Diffracted X-ray tracking: new system for single molecular detection with X-rays

CERN Document Server

Sasaki, Y C; Adachi, S; Suzuki, Y; Yagi, N

2001-01-01

We propose a new X-ray methodology for direct observations of the behaviors of single molecular units in real time and real space. This new system, which we call Diffracted X-ray Tracking (DXT), monitors the Brownian motions of a single molecular unit by observations of X-ray diffracted spots from a nanocrystal, tightly bound to the individual single molecular unit in bio-systems. DXT does not determine any translational movements, but only orientational movements.

Diffracted X-ray tracking: new system for single molecular detection with X-rays

International Nuclear Information System (INIS)

Sasaki, Y.C.; Okumura, Y.; Adachi, S.; Suzuki, Y.; Yagi, N.

2001-01-01

We propose a new X-ray methodology for direct observations of the behaviors of single molecular units in real time and real space. This new system, which we call Diffracted X-ray Tracking (DXT), monitors the Brownian motions of a single molecular unit by observations of X-ray diffracted spots from a nanocrystal, tightly bound to the individual single molecular unit in bio-systems. DXT does not determine any translational movements, but only orientational movements

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto

International Nuclear Information System (INIS)

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

2010-01-01

Nattokinase, a protein found in high levels in the traditional Japanese food natto, has been reported to have high thrombolytic activity. In the present study, the crystallization of native nattokinase and the collection of X-ray diffraction date from a nattokinase crystal to a resolution of 1.74 Å are reported. Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27 724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a = 74.3, b = 49.9, c = 56.3 Å, β = 95.2°. Diffraction images were processed to a resolution of 1.74 Å with an R merge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto

Energy Technology Data Exchange (ETDEWEB)

Yanagisawa, Yasuhide [Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba 288-0025 (Japan); Chatake, Toshiyuki [Research Reactor Institute, Kyoto University, Asashironishi 2, Kumatori, Sennan, Osaka 590-0494 (Japan); Chiba-Kamoshida, Kaori [National Institute of Advanced Industrial Science and Technology (AIST), Umezono 1-1-1, Tsukuba, Ibaraki 305-8568 (Japan); Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki [Kurashiki University of Science and Arts, Nishinoura 2640, Tsurajima-cho, Kurashiki, Okayama 712-8505 (Japan); Yasuda, Ichiro [Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba 288-0025 (Japan); Morimoto, Yukio [Research Reactor Institute, Kyoto University, Asashironishi 2, Kumatori, Sennan, Osaka 590-0494 (Japan); Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba 288-0025 (Japan)

2010-12-01

Nattokinase, a protein found in high levels in the traditional Japanese food natto, has been reported to have high thrombolytic activity. In the present study, the crystallization of native nattokinase and the collection of X-ray diffraction date from a nattokinase crystal to a resolution of 1.74 Å are reported. Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27 724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a = 74.3, b = 49.9, c = 56.3 Å, β = 95.2°. Diffraction images were processed to a resolution of 1.74 Å with an R{sub merge} of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase.

Characterization of an Yb:LuVO{sub 4} single crystal using X-ray topography, high-resolution X-ray diffraction, and X-ray photoelectron spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Paszkowicz, W., E-mail: paszk@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, PL-02668 Warsaw (Poland); Romanowski, P.; Bak-Misiuk, J. [Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, PL-02668 Warsaw (Poland); Wierzchowski, W. [Institute of Electronic Materials Technology, Wolczynska 133, PL-01919 Warsaw (Poland); Wieteska, K. [Institute of Atomic Energy POLATOM, PL-05400 Otwock-Swierk (Poland); Graeff, W. [HASYLAB at DESY, Notkestr. 85, D-22603 Hamburg (Germany); Iwanowski, R.J. [Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, PL-02668 Warsaw (Poland); Heinonen, M.H. [Laboratory of Materials Science, Department of Physics, University of Turku, Vesilinnantie 5, FI-20014, Turku (Finland); Ermakova, O. [Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, PL-02668 Warsaw (Poland); Dabkowska, H. [Department of Physics, McMaster University, Hamilton, Ontario, L8S 4M1 (Canada)

2011-10-15

Knowledge on the defect and electronic structure allows for improved modeling of material properties. A short literature review has shown that the information on defect structure of rare earth orthovanadate single crystals is limited. In this paper, defect and electronic structure of a needle-shaped Yb:LuVO{sub 4} single crystal grown by the slow cooling method have been studied by means of X-ray diffraction topography employing white synchrotron beam, high-resolution diffraction (HRD) and photoelectron spectroscopy (XPS) techniques. Topographic investigations show that the crystal is composed of two blocks disoriented by about 1.5{sup o} and separated by a narrow deformed region. Some contrasts observed within the crystal volume may be attributed to glide bands and sector boundaries. The contrasts appearing in the vicinity of the surface may be interpreted as due to the presence of small inclusions. The HRD study indicates, in particular, that among point defects, the vacancy type defects dominate and that the density of other defects is small in comparison. The XPS measurements enabled, despite highly insulating properties of the studied crystal, an analysis of its bulk electronic structure, including the main core-levels (O 1s, V 2p, Lu 4f) as well as the valence band range.

X-ray and neutron single crystal diffraction on (NH4)3H(SO4)2. II. Refinement of crystal structure of phase II at room temperature

International Nuclear Information System (INIS)

Reehuis, M.; Wozniak, K.; Dominiak, P.; Smirnov, L.S.; Natkaniec, I.; Baranov, A.I.; Dolbinina, V.V.

2006-01-01

The (NH 4 ) 3 H(SO 4 ) 2 is of special interest due to the possible influence of ammonium ions on a series of phase transitions: I => II => III => IV => V => VII. Earlier, the X-ray single crystal diffraction study of phase II of (NH 4 ) 3 H(SO 4 ) 2 showed that the crystal structure of this compound has two crystallographically independent groups of ammonium ions NH 4 (1) and NH 4 (2), but orientational positions of these ammonium ions were not determined exactly. The refinement of NH 4 (1) and NH 4 (2) orientational positions in phase II is carried out with the help of the X-ray and neutron single crystal diffraction study. The analyses of differential Fourier maps of electron charge density and nuclear density point out the possibility of disordering of NH 4 (2) ammonium ions

Surface quality inspection of PbWO4 crystals by grazing incidence X-ray diffraction

International Nuclear Information System (INIS)

Mengucci, P.; Di Cristoforo, A.; Lebeau, M.; Majni, G.; Paone, N.; Pietroni, P.; Rinaldi, D.

