of the Sun. Technology developed as part of the MSFC X Ray Microscope program, showed that high quality, high resolution multilayer x ray imaging microscopes are feasible. Using technology developed at Stanford University and at the DOE Lawrence Livermore National Laboratory (LLNL), Troy W. Barbee, Jr. has fabricated multilayer coatings with near theoretical reflectivities and perfect bandpass matching for a new rocket borne solar observatory, the Multi-Spectral Solar Telescope Array (MSSTA). Advanced Flow Polishing has provided multilayer mirror substrates with sub-angstrom (rms) smoothnesss for the astronomical x ray telescopes and x ray microscopes. The combination of these important technological advancements has paved the way for the development of a Water Window Imaging X Ray Microscope for cancer research.

  14. Evolution of X-ray astronomy

    NASA Technical Reports Server (NTRS)

    Rossj, B.

    1981-01-01

    The evolution of X-ray astronomy up to the launching of the Einstein observatory is presented. The evaluation proceeded through the following major steps: (1) discovery of an extrasolar X-ray source, Sco X-1, orders of magnitude stronger than astronomers believed might exist; (2) identification of a strong X-ray source with the Crab Nebula; (3) identification of Sco X-1 with a faint, peculiar optical object; (4) demonstration that X-ray stars are binary systems, each consisting of a collapsed object accreting matter from an ordinary star; (5) discovery of X-ray bursts; (6) discovery of exceedingly strong X-ray emission from active galaxies, quasars and clusters of galaxies; (7) demonstration that the principal X-ray source is a hot gas filling the space between galaxies.

  15. The Rosat x-ray sky

    NASA Astrophysics Data System (ADS)

    Voges, Wolfgang

    1995-01-01

    The ROSAT (Röntgensatellit) X-ray astronomy satellite has completed the first all-sky x-ray and XUV survey with imaging telescopes. About 60 000 new x-ray and 400 new XUV (1) sources were detected. This contribution will deal with preliminary results from the ROSAT ALL-SKY X-RAY SURVEY. The ROSAT diffuse and point-source x-ray skymaps, the positional accuracy obtained for the x-ray sources, and a few results from correlations performed with available catalogues in various energy bands like the Radio, Infrared, Visible, UV, and hard x-rays as well as identifications from optical follow-up observations will be presented.

  16. Spectral slicing X-ray telescope

    NASA Technical Reports Server (NTRS)

    Hoover, R. B.; Shealy, D.; Chao, S.-H.

    1986-01-01

    Layered synthetic microstructure (LSM) X-ray optics is investigated as a system for coupling a conventional glancing incidence X-ray mirror to a high sensitivity X-ray detector. It is shown that, by the use of figured LSM optics, it is possible to magnify the X-ray image produced by the primary mirrors so as to maintain their high inherent spatial resolution. The results of theoretical and design analyses of several spectral slicing X-ray telescope systems that utilize LSM mirrors of hyperboloidal, spherical, ellipsoidal, and constant optical path aspheric configurations are presented. It is shown that the spherical LSM optics are the preferred configuration, yielding subarcsecond performance over the entire field. The Stanford/Marshall Space Flight Center Rocket X-ray Telescope, which will utilize normal incidence LSM optics to couple a Wolter-Schwarzschild primary mirror to high resolution detectors for solar X-ray/EUV studies, is discussed. Design diagrams are included.

  17. X-ray deconvolution microscopy.

    PubMed

    Ehn, Sebastian; Epple, Franz Michael; Fehringer, Andreas; Pennicard, David; Graafsma, Heinz; Noël, Peter; Pfeiffer, Franz

    2016-04-01

    Recent advances in single-photon-counting detectors are enabling the development of novel approaches to reach micrometer-scale resolution in x-ray imaging. One example of such a technology are the MEDIPIX3RX-based detectors, such as the LAMBDA which can be operated with a small pixel size in combination with real-time on-chip charge-sharing correction. This characteristic results in a close to ideal, box-like point spread function which we made use of in this study. The proposed method is based on raster-scanning the sample with sub-pixel sized steps in front of the detector. Subsequently, a deconvolution algorithm is employed to compensate for blurring introduced by the overlap of pixels with a well defined point spread function during the raster-scanning. The presented approach utilizes standard laboratory x-ray equipment while we report resolutions close to 10 μm. The achieved resolution is shown to follow the relationship [Formula: see text] with the pixel-size p of the detector and the number of raster-scanning steps n.

  18. Submicron X-ray diffraction

    SciTech Connect

    MacDowell, Alastair; Celestre, Richard; Tamura, Nobumichi; Spolenak, Ralph; Valek, Bryan; Brown, Walter; Bravman, John; Padmore, Howard; Batterman, Boris; Patel, Jamshed

    2000-08-17

    At the Advanced Light Source in Berkeley the authors have instrumented a beam line that is devoted exclusively to x-ray micro diffraction problems. By micro diffraction they mean those classes of problems in Physics and Materials Science that require x-ray beam sizes in the sub-micron range. The instrument is for instance, capable of probing a sub-micron size volume inside micron sized aluminum metal grains buried under a silicon dioxide insulating layer. The resulting Laue pattern is collected on a large area CCD detector and automatically indexed to yield the grain orientation and deviatoric (distortional) strain tensor of this sub-micron volume. A four-crystal monochromator is then inserted into the beam, which allows monochromatic light to illuminate the same part of the sample. Measurement of diffracted photon energy allows for the determination of d spacings. The combination of white and monochromatic beam measurements allow for the determination of the total strain/stress tensor (6 components) inside each sub-micron sized illuminated volume of the sample.

  19. X-ray deconvolution microscopy

    PubMed Central

    Ehn, Sebastian; Epple, Franz Michael; Fehringer, Andreas; Pennicard, David; Graafsma, Heinz; Noël, Peter; Pfeiffer, Franz

    2016-01-01

    Recent advances in single-photon-counting detectors are enabling the development of novel approaches to reach micrometer-scale resolution in x-ray imaging. One example of such a technology are the MEDIPIX3RX-based detectors, such as the LAMBDA which can be operated with a small pixel size in combination with real-time on-chip charge-sharing correction. This characteristic results in a close to ideal, box-like point spread function which we made use of in this study. The proposed method is based on raster-scanning the sample with sub-pixel sized steps in front of the detector. Subsequently, a deconvolution algorithm is employed to compensate for blurring introduced by the overlap of pixels with a well defined point spread function during the raster-scanning. The presented approach utilizes standard laboratory x-ray equipment while we report resolutions close to 10 μm. The achieved resolution is shown to follow the relationship pn with the pixel-size p of the detector and the number of raster-scanning steps n. PMID:27446649

  20. X-ray lasing - Theory

    NASA Astrophysics Data System (ADS)

    1985-11-01

    The theoretical basis of lasing at very short wavelengths is discussed, and lasing at soft-X-ray (4-50 nm) wavelengths using the electron-collisional excitation scheme is successfully demonstrated. In research at LLNL, thin foils of selenium and yttrium are irradiated with laser light to generate a roughly cylindrical plasma containing neon-like ions. Excitation of ground state 2p electrons to the 3p state in the lasant medium is followed by very fast radioactive decay out of the 3s state, creating a population inversion between the 3s and 3p states. Stimulated X-ray emission is initiated by slower spontaneous decay from a 3p to 3s state. Design goals are to produce a plasma with a flat electron density of approximately 5 x 10 to the 20th/cu cm, a flat temperature profile, a scale length of at least 100 microns, and a population inversion lasting at least the 100 ps necessary to produce a significant gain. Good correlation is seen between experimental data and LANEX and XRASER theoretical modeling predictions over large variations in intensity, pulse length, and probing times. No explanation is found for the weakness of the J = 0 to J = 1 lasing transition line at 18.3 nm.