2005-01-01

High-quality scintillating crystals are required for applications in radiographic systems and high-energy physics detectors to achieve the specified optical properties. In order to study the state of the single crystals surface we propose the use of the grazing incidence X-ray diffraction (GID) technique. This technique allows performing a depth profiling of the sample by changing the incidence angle of the X-ray beam with respect to the sample surface. In this work, two samples of a large PbWO 4 (PWO) single crystal exhibiting different surface roughness values have been studied. Results have shown that GID is a suitable technique for surface quality inspection

LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae

Energy Technology Data Exchange (ETDEWEB)

Kusakizako, Tsukasa [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Tanaka, Yoshiki [Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 (Japan); Hipolito, Christopher J. [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575 (Japan); Kuroda, Teruo [Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 (Japan); Ishitani, Ryuichiro [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Suga, Hiroaki [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Nureki, Osamu, E-mail: nureki@bs.s.u-tokyo.ac.jp [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)

2016-06-22

A V. cholerae MATE transporter was crystallized using the lipidic cubic phase (LCP) method. X-ray diffraction data sets were collected from single crystals obtained in a sandwich plate and a sitting-drop plate to resolutions of 2.5 and 2.2 Å, respectively. Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-ray diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 52.3, b = 93.7, c = 100.2 Å. As a result of further LCP crystallization trials, crystals of larger size were obtained using sitting-drop plates. X-ray diffraction data were collected to 2.2 Å resolution from a single crystal obtained in a sitting-drop plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.9, b = 91.8, c = 100.9 Å. The present work provides valuable insights into the atomic resolution structure determination of membrane transporters.

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto.

Science.gov (United States)

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

2010-12-01

Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27,724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a=74.3, b=49.9, c=56.3 Å, β=95.2°. Diffraction images were processed to a resolution of 1.74 Å with an Rmerge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase.

Single-pulse x-ray diffraction using polycapillary optics for in situ dynamic diffraction

Energy Technology Data Exchange (ETDEWEB)

Maddox, B. R., E-mail: maddox3@llnl.gov; Akin, M. C., E-mail: akin1@llnl.gov; Teruya, A.; Hunt, D.; Hahn, D.; Cradick, J. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Morgan, D. V. [National Security Technologies LLC, Los Alamos, New Mexico 87544 (United States)

2016-08-15

Diagnostic use of single-pulse x-ray diffraction (XRD) at pulsed power facilities can be challenging due to factors such as the high flux and brightness requirements for diffraction and the geometric constraints of experimental platforms. By necessity, the x-ray source is usually positioned very close, within a few inches of the sample. On dynamic compression platforms, this puts the x-ray source in the debris field. We coupled x-ray polycapillary optics to a single-shot needle-and-washer x-ray diode source using a laser-based alignment scheme to obtain high-quality x-ray diffraction using a single 16 ns x-ray pulse with the source >1 m from the sample. The system was tested on a Mo sample in reflection geometry using 17 keV x-rays from a Mo anode. We also identified an anode conditioning effect that increased the x-ray intensity by 180%. Quantitative measurements of the x-ray focal spot produced by the polycapillary yielded a total x-ray flux on the sample of 3.3 ± 0.5 × 10{sup 7} molybdenum Kα photons.

Micromanipulation and pick-up system for X-Ray diffraction characterization of micrometer-sized single particles

International Nuclear Information System (INIS)

Takeichi, Y; Inami, N; Saito, K; Otori, H; Sagayama, R; Kumai, R; Ono, K; Ueno, T

2014-01-01

We describe a micromanipulation and pick-up system for preparing a micrometer-sized single particle for X-ray diffraction characterization. Combining a microgripper based on microelectromechanical systems, piezo-motor-driven linear stages, and a gamepad, the system provides precise and intuitive handling of the object. Single-crystal X-ray diffraction measurements of Sm-Fe-N permanent magnet were performed using this system. We also describe a method to distinguish crystallographically homogeneous particles found in powder-form samples.

Strength of shock-loaded single-crystal tantalum [100] determined using in situ broadband x-ray Laue diffraction.

Science.gov (United States)

Comley, A J; Maddox, B R; Rudd, R E; Prisbrey, S T; Hawreliak, J A; Orlikowski, D A; Peterson, S C; Satcher, J H; Elsholz, A J; Park, H-S; Remington, B A; Bazin, N; Foster, J M; Graham, P; Park, N; Rosen, P A; Rothman, S R; Higginbotham, A; Suggit, M; Wark, J S

2013-03-15

The strength of shock-loaded single crystal tantalum [100] has been experimentally determined using in situ broadband x-ray Laue diffraction to measure the strain state of the compressed crystal, and elastic constants calculated from first principles. The inferred strength reaches 35 GPa at a shock pressure of 181 GPa and is in excellent agreement with a multiscale strength model [N. R. Barton et al., J. Appl. Phys. 109, 073501 (2011)], which employs a hierarchy of simulation methods over a range of length scales to calculate strength from first principles.

Correct interpretation of diffraction properties of quartz crystals for X-ray optics applications

Energy Technology Data Exchange (ETDEWEB)

Huang, Xian-Rong; Gog, Thomas; Kim, Jungho; Kasman, Elina; Said, Ayman H.; Casa, Diego M.; Wieczorek, Michael; Hönnicke, Marcelo G.; Assoufid, Lahsen

2018-02-01

Quartz has hundreds of strong Bragg reflections that may offer a great number of choices for making fixed-angle X-ray analyzers and polarizers at virtually any hard X-ray energies with selectable resolution. However, quartz crystals, unlike silicon and germanium, are chiral and may thus appear in two different forms of handedness that are mirror images. Furthermore, because of the threefold rotational symmetry along thecaxis, the {h₁h₂h₃L} and {h₂h₁h₃L} Bragg reflections may have quite different Darwin bandwidth, reflectivity and angular acceptance, although they have the same Bragg angle. The design of X-ray optics from quartz crystals therefore requires unambiguous determination of the orientation, handedness and polarity of the crystals. The Laue method and single-axis diffraction technique can provide such information, but the variety of conventions used in the literature to describe quartz structures has caused widespread confusion. The current studies give detailed guidelines for design and fabrication of quartz X-ray optics, with special emphasis on the correct interpretation of Laue patterns in terms of the crystallography and diffraction properties of quartz. Meanwhile, the quartz crystals examined were confirmed by X-ray topography to have acceptably low densities of dislocations and other defects, which is the foundation for developing high-resolution quartz-based X-ray optics.

X-ray and Neutron Diffraction in the Study of Organic Crystalline Hydrates

Directory of Open Access Journals (Sweden)

Katharina Fucke

2010-07-01

Full Text Available A review. Diffraction methods are a powerful tool to investigate the crystal structure of organic compounds in general and their hydrates in particular. The laboratory standard technique of single crystal X-ray diffraction gives information about the molecular conformation, packing and hydrogen bonding in the crystal structure, while powder X-ray diffraction on bulk material can trace hydration/dehydration processes and phase transitions under non-ambient conditions. Neutron diffraction is a valuable complementary technique to X-ray diffraction and gives highly accurate hydrogen atom positions due to the interaction of the radiation with the atomic nuclei. Although not yet often applied to organic hydrates, neutron single crystal and neutron powder diffraction give precise structural data on hydrogen bonding networks which will help explain why hydrates form in the first place.

Variable-metric diffraction crystals for x-ray optics

International Nuclear Information System (INIS)

Smither, R.K.; Fernandez, P.B.

1992-01-01

A variable-metric (VM) crystal is one in which the spacing between the crystalline planes changes with position in the crystal. This variation can be either parallel to the crystalline planes or perpendicular to the crystalline planes of interest and can be produced by either introducing a thermal gradient in the crystal or by growing a crystal made of two or more elements and changing the relative percentages of the two elements as the crystal is grown. A series of experiments were performed in the laboratory to demonstrate the principle of the variable-metric crystal and its potential use in synchrotron beam lines. One of the most useful applications of the VM crystal is to increase the number of photons per unit bandwidth in a diffracted beam without losing any of the overall intensity. In a normal synchrotron beam line that uses a two-crystal monochromator, the bandwidth of the diffracted photon beam is determined by the vertical opening angle of the beam which is typically 0.10--0.30 mrad or 20--60 arcsec. When the VM crystal approach is applied, the bandwidth of the beam can be made as narrow as the rocking curve of the diffracting crystal, which is typically 0.005--0.050 mrad or 1--10 arcsec. Thus a very large increase of photons per unit bandwidth (or per unit energy) can be achieved through the use of VM crystals. When the VM principle is used with bent crystals, new kinds of x-ray optical elements can be generated that can focus and defocus x-ray beams much like simple lenses where the focal length of the lens can be changed to match its application. Thus both large magnifications and large demagnifications can be achieved as well as parallel beams with narrow bandwidths

High pressure single-crystal micro X-ray diffraction analysis with GSE_ADA/RSV software

Science.gov (United States)

Dera, Przemyslaw; Zhuravlev, Kirill; Prakapenka, Vitali; Rivers, Mark L.; Finkelstein, Gregory J.; Grubor-Urosevic, Ognjen; Tschauner, Oliver; Clark, Simon M.; Downs, Robert T.

2013-08-01

GSE_ADA/RSV is a free software package for custom analysis of single-crystal micro X-ray diffraction (SCμXRD) data, developed with particular emphasis on data from samples enclosed in diamond anvil cells and subject to high pressure conditions. The package has been in extensive use at the high pressure beamlines of Advanced Photon Source (APS), Argonne National Laboratory and Advanced Light Source (ALS), Lawrence Berkeley National Laboratory. The software is optimized for processing of wide-rotation images and includes a variety of peak intensity corrections and peak filtering features, which are custom-designed to make processing of high pressure SCμXRD easier and more reliable.

Diffractive-refractive optics: (+,-,-,+) X-ray crystal monochromator with harmonics separation.

Science.gov (United States)

Hrdý, Jaromír; Mikulík, Petr; Oberta, Peter

2011-03-01

A new kind of two channel-cut crystals X-ray monochromator in dispersive (+,-,-,+) position which spatially separates harmonics is proposed. The diffracting surfaces are oriented so that the diffraction is inclined. Owing to refraction the diffracted beam is sagittally deviated. The deviation depends on wavelength and is much higher for the first harmonics than for higher harmonics. This leads to spatial harmonics separation. The idea is supported by ray-tracing simulation.

New structural studies of liquid crystal by reflectivity and resonant X-ray diffraction

International Nuclear Information System (INIS)

Fernandes, P.

2007-04-01

This memory presents three structural studies of smectic Liquid Crystals by reflectivity and resonant diffraction of X-rays. It is divided in five chapters. In the first a short introduction to Liquid Crystals is given. In particular, the smectic phases that are the object of this study are presented. The second chapter is consecrated to the X-ray experimental techniques that were used in this work. The three last chapters present the works on which this thesis can be divided. Chapter three demonstrates on free-standing films of MHPOBC (historic liquid crystal that possesses the antiferroelectric sub-phases) the possibility to extend the technique of resonant X-ray diffraction to liquid crystals without resonant element. In the fourth chapter the structure of the B 2 liquid crystal phase of bent-core molecules (or banana molecules) is elucidated by using resonant X-ray diffraction combined with polarization analysis of the diffracted beam. A model of the polarization of the resonant beam diffracted by four different structures proposed for the B 2 phase is developed in this chapter. In the fifth chapter a smectic binary mixture presenting a very original critical point of phase separation is studied by X-ray reflectivity and optical microscopy. A concentration gradient in the direction perpendicular to the plane of the film seems to be induced by the free-standing film geometry. The results of a simplified model of the system are compatible with this interpretation

Production, crystallization and preliminary X-ray diffraction analysis of the allergen Can f 2 from Canis familiaris

International Nuclear Information System (INIS)

Madhurantakam, Chaithanya; Nilsson, Ola B.; Jönsson, Klas; Grönlund, Hans; Achour, Adnane

2009-01-01

The recombinant form of the allergen Can f 2 from C. familiaris was produced, isolated and crystallized in two different forms. Preliminary X-ray diffraction analyses are reported for the two crystal forms of Can f 2. The allergen Can f 2 from dog (Canis familiaris) present in saliva, dander and fur is an important cause of allergic sensitization worldwide. Here, the production, isolation, crystallization and preliminary X-ray diffraction analysis of two crystal forms of recombinant Can f 2 are reported. The first crystal form belonged to space group C222, with unit-cell parameters a = 68.7, b = 77.3, c = 65.1 Å, and diffracted to 1.55 Å resolution, while the second crystal form belonged to space group C2, with unit-cell parameters a = 75.7, b = 48.3, c = 68.7 Å, β = 126.5°, and diffracted to 2.1 Å resolution. Preliminary data analysis indicated the presence of a single molecule in the asymmetric unit for both crystal forms

Long wave-length x-ray diffraction crystal and method of manufacturing same

International Nuclear Information System (INIS)

Zingaro, W.P.; Sicignano, A.

1980-01-01

An x-ray diffraction crystal of the Langemuir-Blodgett type capable of detecting radiation having a wavelength greater than 50 Arystroms and a method of making such a crystal are described. The crystal consists of a pair of alternate monolayers, one a heavy metal soap, and one a light metal soap. Selecting cation pairs with a significant difference in atomic number and dispersing power, such as Pb and Be, Mg, or Ca, increases the effective interplanar distance since the Pb planes cause the predominant x-ray diffraction. (LL)

Coherent X-ray diffraction studies of mesoscopic materials

International Nuclear Information System (INIS)

Shabalin, Anatoly

2015-12-01

This thesis is devoted to three separate projects, which can be considered as independent. First, the dynamical scattering effects in the Coherent X-ray Diffractive Imaging (CXDI) method are discussed. Based on the simulation results, a straightforward method for correction for the refraction and absorption artifacts in the Bragg CXDI reconstruction is suggested. The second part summarizes the results of an Coherent X-ray Diffractive Imaging experiment with a single colloidal crystal grain. A remarkable result is that positions of individual particles in the crystal lattice have been resolved in three dimensions. The third project is devoted to X-ray diffraction experimental studies of structural evolution of colloidal crystalline films upon incremental heating. Based on the results of the analysis a model of structural evolution of a colloidal crystal upon heating on nanoscopic and mesoscopic length scales is suggested.

Sequential x-ray diffraction topography at 1-BM x-ray optics testing beamline at the advanced photon source

Energy Technology Data Exchange (ETDEWEB)

Stoupin, Stanislav, E-mail: sstoupin@aps.anl.gov; Shvyd’ko, Yuri; Trakhtenberg, Emil; Liu, Zunping; Lang, Keenan; Huang, Xianrong; Wieczorek, Michael; Kasman, Elina; Hammonds, John; Macrander, Albert; Assoufid, Lahsen [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States)

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.