  1. X-ray omni microscopy.

    PubMed

    Paganin, D; Gureyev, T E; Mayo, S C; Stevenson, A W; Nesterets, Ya I; Wilkins, S W

    2004-06-01

    The science of wave-field phase retrieval and phase measurement is sufficiently mature to permit the routine reconstruction, over a given plane, of the complex wave-function associated with certain coherent forward-propagating scalar wave-fields. This reconstruction gives total knowledge of the information that has been encoded in the complex wave-field by passage through a sample of interest. Such total knowledge is powerful, because it permits the emulation in software of the subsequent action of an infinite variety of coherent imaging systems. Such 'virtual optics', in which software forms a natural extension of the 'hardware optics' in an imaging system, may be useful in contexts such as quantitative atom and X-ray imaging, in which optical elements such as beam-splitters and lenses can be realized in software rather than optical hardware. Here, we develop the requisite theory to describe such hybrid virtual-physical imaging systems, which we term 'omni optics' because of their infinite flexibility. We then give an experimental demonstration of these ideas by showing that a lensless X-ray point projection microscope can, when equipped with the appropriate software, emulate an infinite variety of optical imaging systems including those which yield interferograms, Zernike phase contrast, Schlieren imaging and diffraction-enhanced imaging.

  2. Grain orientation measurement of passivated aluminum interconnectsby x-ray micro diffraction

    SciTech Connect

    Chang, Chang-Hwan; Valek, B.C.; Padmore,H.A.; MacDowell, A.A.; Celestre, R.; Marieb, T.; Bravman, J.C.; Koo, Y.M.; Patel, J.R.

    1999-07-01

    The crystallographic orientations of individual grains in apassivated aluminum interconnect line of 0.7-mu m width were investigatedby using an incidentwhite x-ray microbeam at the Advanced Light Source,Berkeley National Laboratory. Intergrain orientation mapping was obtainedwith about 0.05o sensitivity by the micro Laue diffractiontechnique.

  3. X-Ray Attenuation Cell

    SciTech Connect

    Ryutov, D.; Toor, A.

    2000-03-03

    To minimize the pulse-to-pulse variation, the LCLS FEL must operate at saturation, i.e. 10 orders of magnitude brighter spectral brilliance than 3rd-generation light sources. At this intensity, ultra-high vacuums and windowless transport are required. Many of the experiments, however, will need to be conducted at a much lower intensity thereby requiring a reliable means to reduce the x-ray intensity by many orders of magnitude without increasing the pulse-to-pulse variation. In this report we consider a possible solution for controlled attenuation of the LCLS x-ray radiation. We suggest using for this purpose a windowless gas-filled cell with the differential pumping. Although this scheme is easily realizable in principle, it has to be demonstrated that the attenuator can be made short enough to be practical and that the gas loads delivered to the vacuum line of sight (LOS) are acceptable. We are not going to present a final, optimized design. Instead, we will provide a preliminary analysis showing that the whole concept is robust and is worth further study. The spatial structure of the LCLS x-ray pulse at the location of the attenuator is shown in Fig. 1. The central high-intensity component, due to the FEL, has a FWHM of {approx}100 {micro}m. A second component, due to the undulator's broad band spontaneous radiation is seen as a much lower intensity ''halo'' with a FWHM of 1 mm. We discuss two versions of the attenuation cell. The first is directed towards a controlled attenuation of the FEL up to the 4 orders of magnitude in the intensity, with the spontaneous radiation halo being eliminated by collimators. In the second version, the spontaneous radiation is not sacrificed but the FEL component (as well as the first harmonic of the spontaneous radiation) gets attenuated by a more modest factor up to 100. We will make all the estimates assuming that the gas used in the attenuator is Xenon and that the energy of the FEL is 8.25 keV. At lower FEL energies the

  4. Compact Stellar X-ray Sources

    NASA Astrophysics Data System (ADS)

    Lewin, Walter; van der Klis, Michiel

    2010-11-01

    1. Accreting neutron stars and black holes: a decade of discoveries D. Psaltis; 2. Rapid X-ray variability M. van der Klis; 3. New views of thermonuclear bursts T. Strohmayer and L. Bildsten; 4. Black hole binaries J. McClintock and R. Remillard; 5. Optical, ultraviolet and infrared observations of X-ray binaries P. Charles and M. Coe; 6. Fast X-ray transients and X-ray flashes J. Heise and J. in 't Zand; 7. Isolated neutron stars V. Kaspi, M. Roberts and A. Harding; 8. Globular cluster X-ray sources F. Verbunt and W. Lewin; 9. Jets from X-ray binaries R. Fender; 10. X-Rays from cataclysmic variables E. Kuulkers, A. Norton, A. Schwope and B. Warner; 11. Super soft sources P. Kahabka and E. van den Heuvel; 12. Compact stellar X-ray sources in normal galaxies G. Fabbiano and N. White; 13. Accretion in compact binaries A. King; 14. Soft gamma repeaters and anomalous X-ray pulsars: magnetar candidates P. Woods and C. Thompson; 15. Cosmic gamma-ray bursts, their afterglows, and their host galaxies K. Hurley, R. Sari and S. Djorgovski; 16. Formation and evolution of compact stellar X-ray sources T. Tauris and E. van den Heuvel.

  5. Compact Stellar X-ray Sources

    NASA Astrophysics Data System (ADS)

    Lewin, Walter H. G.; van der Klis, Michiel

    2006-04-01

    1. Accreting neutron stars and black holes: a decade of discoveries D. Psaltis; 2. Rapid X-ray variability M. van der Klis; 3. New views of thermonuclear bursts T. Strohmayer and L. Bildsten; 4. Black hole binaries J. McClintock and R. Remillard; 5. Optical, ultraviolet and infrared observations of X-ray binaries P. Charles and M. Coe; 6. Fast X-ray transients and X-ray flashes J. Heise and J. in 't Zand; 7. Isolated neutron stars V. Kaspi, M. Roberts and A. Harding; 8. Globular cluster X-ray sources F. Verbunt and W. Lewin; 9. Jets from X-ray binaries R. Fender; 10. X-Rays from cataclysmic variables E. Kuulkers, A. Norton, A. Schwope and B. Warner; 11. Super soft sources P. Kahabka and E. van den Heuvel; 12. Compact stellar X-ray sources in normal galaxies G. Fabbiano and N. White; 13. Accretion in compact binaries A. King; 14. Soft gamma repeaters and anomalous X-ray pulsars: magnetar candidates P. Woods and C. Thompson; 15. Cosmic gamma-ray bursts, their afterglows, and their host galaxies K. Hurley, R. Sari and S. Djorgovski; 16. Formation and evolution of compact stellar X-ray sources T. Tauris and E. van den Heuvel.

  6. Controlling X-rays With Light

    SciTech Connect

    Glover, Ernie; Hertlein, Marcus; Southworth, Steve; Allison, Tom; van Tilborg, Jeroen; Kanter, Elliot; Krassig, B.; Varma, H.; Rude, Bruce; Santra, Robin; Belkacem, Ali; Young, Linda

    2010-08-02

    Ultrafast x-ray science is an exciting frontier that promises the visualization of electronic, atomic and molecular dynamics on atomic time and length scales. A largelyunexplored area of ultrafast x-ray science is the use of light to control how x-rays interact with matter. In order to extend control concepts established for long wavelengthprobes to the x-ray regime, the optical control field must drive a coherent electronic response on a timescale comparable to femtosecond core-hole lifetimes. An intense field is required to achieve this rapid response. Here an intense optical control pulse isobserved to efficiently modulate photoelectric absorption for x-rays and to create an ultrafast transparency window. We demonstrate an application of x-ray transparencyrelevant to ultrafast x-ray sources: an all-photonic temporal cross-correlation measurement of a femtosecond x-ray pulse. The ability to control x-ray/matterinteractions with light will create new opportunities at current and next-generation x-ray light sources.

  7. Controlling x-rays with light.

    SciTech Connect

    Glover, T. E.; Hertlein, M. P.; Southworth, S. H.; Allison, T. K.; van Tilborg, J.; Kanter, E. P.; Krassig, B.; Varma, H. R.; Rude, B.; Santra, R.; Belkacem, A.; Young, L.; Chemical Sciences and Engineering Division; LBNL; Univ. of California at Berkley; Univ. of Chicago

    2010-01-01

    Ultrafast X-ray science is an exciting frontier that promises the visualization of electronic, atomic and molecular dynamics on atomic time and length scales. A largely unexplored area of ultrafast X-ray science is the use of light to control how X-rays interact with matter. To extend control concepts established for long-wavelength probes to the X-ray regime, the optical control field must drive a coherent electronic response on a timescale comparable to femtosecond core-hole lifetimes. An intense field is required to achieve this rapid response. Here, an intense optical control pulse is observed to efficiently modulate photoelectric absorption for X-rays and to create an ultrafast transparency window. We demonstrate an application of X-ray transparency relevant to ultrafast X-ray sources: an all-photonic temporal cross-correlation measurement of a femtosecond X-ray pulse. The ability to control X-ray-matter interactions with light will create new opportunities for present and next-generation X-ray light sources.

  8. Controlling X-rays with light

    NASA Astrophysics Data System (ADS)

    Glover, T. E.; Hertlein, M. P.; Southworth, S. H.; Allison, T. K.; van Tilborg, J.; Kanter, E. P.; Krässig, B.; Varma, H. R.; Rude, B.; Santra, R.; Belkacem, A.; Young, L.

    2010-01-01

    Ultrafast X-ray science is an exciting frontier that promises the visualization of electronic, atomic and molecular dynamics on atomic time and length scales. A largely unexplored area of ultrafast X-ray science is the use of light to control how X-rays interact with matter. To extend control concepts established for long-wavelength probes to the X-ray regime, the optical control field must drive a coherent electronic response on a timescale comparable to femtosecond core-hole lifetimes. An intense field is required to achieve this rapid response. Here, an intense optical control pulse is observed to efficiently modulate photoelectric absorption for X-rays and to create an ultrafast transparency window. We demonstrate an application of X-ray transparency relevant to ultrafast X-ray sources: an all-photonic temporal cross-correlation measurement of a femtosecond X-ray pulse. The ability to control X-ray-matter interactions with light will create new opportunities for present and next-generation X-ray light sources.

  9. Industrial X-Ray Imaging

    NASA Technical Reports Server (NTRS)

    1997-01-01

    In 1990, Lewis Research Center jointly sponsored a conference with the U.S. Air Force Wright Laboratory focused on high speed imaging. This conference, and early funding by Lewis Research Center, helped to spur work by Silicon Mountain Design, Inc. to break the performance barriers of imaging speed, resolution, and sensitivity through innovative technology. Later, under a Small Business Innovation Research contract with the Jet Propulsion Laboratory, the company designed a real-time image enhancing camera that yields superb, high quality images in 1/30th of a second while limiting distortion. The result is a rapidly available, enhanced image showing significantly greater detail compared to image processing executed on digital computers. Current applications include radiographic and pathology-based medicine, industrial imaging, x-ray inspection devices, and automated semiconductor inspection equipment.

  10. Diffractive X-Ray Telescopes

    NASA Technical Reports Server (NTRS)

    Skinner, Gerald K.

    2010-01-01

    Diffractive X-ray telescopes, using zone plates, phase Fresnel lenses, or related optical elements have the potential to provide astronomers with true imaging capability with resolution many orders of magnitude better than available in any other waveband. Lenses that would be relatively easy to fabricate could have an angular resolution of the order of micro-arc-seconds or even better, that would allow, for example, imaging of the distorted spacetime in the immediate vicinity of the super-massive black holes in the center of active galaxies. What then is precluding their immediate adoption? Extremely long focal lengths, very limited bandwidth, and difficulty stabilizing the image are the main problems. The history, and status of the development of such lenses is reviewed here and the prospects for managing the challenges that they present are discussed.

  11. Soft x-ray interferometry

    SciTech Connect

    Not Available

    1993-09-01

    The purpose of the soft x-ray interferometry workshop held at Lawrence Berkeley Laboratory was to discuss with the scientific community the proposed technical design of the soft x-ray Fourier-transform spectrometer being developed at the ALS. Different design strategies for the instrument`s components were discussed, as well as detection methods, signal processing issues, and how to meet the manufacturing tolerances that are necessary for the instrument to achieve the desired levels of performance. Workshop participants were encouraged to report on their experiences in the field of Fourier transform spectroscopy. The ALS is developing a Fourier transform spectrometer that is intended to operate up to 100 eV. The motivation is solely improved resolution and not the throughput (Jaquinot) or multiplex (Fellgett) advantage, neither of which apply for the sources and detectors used in this spectral range. The proposed implementation of this is via a Mach-Zehnder geometry that has been (1) distorted from a square to a rhombus to get grazing incidence of a suitable angle for 100 eV and (2) provided with a mirror-motion system to make the path difference between the interfering beams tunable. The experiment consists of measuring the emergent light intensity (I(x)) as a function of the path difference (x). The resolving power of the system is limited by the amount of path difference obtainable that is 1 cm (one million half-waves at 200{angstrom} wavelength) in the design thus allowing a resolving power of one million. The free spectral range of the system is limited by the closeness with which the function I(x) is sampled. It is proposed to illuminate a helium absorption cell with roughly 1%-band-width light from a monochromator thus allowing one hundred aliases without spectral overlap even for sampling of I(x) at one hundredth of the Nyquist frequency.

  12. The anomalous X-ray pulsars

    NASA Astrophysics Data System (ADS)

    Chen, Rui; Li, Xiangdong

    2002-03-01

    In the last few years it has been recognized that a group of X-ray pulsars have peculiar properties which set them apart from the majority of accreting pulars in X-ray binaries. They are called the Anomalous X-ray Pulsars (AXP). These objects are characterized by very soft X-ray spectra with low and steady X-ray fluxes, narrow-distributed spin periods, steady spin-down, no optical/infrared counterparts. Some of them may associate with supernova remnants. The nature of AXP remains mysterious. It has been suggested that AXP are accreting neutron stars, or solitary "magnetars", neutron stars with super strong magnetic fields (≍1010-1011T). In this paper we review the recent progress in the studies of AXP, and discuss the possible implications from comparison of AXP with other neutron stars, such as radio pulsars, radio quiet X-ray pulsar candidates and soft γ-ray repeaters.

  13. Hard X-ray imaging from Explorer

    NASA Technical Reports Server (NTRS)

    Grindlay, J. E.; Murray, S. S.

    1981-01-01

    Coded aperture X-ray detectors were applied to obtain large increases in sensitivity as well as angular resolution. A hard X-ray coded aperture detector concept is described which enables very high sensitivity studies persistent hard X-ray sources and gamma ray bursts. Coded aperture imaging is employed so that approx. 2 min source locations can be derived within a 3 deg field of view. Gamma bursts were located initially to within approx. 2 deg and X-ray/hard X-ray spectra and timing, as well as precise locations, derived for possible burst afterglow emission. It is suggested that hard X-ray imaging should be conducted from an Explorer mission where long exposure times are possible.

  14. Stimulated Electronic X-Ray Raman Scattering

    NASA Astrophysics Data System (ADS)

    Weninger, Clemens; Purvis, Michael; Ryan, Duncan; London, Richard A.; Bozek, John D.; Bostedt, Christoph; Graf, Alexander; Brown, Gregory; Rocca, Jorge J.; Rohringer, Nina

    2013-12-01

    We demonstrate strong stimulated inelastic x-ray scattering by resonantly exciting a dense gas target of neon with femtosecond, high-intensity x-ray pulses from an x-ray free-electron laser (XFEL). A small number of lower energy XFEL seed photons drive an avalanche of stimulated resonant inelastic x-ray scattering processes that amplify the Raman scattering signal by several orders of magnitude until it reaches saturation. Despite the large overall spectral width, the internal spiky structure of the XFEL spectrum determines the energy resolution of the scattering process in a statistical sense. This is demonstrated by observing a stochastic line shift of the inelastically scattered x-ray radiation. In conjunction with statistical methods, XFELs can be used for stimulated resonant inelastic x-ray scattering, with spectral resolution smaller than the natural width of the core-excited, intermediate state.

  15. X-Ray Observations of Planetary Nebulae

    NASA Astrophysics Data System (ADS)

    Guerrero, M. A.; Chu, Y.-H.; Gruendl, R. A.