X-ray diffraction studies of NbTe2 single crystal

Indian Academy of Sciences (India)

Unknown

X-ray (EDAX) and remaining structural characterization was also accomplished by X-ray diffraction (XRD) studies. Lattice parameters, volume and ... The layered structure compound, NbTe2, is one of the typical materials which lead to charge .... financial assistance to carry out this work. References. Brown B E 1966 Acta ...

Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction

International Nuclear Information System (INIS)

Emamzadah, Soheila; Petty, Tom J.; De Almeida, Victor; Nishimura, Taisuke; Joly, Jacques; Ferrer, Jean-Luc; Halazonetis, Thanos D.

2009-01-01

A cyclic olefin homopolymer-based microfluidics system has been established for protein crystallization and in situ X-ray diffraction. Microfluidics is a promising technology for the rapid identification of protein crystallization conditions. However, most of the existing systems utilize silicone elastomers as the chip material which, despite its many benefits, is highly permeable to water vapour. This limits the time available for protein crystallization to less than a week. Here, the use of a cyclic olefin homopolymer-based microfluidics system for protein crystallization and in situ X-ray diffraction is described. Liquid handling in this system is performed in 2 mm thin transparent cards which contain 500 chambers, each with a volume of 320 nl. Microbatch, vapour-diffusion and free-interface diffusion protocols for protein crystallization were implemented and crystals were obtained of a number of proteins, including chicken lysozyme, bovine trypsin, a human p53 protein containing both the DNA-binding and oligomerization domains bound to DNA and a functionally important domain of Arabidopsis Morpheus’ molecule 1 (MOM1). The latter two polypeptides have not been crystallized previously. For X-ray diffraction analysis, either the cards were opened to allow mounting of the crystals on loops or the crystals were exposed to X-rays in situ. For lysozyme, an entire X-ray diffraction data set at 1.5 Å resolution was collected without removing the crystal from the card. Thus, cyclic olefin homopolymer-based microfluidics systems have the potential to further automate protein crystallization and structural genomics efforts

X-ray diffraction 2 - diffraction principles

International Nuclear Information System (INIS)

O'Connor, B.

1999-01-01

Full text: The computation of powder diffraction intensities is based on the principle that the powder pattern comprises the summation of the intensity contributions from each of the crystallites (or single crystals) in the material. Therefore, it is of value for powder diffractionists to appreciate the form of the expression for calculating single crystal diffraction pattern intensities. This knowledge is especially important for Rietveld analysis practitioners in terms of the (i) mathematics of the method and (ii) retrieving single crystal structure data from the literature. We consider the integrated intensity from a small single crystal being rotated at velocity ω through the Bragg angle θ for reflection (hkl).... I(hkl) = [l o /ω]. [e 4 /m 2 c 4 ]. [λ 3 δV F(hkl) 2 /υ 2 ].[(1+cos 2 2θ)/2sin2θ] where e, m and c are the usual fundamental constants; λ is the x-ray wavelength, δV is the crystallite volume; F(hkl) is the structure factor; υ is the unit cell volume; and (1+cos 2 θ)/2sin2θ] is the Lorentz-polarisation factor for an unpolarised incident beam. The expression does not include a contribution for extinction. The influence of factors λ, δV, F(hkl) and υ on the intensities should be appreciated by powder diffractionists, especially the structure factor, F(hkl), which is responsible for the fingerprint nature of diffraction patterns, such as the rise and fall of intensity from peak to peak. The structure factor expression represents the summation of the scattered waves from each of the j scattering centres (i e atoms) in the unit cell: F(hkl) Σ f j exp[2πi (h.x j +k.y i +l. z i )] T j . Symbol f is the scattering factor (representing the atom-type scattering efficiency); (x, y, z) are the fractional position coordinates of atom j within the unit cell; and T is the thermal vibration factor for the atom given by: T j = 8π 2 2 > sin 2 θ/λ 2 with 2 > being the mean-square vibration amplitude of the atom (assumed to be isotropic). The

Diffractive-refractive optics: (+,-,-,+) X-ray crystal monochromator with harmonics separation

Czech Academy of Sciences Publication Activity Database

Hrdý, Jaromír; Mikulík, P.; Oberta, Peter

2011-01-01

Roč. 18, č. 2 (2011), s. 299-301 ISSN 0909-0495 R&D Projects: GA MPO FR-TI1/412 Institutional research plan: CEZ:AV0Z10100522 Keywords : diffractive-refractive optics * x-ray synchrotron radiation monochromator * x-ray crystal monochromator * harmonics separation Subject RIV: BH - Optics, Masers, Lasers Impact factor: 2.726, year: 2011

Measuring the x-ray resolving power of bent potassium acid phthalate diffraction crystals

International Nuclear Information System (INIS)

Haugh, M. J.; Jacoby, K. D.; Wu, M.; Loisel, G. P.

2014-01-01

This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals that we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories in Albuquerque, New Mexico. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a double crystal diffractometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed

Measuring the x-ray resolving power of bent potassium acid phthalate diffraction crystals

Energy Technology Data Exchange (ETDEWEB)

Haugh, M. J., E-mail: haughmj@nv.doe.gov; Jacoby, K. D. [National Security Technologies, LLC, Livermore, California 94550 (United States); Wu, M.; Loisel, G. P. [Sandia National Laboratories, Albuquerque, New Mexico 87123 (United States)

2014-11-15

This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals that we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories in Albuquerque, New Mexico. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a double crystal diffractometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed.

Diffraction. Single crystal, magnetic

International Nuclear Information System (INIS)

Heger, G.

1999-01-01

The analysis of crystal structure and magnetic ordering is usually based on diffraction phenomena caused by the interaction of matter with X-rays, neutrons, or electrons. Complementary information is achieved due to the different character of X-rays, neutrons and electrons, and hence their different interactions with matter and further practical aspects. X-ray diffraction using conventional laboratory equipment and/or synchrotron installations is the most important method for structure analyses. The purpose of this paper is to discuss special cases, for which, in addition to this indispensable part, neutrons are required to solve structural problems. Even though the huge intensity of modern synchrotron sources allows in principle the study of magnetic X-ray scattering the investigation of magnetic structures is still one of the most important applications of neutron diffraction. (K.A.)

Diffraction peaks in x-ray spectroscopy: Friend or foe?

International Nuclear Information System (INIS)

Tissot, R.G.; Goehner, R.P.