    2004-07-01

    Planetary nebulae (PNe) are an exciting addition to the zoo of X-ray sources. Recent Chandra and XMM-Newton observations have detected diffuse X-ray emission from shocked fast winds in PN interiors as well as bow-shocks of fast collimated outflows impinging on the nebular envelope. Point X-ray sources associated with PN central stars are also detected, with the soft X-ray (<0.5 keV) emission originating from the photospheres of stars hotter than ˜100,000 K, and the hard X-ray (≫0.5 keV) emission from instability shocks in the fast stellar wind itself or from a low-mass companion's coronal activity. X-ray observations of PNe offer a unique opportunity to directly examine the dynamic effects of fast stellar winds and collimated outflows, and help us understand the formation and evolution of PNe.

  16. Stimulated electronic x-ray Raman scattering.

    PubMed

    Weninger, Clemens; Purvis, Michael; Ryan, Duncan; London, Richard A; Bozek, John D; Bostedt, Christoph; Graf, Alexander; Brown, Gregory; Rocca, Jorge J; Rohringer, Nina

    2013-12-06

    We demonstrate strong stimulated inelastic x-ray scattering by resonantly exciting a dense gas target of neon with femtosecond, high-intensity x-ray pulses from an x-ray free-electron laser (XFEL). A small number of lower energy XFEL seed photons drive an avalanche of stimulated resonant inelastic x-ray scattering processes that amplify the Raman scattering signal by several orders of magnitude until it reaches saturation. Despite the large overall spectral width, the internal spiky structure of the XFEL spectrum determines the energy resolution of the scattering process in a statistical sense. This is demonstrated by observing a stochastic line shift of the inelastically scattered x-ray radiation. In conjunction with statistical methods, XFELs can be used for stimulated resonant inelastic x-ray scattering, with spectral resolution smaller than the natural width of the core-excited, intermediate state.

  17. The Overutilization of X-rays

    PubMed Central

    Lyon, W. K.

    1981-01-01

    Within 20 years of Roentgen's discovery of X-rays in 1895, it became apparent that large doses of radiation damaged human tissue.1 Yet the medical profession continues to contribute to the overutilization of X-rays, occasionally spending health care dollars to subject our patients to a health risk. This paper discusses the evidence to support the claim that X-rays are overutilized, and offers recommendations to rectify the situation. PMID:21289771

  18. X-ray transmissive debris shield

    DOEpatents

    Spielman, Rick B.

    1994-01-01

    A composite window structure is described for transmitting x-ray radiation and for shielding radiation generated debris. In particular, separate layers of different x-ray transmissive materials are laminated together to form a high strength, x-ray transmissive debris shield which is particularly suited for use in high energy fluences. In one embodiment, the composite window comprises alternating layers of beryllium and a thermoset polymer.

  19. Topological X-Rays and MRIs

    ERIC Educational Resources Information Center

    Lynch, Mark

    2002-01-01

    Let K be a compact subset of the interior of the unit disk D in the plane and suppose one can't see through the boundary of D and identify K. However, assume that one can take "topological X-rays" of D which measure the "density" of K along the lines of the X-rays. By taking these X-rays from all directions, a "topological MRI" is generated for…

  20. X-ray data booklet. Revision

    SciTech Connect

    Vaughan, D.

    1986-04-01

    A compilation of data is presented. Included are properties of the elements, electron binding energies, characteristic x-ray energies, fluorescence yields for K and L shells, Auger energies, energy levels for hydrogen-, helium-, and neonlike ions, scattering factors and mass absorption coefficients, and transmission bands of selected filters. Also included are selected reprints on scattering processes, x-ray sources, optics, x-ray detectors, and synchrotron radiation facilities. (WRF)

  1. UV observations of x ray binaries

    NASA Technical Reports Server (NTRS)

    Raymond, John C.

    1990-01-01

    IUE (International Ultraviolet Explorer) has observed both high and low mass x ray binaries throughout its life. The UV spectra of high mass systems reveal the nature of the massive companion star and the effects of the x ray illumination of the stellar wind. In loss mass systems, the x ray illuminated disk or companion star dominates the UV light. System parameters and the characteristics of the accretion disk can be inferred.

  2. Topological X-Rays and MRIs

    ERIC Educational Resources Information Center

    Lynch, Mark

    2002-01-01

    Let K be a compact subset of the interior of the unit disk D in the plane and suppose one can't see through the boundary of D and identify K. However, assume that one can take "topological X-rays" of D which measure the "density" of K along the lines of the X-rays. By taking these X-rays from all directions, a "topological MRI" is generated for…

  3. Applications of soft x-ray lasers

    SciTech Connect

    Skinner, C.H.

    1993-08-01

    The high brightness and short pulse duration of soft x-ray lasers provide unique advantages for novel applications. Imaging of biological specimens using x-ray lasers has been demonstrated by several groups. Other applications to fields such as chemistry, material science, plasma diagnostics, and lithography are beginning to emerge. We review the current status of soft x-ray lasers from the perspective of applications, and present an overview of the applications currently being developed.

  4. Negative affinity X-ray photocathodes

    NASA Technical Reports Server (NTRS)

    Vanspeybroeck, L.; Kellogg, E.; Murray, S.; Duckett, S.

    1974-01-01

    A new X-ray image intensifier is described. The device should eventually have a quantum efficiency which is an order of magnitude greater than that of presently available high spatial resolution X-ray detectors, such as microchannel plates. The new intesifier is based upon a GaAs crystal photocathode which is activated to achieve negative electron affinity. Details concerning the detector concept are discussed together with the theoretical relations involved, X-ray data, and optical data.

  5. High speed x-ray beam chopper

    DOEpatents

    McPherson, Armon; Mills, Dennis M.

    2002-01-01

    A fast, economical, and compact x-ray beam chopper with a small mass and a small moment of inertia whose rotation can be synchronized and phase locked to an electronic signal from an x-ray source and be monitored by a light beam is disclosed. X-ray bursts shorter than 2.5 microseconds have been produced with a jitter time of less than 3 ns.

  6. Lobster-Eye X-Ray Astronomy

    SciTech Connect

    Hudec, R.; Pina, L.; Marsikova, V.; Inneman, A.

    2010-07-15

    We report on technical and astrophysical aspects of Lobster-Eye wide-field X-ray telescopes expected to monitor the sky with high sensitivity and angular resolution of order of 1 arcmin. They will contribute essentially to study of various astrophysical objects such as AGN, SNe, Gamma-ray bursts (GRBs), X-ray flashes (XRFs), galactic binary sources, stars, CVs, X-ray novae, various transient sources, etc.

  7. X-ray microlaminography with polycapillary optics

    SciTech Connect

    Dabrowski, K. M.; Dul, D. T.; Wrobel, A.; Korecki, P.

    2013-06-03

    We demonstrate layer-by-layer x-ray microimaging using polycapillary optics. The depth resolution is achieved without sample or source rotation and in a way similar to classical tomography or laminography. The method takes advantage from large angular apertures of polycapillary optics and from their specific microstructure, which is treated as a coded aperture. The imaging geometry is compatible with polychromatic x-ray sources and with scanning and confocal x-ray fluorescence setups.

  8. X-ray line emission from Capella

    NASA Technical Reports Server (NTRS)

    Holt, S. S.; Boldt, E. A.; Serlemitsos, P. J.; White, N. E.; Becker, R. H.; Mushotzky, R. F.; Smith, B. W.

    1979-01-01

    X-ray emission-line components from Mg, Si, S, and Fe are unambiguously detected from Capella with the solid-state spectrometer onboard the Einstein Observatory. The X-ray spectrum is inconsistent with an isothermal corona, and requires components between 6-million K and at least 24-million K for an adequate fit. An inhomogeneous corona in which the X-ray emitting plasma is confined to magnetically contained loops appears to be reconcilable with all of the experimental evidence.

  9. X ray microcalorimeters: Principles and performance

    NASA Technical Reports Server (NTRS)

    Moseley, S. H.; Juda, M.; Kelley, R. L.; Mccammon, D.; Stahle, C. K.; Szymkowiak, A. E.; Zhang, J.

    1992-01-01

    Microcalorimeters operating at cryogenic temperatures can be excellent X-ray spectrometers. They simultaneously offer very high spectral resolving power and high efficiency. These attributes are important for X-ray astronomy where most sources have low fluxes and where high spectral resolution is essential for understanding the physics of the emitting regions. The principles of operation of these detectors, limits to their sensitivity, design considerations, techniques of fabrication, and their performance as X-ray spectrometers, are reviewed.