1992-01-01

Diffraction peaks can occur as unidentifiable peaks in the energy spectrum of an x-ray spectrometric analysis. Recently, there has been increased interest in oriented polycrystalline films and epitaxial films on single crystal substrates for electronic applications. Since these materials diffract x-rays more efficiently than randomly oriented polycrystalline materials, diffraction peaks are being observed more frequently in x-ray fluorescent spectra. In addition, micro x-ray spectrometric analysis utilizes a small, intense, collimated x-ray beam that can yield well defined diffraction peaks. In some cases these diffraction peaks can occur at the same position as elemental peaks. These diffraction peaks, although a possible problem in qualitative and quantitative elemental analysis, can give very useful information about the crystallographic structure and orientation of the material being analyzed. The observed diffraction peaks are dependent on the geometry of the x-ray spectrometer, the degree of collimation and the distribution of wavelengths (energies) originating from the x-ray tube and striking the sample

Simultaneous, single-pulse, synchrotron x-ray imaging and diffraction under gas gun loading

Energy Technology Data Exchange (ETDEWEB)

Fan, D.; Luo, S. N., E-mail: sluo@pims.ac.cn [The Peac Institute of Multiscale Sciences, Chengdu, Sichuan 610031 (China); Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China); Huang, J. W.; Zeng, X. L.; Li, Y.; E, J. C.; Huang, J. Y. [The Peac Institute of Multiscale Sciences, Chengdu, Sichuan 610031 (China); Sun, T.; Fezzaa, K. [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Wang, Z. [Physics Division P-25, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2016-05-15

We develop a mini gas gun system for simultaneous, single-pulse, x-ray diffraction and imaging under high strain-rate loading at the beamline 32-ID of the Advanced Photon Source. In order to increase the reciprocal space covered by a small-area detector, a conventional target chamber is split into two chambers: a narrowed measurement chamber and a relief chamber. The gas gun impact is synchronized with synchrotron x-ray pulses and high-speed cameras. Depending on a camera’s capability, multiframe imaging and diffraction can be achieved. The proof-of-principle experiments are performed on single-crystal sapphire. The diffraction spots and images during impact are analyzed to quantify lattice deformation and fracture; fracture is dominated by splitting cracks followed by wing cracks, and diffraction peaks are broadened likely due to mosaic spread. Our results demonstrate the potential of such multiscale measurements for studying high strain-rate phenomena at dynamic extremes.

Spatially resolved single crystal x-ray spectropolarimetry of wire array z-pinch plasmas.

Science.gov (United States)

Wallace, M S; Haque, S; Neill, P; Pereira, N R; Presura, R

2018-01-01

A recently developed single-crystal x-ray spectropolarimeter has been used to record paired sets of polarization-dependent and axially resolved x-ray spectra emitted by wire array z-pinches. In this measurement, two internal planes inside a suitable crystal diffract the x-rays into two perpendicular directions that are normal to each other, thereby separating incident x-rays into their linearly polarized components. This paper gives considerations for fielding the instrument on extended sources. Results from extended sources are difficult to interpret because generally the incident x-rays are not separated properly by the crystal. This difficulty is mitigated by using a series of collimating slits to select incident x-rays that propagate in a plane of symmetry between the polarization-splitting planes. The resulting instrument and some of the spatially resolved polarized x-ray spectra recorded for a 1-MA aluminum wire array z-pinch at the Nevada Terawatt Facility at the University of Nevada, Reno will be presented.

Accurate X-ray diffraction studies of KTiOPO{sub 4} single crystals doped with niobium

Energy Technology Data Exchange (ETDEWEB)

Novikova, N. E., E-mail: natnov@ns.crys.ras.ru; Sorokina, N. I.; Alekseeva, O. A.; Verin, I. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Center (Russian Federation); Kharitonova, E. P.; Orlova, E. I.; Voronkova, V. I. [Moscow State University, Faculty of Physics (Russian Federation)

2017-01-15

Single crystals of potassium titanyl phosphate doped with 4% of niobium (КТР:4%Nb) and 6% of niobium (KTP:6%Nb) are studied by accurate X-ray diffraction at room temperature. The niobium atoms are localized near the Ti1 and Ti2 atomic positions, and their positions are for the first time refined independent of the titanium atomic positions. Maps of difference electron density in the vicinity of K1 and K2 atomic positions are analyzed. It is found that in the structure of crystal КТР:4%Nb, additional positions of K atoms are located farther from the main positions and from each other than in КТР and KTP:6%Nb crystals. The nonuniform distribution of electron density found in the channels of the КТР:4%Nb structure is responsible for ~20% increase in the signal of second harmonic generation.

First indirect x-ray imaging tests with an 88-mm diameter single crystal

Energy Technology Data Exchange (ETDEWEB)

Lumpkin, A. H. [Fermilab; Macrander, A. T. [Argonne

2017-02-01

Using the 1-BM-C beamline at the Advanced Photon Source (APS), we have performed the initial indirect x - ray imaging point-spread-function (PSF) test of a unique 88-mm diameter YAG:Ce single crystal of only 100 - micron thickness. The crystal was bonded to a fiber optic plat e (FOP) for mechanical support and to allow the option for FO coupling to a large format camera. This configuration resolution was compared to that of self - supported 25-mm diameter crystals, with and without an Al reflective coating. An upstream monochromator was used to select 17-keV x-rays from the broadband APS bending magnet source of synchrotron radiation. The upstream , adjustable Mo collimators were then used to provide a series of x-ray source transverse sizes from 200 microns down to about 15-20 microns (FWHM) at the crystal surface. The emitted scintillator radiation was in this case lens coupled to the ANDOR Neo sCMOS camera, and the indirect x-ray images were processed offline by a MATLAB - based image processing program. Based on single Gaussian peak fits to the x-ray image projected profiles, we observed a 10.5 micron PSF. This sample thus exhibited superior spatial resolution to standard P43 polycrystalline phosphors of the same thickness which would have about a 100-micron PSF. Lastly, this single crystal resolution combined with the 88-mm diameter makes it a candidate to support future x-ray diffraction or wafer topography experiments.

The accuracy of the crystal chemical parameters at high-pressure conditions from single-crystal X-ray diffraction in diamond-anvil cell

DEFF Research Database (Denmark)

Periotto, Benedetta

-ray instruments. At the same time, the high-pressure experiments have benefited by the strong improvements on the high-pressure devices, in particular the diamond-anvil cell (DAC). The aim of this research project is to assess the quality of the data obtained by means of the single-crystal X-ray diffraction...... technique through the study of different mineral phases. The procedure for setting up an experiment under high-pressure conditions, using a single crystal as sample held within a DAC, are presented here with all the details of the in situ measurements at high-pressure conditions. The research project...... started with a comparison between two different DACs, in order to define the capabilities of one of the most common types of pressure device, the ETH-type DAC. Application examples of data quality analysis have been conducted on pyroxenes (NaInSi2O6, orthoenstatite MgSiO3 and LiCrSi2O6), which...

Single-Crystal Diffraction from Two-Dimensional Block Copolymer Arrays

International Nuclear Information System (INIS)

Stein, G. E.; Kramer, E. J.; Li, X.; Wang, J.