  10. Electron channeling: a problem for x-ray microanalysis in materials science.

    PubMed

    Meisenkothen, Frederick; Wheeler, Robert; Uchic, Michael D; Kerns, Robert D; Scheltens, Frank J

    2009-04-01

    Electron channeling effects can create measurable signal intensity variations in all product signals that result from the scattering of the electron beam within a crystalline specimen. Of particular interest to the X-ray microanalyst are any variations that occur within the characteristic X-ray signal that are not directly related to a specimen composition variation. Many studies have documented the effect of crystallographic orientation on the local X-ray yield; however, the vast majority of these studies were carried out on thin foil specimens examined in transmission. Only a few studies have addressed these effects in bulk specimen materials, and these analyses were generally carried out at common scanning electron microscope microanalysis overvoltages (>1.5). At these overvoltage levels, the anomalous transmission effect is weak. As a result, the effect of electron channeling on the characteristic X-ray signal intensity has traditionally been overlooked in the field of quantitative electron probe microanalysis. The present work will demonstrate that electron channeling can produce X-ray variations of up to 26%, between intensity maxima and minima, in low overvoltage X-ray microanalyses of bulk specimens. Intensity variations of this magnitude will significantly impact the accuracy of qualitative and quantitative X-ray microanalyses at low overvoltage on engineering structural materials.

  11. Observation of femtosecond X-ray interactions with matter using an X-ray-X-ray pump-probe scheme.

    PubMed

    Inoue, Ichiro; Inubushi, Yuichi; Sato, Takahiro; Tono, Kensuke; Katayama, Tetsuo; Kameshima, Takashi; Ogawa, Kanade; Togashi, Tadashi; Owada, Shigeki; Amemiya, Yoshiyuki; Tanaka, Takashi; Hara, Toru; Yabashi, Makina

    2016-02-09

    Resolution in the X-ray structure determination of noncrystalline samples has been limited to several tens of nanometers, because deep X-ray irradiation required for enhanced resolution causes radiation damage to samples. However, theoretical studies predict that the femtosecond (fs) durations of X-ray free-electron laser (XFEL) pulses make it possible to record scattering signals before the initiation of X-ray damage processes; thus, an ultraintense X-ray beam can be used beyond the conventional limit of radiation dose. Here, we verify this scenario by directly observing femtosecond X-ray damage processes in diamond irradiated with extraordinarily intense (∼10(19) W/cm(2)) XFEL pulses. An X-ray pump-probe diffraction scheme was developed in this study; tightly focused double-5-fs XFEL pulses with time separations ranging from sub-fs to 80 fs were used to excite (i.e., pump) the diamond and characterize (i.e., probe) the temporal changes of the crystalline structures through Bragg reflection. It was found that the pump and probe diffraction intensities remain almost constant for shorter time separations of the double pulse, whereas the probe diffraction intensities decreased after 20 fs following pump pulse irradiation due to the X-ray-induced atomic displacement. This result indicates that sub-10-fs XFEL pulses enable conductions of damageless structural determinations and supports the validity of the theoretical predictions of ultraintense X-ray-matter interactions. The X-ray pump-probe scheme demonstrated here would be effective for understanding ultraintense X-ray-matter interactions, which will greatly stimulate advanced XFEL applications, such as atomic structure determination of a single molecule and generation of exotic matters with high energy densities.

  12. Exploring ribozyme conformational changes with X-ray crystallography.

    PubMed

    Spitale, Robert C; Wedekind, Joseph E

    2009-10-01

    Relating three-dimensional fold to function is a central challenge in RNA structural biology. Toward this goal, X-ray crystallography has long been considered the "gold standard" for structure determinations at atomic resolution, although NMR spectroscopy has become a powerhouse in this arena as well. In the area of dynamics, NMR remains the dominant technique to probe the magnitude and timescales of molecular motion. Although the latter area remains largely unassailable by conventional crystallographic methods, inroads have been made on proteins using Laue radiation on timescales of ms to ns. Proposed 'fourth generation' radiation sources, such as free-electron X-ray lasers, promise ps- to fs-timescale resolution, and credible evidence is emerging that supports the feasibility of single molecule imaging. At present however, the preponderance of RNA structural information has been derived from timescale and motion insensitive crystallographic techniques. Importantly, developments in computing, automation and high-flux synchrotron sources have propelled the rapidity of 'conventional' RNA crystal structure determinations to timeframes of hours once a suitable set of phases is obtained. With a sufficient number of crystal structures, it is possible to create a structural ensemble that can provide insight into global and local molecular motion characteristics that are relevant to biological function. Here we describe techniques to explore conformational changes in the hairpin ribozyme, a representative non-protein-coding RNA catalyst. The approaches discussed include: (i) construct choice and design using prior knowledge to improve X-ray diffraction; (ii) recognition of long-range conformational changes and (iii) use of single-base or single-atom changes to create ensembles. The methods are broadly applicable to other RNA systems.

  13. Symbiotic Stars in X-rays

    NASA Technical Reports Server (NTRS)

    Luna, G. J. M.; Sokoloski, J. L.; Mukai, K.; Nelson, T.

    2014-01-01

    Until recently, symbiotic binary systems in which a white dwarf accretes from a red giant were thought to be mainly a soft X-ray population. Here we describe the detection with the X-ray Telescope (XRT) on the Swift satellite of 9 white dwarf symbiotics that were not previously known to be X-ray sources and one that was previously detected as a supersoft X-ray source. The 9 new X-ray detections were the result of a survey of 41 symbiotic stars, and they increase the number of symbiotic stars known to be X-ray sources by approximately 30%. Swift/XRT detected all of the new X-ray sources at energies greater than 2 keV. Their X-ray spectra are consistent with thermal emission and fall naturally into three distinct groups. The first group contains those sources with a single, highly absorbed hard component, which we identify as probably coming from an accretion-disk boundary layer. The second group is composed of those sources with a single, soft X-ray spectral component, which likely arises in a region where low-velocity shocks produce X-ray emission, i.e. a colliding-wind region. The third group consists of those sources with both hard and soft X-ray spectral components. We also find that unlike in the optical, where rapid, stochastic brightness variations from the accretion disk typically are not seen, detectable UV flickering is a common property of symbiotic stars. Supporting our physical interpretation of the two X-ray spectral components, simultaneous Swift UV photometry shows that symbiotic stars with harder X-ray emission tend to have stronger UV flickering, which is usually associated with accretion through a disk. To place these new observations in the context of previous work on X-ray emission from symbiotic stars, we modified and extended the alpha/beta/gamma classification scheme for symbiotic-star X-ray spectra that was introduced by Muerset et al. based upon observations with the ROSAT satellite, to include a new sigma classification for sources with

  14. Ultrafast X-Ray Crystallography and Liquidography

    NASA Astrophysics Data System (ADS)

    Ki, Hosung; Oang, Key Young; Kim, Jeongho; Ihee, Hyotcherl

    2017-05-01

    Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.

  15. Compound refractive X-ray lens

    DOEpatents

    Nygren, David R.; Cahn, Robert; Cederstrom, Bjorn; Danielsson, Mats; Vestlund, Jonas

    2000-01-01

    An apparatus and method for focusing X-rays. In one embodiment, his invention is a commercial-grade compound refractive X-ray lens. The commercial-grade compound refractive X-ray lens includes a volume of low-Z material. The volume of low-Z material has a first surface which is adapted to receive X-rays of commercially-applicable power emitted from a commercial-grade X-ray source. The volume of low-Z material also has a second surface from which emerge the X-rays of commercially-applicable power which were received at the first surface. Additionally, the commercial-grade compound refractive X-ray lens includes a plurality of openings which are disposed between the first surface and the second surface. The plurality of openings are oriented such that the X-rays of commercially-applicable power which are received at the first surface, pass through the volume of low-Z material and through the plurality openings. In so doing, the X-rays which emerge from the second surface are refracted to a focal point.