2007-01-01

The structure of oriented 2D block copolymer single crystals is characterized by grazing-incidence small-angle x-ray diffraction, demonstrating long-range sixfold orientational order. From line shape analysis of the higher-order Bragg diffraction peaks, we determine that translational order decays algebraically with a decay exponent η=0.2, consistent with the Kosterlitz-Thouless-Halperin-Nelson-Young theory for a 2D crystal with a shear modulus μ=2x10 -4 N/m

Single photon energy dispersive x-ray diffraction

International Nuclear Information System (INIS)

Higginbotham, Andrew; Patel, Shamim; Ciricosta, Orlando; Suggit, Matthew J.; Wark, Justin S.; Hawreliak, James A.; Collins, Gilbert W.; Coppari, Federica; Eggert, Jon H.; Tang, Henry

2014-01-01

With the pressure range accessible to laser driven compression experiments on solid material rising rapidly, new challenges in the diagnosis of samples in harsh laser environments are emerging. When driving to TPa pressures (conditions highly relevant to planetary interiors), traditional x-ray diffraction techniques are plagued by increased sources of background and noise, as well as a potential reduction in signal. In this paper we present a new diffraction diagnostic designed to record x-ray diffraction in low signal-to-noise environments. By utilising single photon counting techniques we demonstrate the ability to record diffraction patterns on nanosecond timescales, and subsequently separate, photon-by-photon, signal from background. In doing this, we mitigate many of the issues surrounding the use of high intensity lasers to drive samples to extremes of pressure, allowing for structural information to be obtained in a regime which is currently largely unexplored

Single photon energy dispersive x-ray diffraction

Energy Technology Data Exchange (ETDEWEB)

Higginbotham, Andrew; Patel, Shamim; Ciricosta, Orlando; Suggit, Matthew J.; Wark, Justin S. [Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU (United Kingdom); Hawreliak, James A.; Collins, Gilbert W.; Coppari, Federica; Eggert, Jon H. [Lawrence Livermore National Laboratory, Livermore, California 94551 (United States); Tang, Henry [Department of Earth and Planetary Science, University of California Berkeley, Berkeley, California 94720 (United States)

2014-03-15

With the pressure range accessible to laser driven compression experiments on solid material rising rapidly, new challenges in the diagnosis of samples in harsh laser environments are emerging. When driving to TPa pressures (conditions highly relevant to planetary interiors), traditional x-ray diffraction techniques are plagued by increased sources of background and noise, as well as a potential reduction in signal. In this paper we present a new diffraction diagnostic designed to record x-ray diffraction in low signal-to-noise environments. By utilising single photon counting techniques we demonstrate the ability to record diffraction patterns on nanosecond timescales, and subsequently separate, photon-by-photon, signal from background. In doing this, we mitigate many of the issues surrounding the use of high intensity lasers to drive samples to extremes of pressure, allowing for structural information to be obtained in a regime which is currently largely unexplored.

The discovery of X-ray diffraction by crystals and its great impact on science

International Nuclear Information System (INIS)

Mai Zhenhong

2012-01-01

In April 1912, Friedrich, Knipping and Laue discovered X-ray diffraction in a CuSO 4 crystal. Later, Laue derived the famous Laue equations which explain the diffraction phenomenon. For this, Laue was awarded a Nobel Prize for Physics in 1914. In 1912 W. H. Bragg and W. L. Bragg received news of Laue 's discovery, and from X-ray diffraction experiments in a ZnS crystal they derived the famous Bragg equation. For this work, father and son were together awarded the Nobel Prize for Physics in 1915, To commemorate the 100th anniversary of the discovery of X-ray diffraction, this article reviews the important contributions of the early pioneers and their historic impact on science and technology worldwide. (author)

Crystallization and preliminary X-ray diffraction analysis of recombinant hepatitis E virus-like particle

International Nuclear Information System (INIS)

Wang, Che-Yen; Miyazaki, Naoyuki; Yamashita, Tetsuo; Higashiura, Akifumi; Nakagawa, Atsushi; Li, Tian-Cheng; Takeda, Naokazu; Xing, Li; Hjalmarsson, Erik; Friberg, Claes; Liou, Der-Ming; Sung, Yen-Jen; Tsukihara, Tomitake; Matsuura, Yoshiharu; Miyamura, Tatsuo; Cheng, R. Holland

2008-01-01

A recombinant virus-like particle that is a potential oral hepatitis E vaccine was crystallized. Diffraction data were collected to 8.3 Å resolution and the X-ray structure was phased with the aid of a low-resolution density map determined using cryo-electron microscopy data. Hepatitis E virus (HEV) accounts for the majority of enterically transmitted hepatitis infections worldwide. Currently, there is no specific treatment for or vaccine against HEV. The major structural protein is derived from open reading frame (ORF) 2 of the viral genome. A potential oral vaccine is provided by the virus-like particles formed by a protein construct of partial ORF3 protein (residue 70–123) fused to the N-terminus of the ORF2 protein (residues 112–608). Single crystals obtained by the hanging-drop vapour-diffusion method at 293 K diffract X-rays to 8.3 Å resolution. The crystals belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 337, b = 343, c = 346 Å, α = β = γ = 90°, and contain one particle per asymmetric unit

Single-shot full strain tensor determination with microbeam X-ray Laue diffraction and a two-dimensional energy-dispersive detector.

Science.gov (United States)

Abboud, A; Kirchlechner, C; Keckes, J; Conka Nurdan, T; Send, S; Micha, J S; Ulrich, O; Hartmann, R; Strüder, L; Pietsch, U

2017-06-01

The full strain and stress tensor determination in a triaxially stressed single crystal using X-ray diffraction requires a series of lattice spacing measurements at different crystal orientations. This can be achieved using a tunable X-ray source. This article reports on a novel experimental procedure for single-shot full strain tensor determination using polychromatic synchrotron radiation with an energy range from 5 to 23 keV. Microbeam X-ray Laue diffraction patterns were collected from a copper micro-bending beam along the central axis (centroid of the cross section). Taking advantage of a two-dimensional energy-dispersive X-ray detector (pnCCD), the position and energy of the collected Laue spots were measured for multiple positions on the sample, allowing the measurement of variations in the local microstructure. At the same time, both the deviatoric and hydrostatic components of the elastic strain and stress tensors were calculated.

Development of a new micro-furnace for "in situ" high-temperature single crystal X-ray diffraction measurements

Science.gov (United States)

Alvaro, Matteo; Angel, Ross J.; Marciano, Claudio; Zaffiro, Gabriele; Scandolo, Lorenzo; Mazzucchelli, Mattia L.; Milani, Sula; Rustioni, Greta; Domeneghetti, Chiara M.; Nestola, Fabrizio

2015-04-01

Several experimental methods to reliably determine elastic properties of minerals at non-ambient conditions have been developed. In particular, different techniques for generating high-pressure and high-temperature have been successfully adopted for single-crystal and powder X-ray diffraction measurements. High temperature devices for "in-situ" measurements should provide the most controlled isothermal environment as possible across the entire sample. It is intuitive that in general, thermal gradients across the sample increase as the temperature increases. Even if the small isothermal volume required for single-crystal X-ray diffraction experiments makes such phenomena almost negligible, the design of a furnace should also aim to reduce thermal gradients by including a large thermal mass that encloses the sample. However this solution often leads to complex design that results in a restricted access to reciprocal space or attenuation of the incident or diffracted intensity (with consequent reduction of the accuracy and/or precision in lattice parameter determination). Here we present a newly-developed H-shaped Pt-Pt/Rh resistance microfurnace for in-situ high-temperature single-crystal X-ray diffraction measurements. The compact design of the furnace together with the long collimator-sample-detector distance allows us to perform measurements up to 2θ = 70° with no further restrictions on any other angular movement. The microfurnace is equipped with a water cooling system that allows a constant thermal gradient to be maintained that in turn guarantees thermal stability with oscillations smaller than 5°C in the whole range of operating T of room-T to 1200°C. The furnace has been built for use with a conventional 4-circle Eulerian geometry equipped with point detector and automated with the SINGLE software (Angel and Finger 2011) that allows the effects of crystal offsets and diffractometer aberrations to be eliminated from the refined peak positions by the 8

Crystallization and preliminary X-ray diffraction analysis of rat autotaxin

International Nuclear Information System (INIS)

Day, Jacqueline E.; Hall, Troii; Pegg, Lyle E.; Benson, Timothy E.; Hausmann, Jens; Kamtekar, Satwik

2010-01-01

Autotaxin (ATX), a pyrophosphatase/phosphodiesterase enzyme, is a promising drug target for many indications and is only distantly related to enzymes of previously determined structure. Here, the cloning, expression, purification, crystallization and preliminary diffraction analysis of ATX are reported. Rat autotaxin has been cloned, expressed, purified to homogeneity and crystallized via hanging-drop vapour diffusion using PEG 3350 as precipitant and ammonium iodide and sodium thiocyanate as salts. The crystals diffracted to a maximum resolution of 2.05 Å and belonged to space group P1, with unit-cell parameters a = 53.8, b = 63.3, c = 70.5 Å, α = 98.8, β = 106.2, γ = 99.8°. Preliminary X-ray diffraction analysis indicated the presence of one molecule per asymmetric unit, with a solvent content of 47%

Parametric X-rays and diffracted transition radiation in perfect and mosaic crystals

International Nuclear Information System (INIS)

Artru, X.; Rullhusen, P.

1998-01-01

The amplitude of X-ray emission by relativistic electrons in a single crystal, calculated in the kinematical approach, is decomposed unambiguously in Diffracted Transition Radiation (DTR) and Parametric X-rays (PXR). DTR becomes significant for γ > or similar to ω P ,γ being the Lorentz factor and ω P the plasma frequency. It is more collimated than PXR and, above threshold, its flux increases logarithmically with γ. However, it saturates with thickness at the Bragg primary extinction length l e . This saturation is accounted for only in the dynamical approach, the formulas of which are compared to the kinematical ones. The respective contributions of DTR and PXR are calculated for a simple model of mosaic crystal, taking into account saturation of DTR with thickness. The PXR flux is basically the same as in a perfect crystal. If the size of the domains is larger than l e , the DTR flux is multiplied by the number of domains crossed by the electron. For domains smaller than l e and γ > or similar to ω P , the DTR and PXR fluxes are of the same order of magnitude, up to logarithmic factors. In any case, mosaicity increases the total yield of X-ray photons. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

X-ray Excited Optical Fluorescence and Diffraction Imaging of Reactivity and Crystallinity in a Zeolite Crystal : Crystallography and Molecular Spectroscopy in One

NARCIS (Netherlands)

Ristanovic, Zoran; Hofmann, Jan P; Richard, Marie-Ingrid; Jiang, Tao; Chahine, Gilbert A; Schülli, Tobias U; Meirer, Florian; Weckhuysen, Bert M

2016-01-01

Structure-activity relationships in heterogeneous catalysis are challenging to be measured on a single-particle level. For the first time, one X-ray beam is used to determine the crystallographic structure and reactivity of a single zeolite crystal. The method generates μm-resolved X-ray diffraction

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

Directory of Open Access Journals (Sweden)

Michael Heymann

2014-09-01

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

Synthesis and single crystal x-ray diffraction study of a Schiff base derived from 4-acylpyrazolone and 2-aminophenol

Energy Technology Data Exchange (ETDEWEB)

Sharma, Naresh; Kant, Rajni, E-mail: vivek-gupta2k2@hotmail.com; Gupta, Vivek K., E-mail: vivek-gupta2k2@hotmail.com [Department of Physics and Electronics, University of Jammu, Jammu Tawi - 180006 (India); Jadeja, R. N. [Department of Chemistry, Faculty of Science, The M. S. University of Baroda, Vadodara-390002 (India)

2014-04-24

The title compound, (Z)-1-(3-chlorophenyl)-4[1((2hydroxyphenyl)amino)propylidene] -3-methyl-1H-pyrazol-5(4H)-one was synthesized by refluxing compound 1-(m-chlorophenyl)-3-methyl-4-propionyl-5-pyrazolone, with 2-aminophenol in ethanol. The compound crystallizes in the orthorhombic crystal system with space group Pca2{sub 1} having unit cell parameters: a = 26.2993(8), b = 7.0724(2) and c = 18.7170(5)Å. The structure contains two crystallographically independent molecules, A, and, B, in the asymmetric unit cell. The crystal structure was solved by direct method 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 0.049 for 5207 observed reflections.

High pressure Raman and single crystal X-ray diffraction of the alkali/calcium carbonate, shortite

Science.gov (United States)

Williams, Q. C.; Vennari, C.; O'Bannon, E. F., III

2015-12-01

Raman and synchrotron-based single crystal x-ray diffraction data have been collected on shortite (Na2Ca2(CO3)3) up to 10 GPa at 300 K. Shortite is of geological importance due to its presence in the ground-mass of kimberlites, and the alkaline-/carbon-rich character of kimberlitic eruptions. This investigation focuses on shortite's high pressure behavior and is relevant to the behavior of alkali-carbonate systems within Earth's upper mantle. X-ray data demonstrate that shortite's symmetry remains stable at high pressures—retaining orthorhombic C crystal system (Amm2) up to 10 GPa; diffraction data show a 12% volume decrease from room pressure, and a bulk modulus of 71.0(3) GPa. These also demonstrate that the c-axis is twice as compressible as the a- and b-axes. This anisotropic compression is likely due to the orientation of the relatively stiff carbonate groups, a third of which are oriented close to the plane of the a- and b-axes, c axis compression primarily involves the compaction of the 9-fold coordinate sodium and calcium polyhedral. The two distinct carbonate sites within the unit cell give rise to two Raman symmetric stretching modes of the symmetric stretch; the carbonate group stretching vibration which is close to in plane with the a- and b-axes shifts at 3.75 cm-1/GPa as opposed to the carbonate groups which is closer to in plane with the b- and c-axes which shift at 4.25 cm-1/GPa. This furthers evidence for anisotropic compression observed using x-ray diffraction--as the carbonate in plane with the a- and b-axes is compressed, the strength of oxygen bonds along the c-axis with the cations increases, thus decreasing the pressure shift of the mode. The out of plane bending vibration shifts at -0.48 cm-1/GPa, indicating an enhanced interaction of the oxygens with the cations. The multiple in plane bending modes all shift positively, as do at the low frequency lattice modes, indicating that major changes in bonding do not occur up to 10 GPa. The data

X-ray diffraction from single GaAs nanowires

Energy Technology Data Exchange (ETDEWEB)