  16. An Imaging X-Ray Polarimetry Mission

    NASA Technical Reports Server (NTRS)

    Weisskopf, Martin C.; Bellazini, Ronaldo; Costa, Enrico; Ramsey, Brian; O'Dell, Steve; Elsner, Ronald; Pavlov, George; Matt, Giorgio; Kaspi, Victoria; Tennant, Allyn; hide

    2008-01-01

    Technical progress both in x-ray optics and in polarization-sensitive x-ray detectors, which our groups have pioneered, enables a scientifically powerful---yet inexpensive---dedicated mission for imaging x-ray polarimetry. Such a mission is sufficiently sensitive to measure x-ray (linear) polarization for a broad range of cosmic sources --particularly those involving neutron stars, stellar black holes, and supermassive black holes (active galactic nuclei). We describe the technical elements, discuss a mission concept, and synopsize the important physical and astrophysical questions such a mission would address.

  17. An Imaging X-Ray Polarimetry Mission

    NASA Technical Reports Server (NTRS)

    Weisskopf, Martin C.; Bellazini, Ronaldo; Costa, Enrico; Ramsey, Brian; O'Dell, Steve; Tennant, Allyn; Elsner, Ronald; Pavlov, George; Matt, Girogio; Kaspi, Vicky; hide

    2008-01-01

    Technical progress both in x-ray optics and in polarization-sensitive x-ray detectors, which our groups have pioneered, enables a scientifically powerful - yet inexpensive - dedicated mission for imaging x-ray polarimetry. Such a mission is sufficiently sensitive to measure x-ray (linear) polarization for a broad range of cosmic sources --- particularly those involving neutron stars, stellar black holes, and supermassive black holes (active galactic nuclei). We describe the technical elements, discuss a mission concept, and synopsiz:e the important physical and astrophysical questions such as mission would address.

  18. Colloid Coalescence with Focused X Rays

    SciTech Connect

    Weon, B. M.; Kim, J. T.; Je, J. H.; Yi, J. M.; Wang, S.; Lee, W.-K.

    2011-07-01

    We show direct evidence that focused x rays enable us to merge polymer colloidal particles at room temperature. This phenomenon is ascribed to the photochemical scission of colloids with x rays, reducing the molecular weight, glass transition temperature, surface tension, and viscosity of colloids. The observation of the neck bridge growth with time shows that the x-ray-induced colloid coalescence is analogous to viscoelastic coalescence. This finding suggests a feasible protocol of photonic nanofabrication by sintering or welding of polymers, without thermal damage, using x-ray photonics.

  19. X-rays from stellar flares

    NASA Technical Reports Server (NTRS)

    Linsky, Jeffrey L.

    1991-01-01

    A summary of X-ray observations of flares on dMe, active spectroscopic binaries and young stars is presented. Consideration is given to the energy associated with the X-ray emission and its relation to other components of the flare energy budget, the time behavior of the flaring plasma as seen by the X-ray emission, and comparisons of stellar flare parameters with solar compact and two ribbon flares. Flares are easily detected when the contrast in the emission from the flaring plasma relative to the stellar photosphere is large as in the X-ray, microwave, and UV regions of the spectrum.

  20. Bent crystal X-ray topography

    NASA Technical Reports Server (NTRS)

    Parker, D. L.

    1978-01-01

    A television X-ray topographic camera system was constructed. The system differs from the previous system in that it incorporates the X-ray TV imaging system and has a semi-automatic wafer loading system. Also the X-ray diffraction is in a vertical plane. This feature makes wafer loading easier and makes the system compatible with any commercial X-ray generating system. Topographs and results obtained from a study of the diffraction contrast variation with impurity concentration for both boron implanted and boron diffused silicon are included.

  1. Ultrafast X-Ray Crystallography and Liquidography.

    PubMed

    Ki, Hosung; Oang, Key Young; Kim, Jeongho; Ihee, Hyotcherl

    2017-05-05

    Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.

  2. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1996-12-16

    This is a photograph of the Chandra X-Ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF), High Resolution Mirror Assembly (HRMA) integration at the X-Ray Calibration Facility (XRCF) at the Marshall Space Flight Center (MSFC). The AXAF was renamed CXO in 1999. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It observes x-rays from high-energy regions of the universe, such as hot gas in the remnants of exploded stars. The HRMA, the heart of the telescope system, is contained in the cylindrical "telescope" portion of the observatory. Since high-energy x-rays would penetrate a normal mirror, special cylindrical mirrors were created. The two sets of four nested mirrors resemble tubes within tubes. Incoming x-rays graze off the highly polished mirror surface and are furneled to the instrument section for detection and study. MSFC's XRCF is the world's largest, most advanced laboratory for simulating x-ray emissions from distant celestial objects. It produces a space-like environment in which components related to x-ray telescope imaging are tested and the quality of their performances in space is predicted. TRW, Inc. was the prime contractor for the development of the CXO and NASA's MSFC was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The CXO was launched July 22, 1999 aboard the Space Shuttle Columbia (STS-93).

  3. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1997-12-16

    This is a photograph of the Chandra X-Ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF), High Resolution Mirror Assembly (HRMA) integration at the X-Ray Calibration Facility (XRCF) at the Marshall Space Flight Center (MSFC). The AXAF was renamed CXO in 1999. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It observes x-rays from high-energy regions of the universe, such as hot gas in the remnants of exploded stars. The HRMA, the heart of the telescope system, is contained in the cylindrical "telescope" portion of the observatory. Since high-energy x-rays would penetrate a normal mirror, special cylindrical mirrors were created. The two sets of four nested mirrors resemble tubes within tubes. Incoming x-rays graze off the highly polished mirror surface and are furneled to the instrument section for detection and study. MSFC's XRCF is the world's largest, most advanced laboratory for simulating x-ray emissions from distant celestial objects. It produces a space-like environment in which components related to x-ray telescope imaging are tested and the quality of their performances in space is predicted. TRW, Inc. was the prime contractor for the development of the CXO and NASA's MSCF was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The CXO was launched July 22, 1999 aboard the Space Shuttle Columbia (STS-93).

  4. Ultrashort X-ray pulse science

    SciTech Connect

    Chin, Alan Hap

    1998-05-01

    A variety of phenomena involves atomic motion on the femtosecond time-scale. These phenomena have been studied using ultrashort optical pulses, which indirectly probe atomic positions through changes in optical properties. Because x-rays can more directly probe atomic positions, ultrashort x-ray pulses are better suited for the study of ultrafast structural dynamics. One approach towards generating ultrashort x-ray pulses is by 90° Thomson scattering between terawatt laser pulses and relativistic electrons. Using this technique, the author generated ~ 300 fs, 30 keV (0.4 Å) x-ray pulses. These x-ray pulses are absolutely synchronized with ultrashort laser pulses, allowing femtosecond optical pump/x-ray probe experiments to be performed. Using the right-angle Thomson scattering x-ray source, the author performed time-resolved x-ray diffraction studies of laser-perturbated InSb. These experiments revealed a delayed onset of lattice expansion. This delay is due to the energy relaxation from a dense electron-hole plasma to the lattice. The dense electron-hole plasma first undergoes Auger recombination, which reduces the carrier concentration while maintaining energy content. Longitudinal-optic (LO) phonon emission then couples energy to the lattice. LO phonon decay into acoustic phonons, and acoustic phonon propagation then causes the growth of a thermally expanded layer. Source characterization is instrumental in utilizing ultrashort x-ray pulses in time-resolved x-ray spectroscopies. By measurement of the electron beam diameter at the generation point, the pulse duration of the Thomson scattered x-rays is determined. Analysis of the Thomson scattered x-ray beam properties also provides a novel means of electron bunch characterization. Although the pulse duration is inferred for the Thomson scattering x-ray source, direct measurement is required for other x-ray pulse sources. A method based on the laser-assisted photoelectric effect (LAPE) has been demonstrated as a

  5. X-rays from the youngest stars

    NASA Technical Reports Server (NTRS)

    Feigelson, Eric D.

    1994-01-01

    The X-ray properties of classical and weak-lined T Tauri stars are briefly reviewed, emphasizing recent results from the ROSAT satellite and prospects for ASCA. The interpretation of the high level of T Tauri X-rays as enhanced solar-type magnetic activity is discussed and criticized. The census of X-ray emitters is significantly increasing estimates of galactic star formation efficiency, and X-ray emission may be important for self-regulation of star formation. ASCA images will detect star formation regions out to several kiloparsecs and will study the magnetically heated plasma around T Tauri stars. However, images will often suffer from crowding effects.

  6. Separating Peaks in X-Ray Spectra

    NASA Technical Reports Server (NTRS)

    Nicolas, David; Taylor, Clayborne; Wade, Thomas

    1987-01-01

    Deconvolution algorithm assists in analysis of x-ray spectra from scanning electron microscopes, electron microprobe analyzers, x-ray fluorescence spectrometers, and like. New algorithm automatically deconvolves x-ray spectrum, identifies locations of spectral peaks, and selects chemical elements most likely producing peaks. Technique based on similarities between zero- and second-order terms of Taylor-series expansions of Gaussian distribution and of damped sinusoid. Principal advantage of algorithm: no requirement to adjust weighting factors or other parameters when analyzing general x-ray spectra.

  7. X-ray laser microscope apparatus

    DOEpatents

    Suckewer, Szymon; DiCicco, Darrell S.; Hirschberg, Joseph G.; Meixler, Lewis D.; Sathre, Robert; Skinner, Charles H.

    1990-01-01

    A microscope consisting of an x-ray contact microscope and an optical microscope. The optical, phase contrast, microscope is used to align a target with respect to a source of soft x-rays. The source of soft x-rays preferably comprises an x-ray laser but could comprise a synchrotron or other pulse source of x-rays. Transparent resist material is used to support the target. The optical microscope is located on the opposite side of the transparent resist material from the target and is employed to align the target with respect to the anticipated soft x-ray laser beam. After alignment with the use of the optical microscope, the target is exposed to the soft x-ray laser beam. The x-ray sensitive transparent resist material whose chemical bonds are altered by the x-ray beam passing through the target mater GOVERNMENT LICENSE RIGHTS This invention was made with government support under Contract No. De-FG02-86ER13609 awarded by the Department of Energy. The Government has certain rights in this invention.

  8. Imaging with x-ray lasers

    SciTech Connect

    Da Silva, L.B.; Cauble, B.; Frieders, G.; Koch, J.A.; MacGowan, B.J.; Matthews, D.L.; Mrowka, S.; Ress, D.; Trebes, J.E.; Weiland, T.L.

    1993-11-01

    Collisionally pumped soft x-ray lasers now operate over a wavelength range extending from 35--300 {Angstrom}. These sources have high peak brightness and are now being utilized for x-ray imaging and plasma interferometry. In this paper we will describe our efforts to probe long scalelength plasmas using Moire deflectrometry and soft x-ray imaging. The progress in the development of short pulse x-ray lasers using a double pulse irradiation technique which incorporates a travelling wave pump will also be presented.

  9. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    2000-04-01

    This Chandra X-Ray Observatory (CXO) image is a spectrum of a black hole, which is similar to the colorful spectrum of sunlight produced by a prism. The x-rays of interest are shown here recorded in bright stripes that run rightward and leftward from the center of the image. These x-rays are sorted precisely according to their energy with the highest-energy x-rays near the center of the image and the lower-energy x-rays farther out. The spectrum was obtained by using the Low Energy Transmission Grating (LETG), which intercepts x-rays and changes their direction by the amounts that depend sensitively on the x-ray energy. The assembly holds 540 gold transmission gratings. When in place behind the mirrors, the gratings intercept the x-rays reflected from the telescope. The bright spot at the center is due to a fraction of the x-ray radiation that is not deflected by the LETG. The spokes that intersect the central spot and the faint diagonal rays that flank the spectrum itself are artifacts due to the structure that supports the LETG grating elements. (Photo credit: NASA Cfa/J. McClintock et al)

  10. An Imaging X-Ray Polarimetry Mission

    NASA Technical Reports Server (NTRS)

    Weisskopf, Martin C.; Bellazini, Ronaldo; Costa, Enrico; Ramsey, Brian; O'Dell, Steve; Tennant, Allyn; Elsner, Ronald; Pavlov, George; Matt, Girogio; Kaspi, Vicky; Coppi, Paolo; Wu, Kinwah; Siegmund, Oswald

    2008-01-01

    Technical progress both in x-ray optics and in polarization-sensitive x-ray detectors, which our groups have pioneered, enables a scientifically powerful - yet inexpensive - dedicated mission for imaging x-ray polarimetry. Such a mission is sufficiently sensitive to measure x-ray (linear) polarization for a broad range of cosmic sources --- particularly those involving neutron stars, stellar black holes, and supermassive black holes (active galactic nuclei). We describe the technical elements, discuss a mission concept, and synopsiz:e the important physical and astrophysical questions such as mission would address.

  11. An Imaging X-Ray Polarimetry Mission

    NASA Technical Reports Server (NTRS)

    Weisskopf, Martin C.; Bellazini, Ronaldo; Costa, Enrico; Ramsey, Brian; O'Dell, Steve; Elsner, Ronald; Pavlov, George; Matt, Giorgio; Kaspi, Victoria; Tennant, Allyn; Coppi, Paolo; Wu, Kinwah; Siegmund, Oswald

    2008-01-01

    Technical progress both in x-ray optics and in polarization-sensitive x-ray detectors, which our groups have pioneered, enables a scientifically powerful---yet inexpensive---dedicated mission for imaging x-ray polarimetry. Such a mission is sufficiently sensitive to measure x-ray (linear) polarization for a broad range of cosmic sources --particularly those involving neutron stars, stellar black holes, and supermassive black holes (active galactic nuclei). We describe the technical elements, discuss a mission concept, and synopsize the important physical and astrophysical questions such a mission would address.

  12. Planetary X-rays: Relationship with solar X-rays and solar wind

    NASA Astrophysics Data System (ADS)

    Bhardwaj, A.

    Recently X-ray flares are observed from the low-latitude disk of giant planets Jupiter and Saturn in the energy range of 0.2-2 keV. These flares are found to occur in tandem with the occurrence of solar X-ray flare, when light travel time delay is accounted. These studies suggest that disk of outer planets Jupiter and Saturn acts as "diffuse mirror" for solar X-rays and that X-rays from these planets can be used to study flaring on the hemisphere of the Sun that in invisible to near-Earth space weather satellites. Also by proper modeling of the observed planetary X-rays the solar soft X-ray flux can be derived. X-ray flares are also observed on the Mars. On the other hand, X-rays from comets are produced mainly in charge exchange interaction between highly ionized heavy solar wind ions and cometary neutrals. Thus cometary X-rays provide a diagnostics of the solar wind properties. X-rays from Martian exosphere is also dominantly produced via charge exchange interaction between Martian corona and solar wind, providing proxy for solar wind. This paper provides a brief overview on the X-rays from some of the planets and comets and their connection with solar X-rays and solar wind, and how planetary X-rays can be used to study the Sun.

  13. X-Ray Imaging Study

    NASA Technical Reports Server (NTRS)

    OBrien, Susan K.; Workman, Gary L.

    1996-01-01

    The space environment in which the Space Station Freedom and other space platforms will orbit is truly a hostile environment. For example, the currently estimated integral fluence for electrons above 1 Mev at 2000 nautical miles is above 2 x 1O(exp 10) electrons/sq cm/day and the proton integral fluence is above 1 x 10(exp 9) protons/sq cm/day. At the 200 - 400 nautical miles, which is more representative of the altitude which will provide the environment for the Space Station, each of these fluences will be proportionally less; however, the data indicates that the radiation environment will obviously have an effect on structural materials exposed to the environment for long durations. The effects of this combined environment is the issue which needs to be understood for the long term exposure of structures in space. At the same time, there will be substantial potential for collisions between the space platforms and space debris. The current NASA catalogue contains over 4500 objects floating in space which are not considered payloads. This debris can have significant effects on collision with orbiting spacecraft. In order to better understand the effect of these hostile phenomena on spacecraft, several types of studies are being performed to simulate at some level the effect of the environment. In particular the study of debris clouds produced by hypervelocity impact on the various surfaces anticipated on the Space Station is very important at this point in time. The need to assess the threat of such debris clouds on space structures is an on-going activity. The Space Debris Impact facility in Building 4612 provides a test facility to monitor the types of damage produced with hypervelocity impact. These facilities are used to simulate space environmental effects from energetic particles. Flash radiography or x-ray imaging has traditionally provided such information and as such has been an important tool for recording damage in situ with the event. The proper

  14. X-rays from Saturn Pose Puzzles

    NASA Astrophysics Data System (ADS)

    2004-03-01

    The first clear detection of X-rays from the giant, gaseous planet Saturn has been made with NASA's Chandra X-ray Observatory. Chandra's image shows that the X-rays are concentrated near Saturn's equator, a surprising result since Jupiter's X-ray emission is mainly concentrated near the poles. Existing theories cannot easily explain the intensity or distribution of Saturn's X-rays. Chandra observed Saturn for about 20 hours in April of 2003. The spectrum, or distribution with energy of the X-rays, was found to be very similar to that of X-rays from the Sun. "This indicates that Saturn's X-ray emission is due to the scattering of solar X-rays by Saturn's atmosphere," said Jan-Uwe Ness, of the University of Hamburg in Germany and lead author of a paper discussing the Saturn results in an upcoming issue of Astronomy & Astrophysics. "It's a puzzle, since the intensity of Saturn's X-rays requires that Saturn reflects X-rays fifty times more efficiently than the Moon." The observed 90 megawatts of X-ray power from Saturn's equatorial region is roughly consistent with previous observations of the X-radiation from Jupiter's equatorial region. This suggests that both giant, gaseous planets reflect solar X-rays at unexpectedly high rates. Further observations of Jupiter will be needed to test this possibility. The weak X-radiation from Saturn's south-polar region presents another puzzle (the north pole was blocked by Saturn's rings during this observation). Saturn's magnetic field, like that of Jupiter, is strongest near the poles. X-radiation from Jupiter is brightest at the poles because of auroral activity due to the enhanced interaction of high-energy particles from the Sun with its magnetic field. Since spectacular ultraviolet polar auroras have been observed to occur on Saturn, Ness and colleagues expected that Saturn's south pole might be bright in X-rays. It is not clear whether the auroral mechanism does not produce X-rays on Saturn, or for some reason concentrates

  15. Teaching Biochemists and Pharmacologists How to Use Crystallographic Data.

    ERIC Educational Resources Information Center

    Duax, William L.

    1988-01-01

    Describes a one-semester course designed to teach first year graduate students how to extract, interpret, evaluate, and use the information provided by an X-ray crystallographic crystal structure determination. Presents a course outline and discusses the treatment of crystal composition, crystallographic parameters, molecular geometry and…

  16. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1998-01-01

    This is a computer rendering of the fully developed Chandra X-Ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF). In 1999, the AXAF was renamed the CXO in honor of the late Indian-American Novel Laureate Subrahmanyan Chandrasekhar. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It is designed to observe x-rays from high energy regions of the Universe, such as hot gas in the renmants of exploded stars. It produces picture-like images of x-ray emissions analogous to those made in visible light, as well as gathers data on the chemical composition of x-ray radiating objects. The CXO helps astronomers world-wide better understand the structure and evolution of the universe by studying powerful sources of x-ray such as exploding stars, matter falling into black holes, and other exotic celestial objects. The Observatory has three major parts: (1) the x-ray telescope, whose mirrors will focus x-rays from celestial objects; (2) the science instruments that record the x-rays so that x-ray images can be produced and analyzed; and (3) the spacecraft, which provides the environment necessary for the telescope and the instruments to work. TRW, Inc. was the prime contractor for the development of the CXO and NASA's Marshall Space Flight Center was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The Observatory was launched July 22, 1999 aboard the Space Shuttle Columbia, STS-93 mission. (Image courtesy of TRW).

  17. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1997-04-15

    This photograph captures the installation of the Chandra X-Ray Observatory, formerly Advanced X-Ray Astrophysics Facility (AXAF), Advanced Charged-Coupled Device (CCD) Imaging Spectrometer (ACIS) into the Vacuum Chamber at the X-Ray Calibration Facility (XRCF) at Marshall Space Flight Center (MSFC). The AXAF was renamed Chandra X-Ray Observatory (CXO) in 1999. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It observes x-rays from high-energy regions of the universe, such as hot gas in the remnants of exploded stars. The ACIS is one of two focal plane instruments. As the name suggests, this instrument is an array of CCDs similar to those used in a camcorder. This instrument will be especially useful because it can make x-ray images and measure the energies of incoming x-rays. It is the instrument of choice for studying the temperature variation across x-ray sources, such as vast clouds of hot-gas intergalactic space. MSFC's XRCF is the world's largest, most advanced laboratory for simulating x-ray emissions from distant celestial objects. It produces a space-like environment in which components related to x-ray telescope imaging are tested and the quality of their performances in space is predicted. TRW, Inc. was the prime contractor for the development of the CXO and NASA's MSFC was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The CXO was launched July 22, 1999 aboard the Space Shuttle Columbia (STS-93).

  18. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1999-01-01

    This is a computer rendering of the fully developed Chandra X-ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF), in orbit in a star field. In 1999, the AXAF was renamed the CXO in honor of the late Indian-American Novel Laureate Subrahmanyan Chandrasekhar. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It is designed to observe x-rays from high energy regions of the Universe, such as hot gas in the renmants of exploded stars. It produces picture-like images of x-ray emissions analogous to those made in visible light, as well as gathers data on the chemical composition of x-ray radiating objects. The CXO helps astronomers world-wide better understand the structure and evolution of the universe by studying powerful sources of x-rays such as exploding stars, matter falling into black holes, and other exotic celestial objects. The Observatory has three major parts: (1) the x-ray telescope, whose mirrors will focus x-rays from celestial objects; (2) the science instruments that record the x-rays so that x-ray images can be produced and analyzed; and (3) the spacecraft, which provides the environment necessary for the telescope and the instruments to work. TRW, Inc. was the prime contractor for the development of the CXO and NASA's Marshall Space Flight Center was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The Observatory was launched July 22, 1999 aboard the Space Shuttle Columbia, STS-93 mission. (Image courtesy of TRW).

  19. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1995-01-14

    This is an artist's concept of the Chandra X-Ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF), fully developed in orbit in a star field with Earth. In 1999, the AXAF was renamed the CXO in honor of the late Indian-American Novel Laureate Subrahmanyan Chandrasekhar. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It is designed to observe x-rays from high energy regions of the Universe, such as hot gas in the renmants of exploded stars. It produces picture-like images of x-ray emissions analogous to those made in visible light, as well as gathers data on the chemical composition of x-ray radiating objects. The CXO helps astronomers world-wide better understand the structure and evolution of the universe by studying powerful sources of x-ray such as exploding stars, matter falling into black holes, and other exotic celestial objects. The Observatory has three major parts: (1) the x-ray telescope, whose mirrors will focus x-rays from celestial objects; (2) the science instruments that record the x-rays so that x-ray images can be produced and analyzed; and (3) the spacecraft, which provides the environment necessary for the telescope and the instruments to work. TRW, Inc. was the prime contractor for the development the CXO and NASA's Marshall Space Flight Center was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The Observatory was launched July 22, 1999 aboard the Space Shuttle Columbia, STS-93 mission. (Image courtesy of TRW).

  20. Wide field x-ray telescopes: Detecting x-ray transients/afterglows related to GRBs

    SciTech Connect

    Hudec, Rene; Pina, Ladislav; Inneman, Adolf; Gorenstein, Paul

    1998-05-16

    The recent discovery of X-ray afterglows of GRBs opens the possibility of analyses of GRBs by their X-ray detections. However, imaging X-ray telescopes in current use mostly have limited fields of view. Alternative X-ray optics geometries achieving very large fields of view have been theoretically suggested in the 70's but not constructed and used so far. We review the geometries and basic properties of the wide-field X-ray optical systems based on one- and two-dimensional lobster-eye geometry and suggest technologies for their development and construction. First results of the development of double replicated X-ray reflecting flats for use in one-dimensional X-ray optics of lobster-eye type are presented and discussed. The optimum strategy for locating GRBs upon their X-ray counterparts is also presented and discussed.