Biermanns, Andreas

2012-11-12

In recent years, developments in X-ray focussing optics have allowed to produce highly intense, coherent X-ray beams with spot sizes in the range of 100 nm and below. Together with the development of new experimental stations, X-ray diffraction techniques can now be applied to study single nanometer-sized objects. In the present work, X-ray diffraction is applied to study different aspects of the epitaxial growth of GaAs nanowires. Besides conventional diffraction methods, which employ X-ray beams with dimensions of several tens of {mu}m, special emphasis lies on the use of nanodiffraction methods which allow to study single nanowires in their as-grown state without further preparation. In particular, coherent X-ray diffraction is applied to measure simultaneously the 3-dimensional shape and lattice parameters of GaAs nanowires grown by metal-organic vapor phase epitaxy. It is observed that due to a high density of zinc-blende rotational twins within the nanowires, their lattice parameter deviates systematically from the bulk zinc-blende phase. In a second step, the initial stage in the growth of GaAs nanowires on Si (1 1 1) surfaces is studied. This nanowires, obtained by Ga-assisted growth in molecular beam epitaxy, grow predominantly in the cubic zinc-blende structure, but contain inclusions of the hexagonal wurtzite phase close to their bottom interface. Using nanodiffraction methods, the position of the different structural units along the growth axis is determined. Because the GaAs lattice is 4% larger than silicon, these nanowires release their lattice mismatch by the inclusion of dislocations at the interface. Whereas NWs with diameters below 50 nm are free of strain, a rough interface structure in nanowires with diameters above 100 nm prevents a complete plastic relaxation, leading to a residual strain at the interface that decays elastically along the growth direction. Finally, measurements on GaAs-core/InAs-shell nanowire heterostructures are presented

An in-situ X-ray diffraction study on the electrochemical formation of PtZn alloys on Pt(1 1 1) single crystal electrode

Energy Technology Data Exchange (ETDEWEB)

Drnec, J., E-mail: drnec@esrf.fr [ESRF, Grenoble (France); Bizzotto, D. [Department of Chemistry, AMPEL, University of British Columbia, Vancouver, BC (Canada); Carlà, F. [ESRF, Grenoble (France); Fiala, R. [Charles University, Faculty of Mathematics and Physics, Prague (Czech Republic); Sode, A. [Ruhr-Universität Bochum, Bochum (Germany); Balmes, O.; Detlefs, B.; Dufrane, T. [ESRF, Grenoble (France); Felici, R., E-mail: felici@esrf.fr [ESRF, Grenoble (France)

2015-11-01

Highlights: • PtZn electrochemical alloying is observed on single crystal Pt electrodes. • In-situ X-ray characterization during alloy formation and dissolution is provided. • Structural model of the surface during alloying and dissolution is discussed. • X-ray based techniques can be used in in-operando studies of bimetallic fuel cell catalysts. - Abstract: The electrochemical formation and dissolution of the oxygen reduction reaction (ORR) PtZn catalyst on Pt(1 1 1) surface is followed by in-situ X-ray diffraction (XRD) and X-ray reflectivity (XRR) measurements. When the crystalline Pt surface is polarized to sufficiently negative potential values, with respect to an Ag/AgCl|KCl reference electrode, the electrodeposited zinc atoms diffuse into the bulk and characteristic features are observed in the X-ray patterns. The surface structure and composition during deposition and dissolution is determined from analysis of XRR curves and measurements of crystal truncation rods. Thin Zn-rich surface layer is present during the alloy formation while a Zn-depleted layer forms during dissolution.

Local layer structure of smectic liquid crystals by X-ray micro-diffraction

CERN Document Server

Takanishi, Y

2003-01-01

The local layer structure of smectic liquid crystal has been measured using time-resolved synchrotron X-ray micro-diffraction. Typical layer disorders observed in surface stabilized (anti-) ferroelectric liquid crystals, i.e. a stripe texture, a needed-like defect and a zigzag defect, are directly analyzed. The detailed analysis slows that the surface anchoring force due to the interaction between the liquid crystal molecule and the alignment thin film plays an important role to realize both the static and dynamic local layer structures. The layer structure of the circular domain observed in the liquid crystal of bent-shaped molecules found to depend on the applied electric field though the optical micrograph shows little difference. The frustrated, double and single layer structures of the bent-shaped molecule liquid crystal are determined depending on the terminal alkyl chain length. (author)

Preparation, crystallization, and preliminary X-ray diffraction study of mutant carboxypeptidase T containing the primary specificity pocket of carboxypeptidase B

International Nuclear Information System (INIS)

Akparov, V. Kh.; Grishin, A. M.; Timofeev, V. I.; Kuranova, I. P.

2010-01-01

Recombinant G215S, A251G, T257A, D260G, T262D mutant carboxypeptidase T from Thermoactinomyces vulgaris containing mutations in the primary specificity pocket was prepared and crystallized. Single crystals with a size of up to 0.3 mm were grown and investigated by X-ray diffraction. Recombinant mutant carboxypeptidase T containing the primary specificity subsite compositionally identical to that of pancreatic carboxypeptidase B crystallizes in the same space group as the natural enzyme. The crystals belong to sp. gr. P6 3 22; the unit-cell parameters are a = b = 157.867 A, c = 104.304 A, α = β = 90 deg., γ = 120 deg. X-ray diffraction data suitable for determining the three-dimensional structure at atomic resolution were collected from one crystal.

X-Ray Diffraction Project Final Report, Fiscal Year 2006

International Nuclear Information System (INIS)

Dane V. Morgan

2006-01-01

An x-ray diffraction diagnostic system was developed for determining real-time shock-driven lattice parameter shifts in single crystals at the gas gun at TA-IV at Sandia National Laboratories (SNL). The signal-to-noise ratio and resolution of the system were measured using imaging plates as the detector and by varying the slit width. This report includes tests of the x-ray diffraction system using a phosphor coupled to a charge-coupled device (CCD) camera by a coherent fiber-optic bundle. The system timing delay was measured with a newly installed transistor-transistor logic (TTL) bypass designed to reduce the x-ray delay time. The axial misalignment of the Bragg planes was determined with respect to the optical axis for a set of eight LiF [lithium fluoride] crystals provided by SNL to determine their suitability for gas gun experiments

X-ray diffraction and imaging with a coherent beam: application to X-ray optical elements and to crystals exhibiting phase inhomogeneities

International Nuclear Information System (INIS)

Masiello, F.

2011-05-01

The exceptional properties of synchrotron light sources have been exploited in very different disciplines, from archaeology to chemistry, from material science to biology, from medicine to physics. Among these properties it is important to mention the high brilliance, continuum spectrum, high degree of polarization, time structure, small source size and divergence of the beam, the last resulting in a high transversal coherence of the produced radiation. This high transversal coherence of the synchrotron sources has permitted the development of new techniques, e.g. phase contrast imaging, X-ray photon correlation spectroscopy and coherent X-ray diffraction imaging (CXDI). This thesis work will consist essentially of three parts. In the first part it will be presented the work done as a member of the X-ray Optics Group of ESRF in the characterization of high quality diamond crystals foreseen as X-ray optical elements. The characterization has been done using different complementary X-ray techniques, such as high resolution diffraction, topography, grazing incidence diffraction, reflectivity and measurements of the coherence preservation using the Talbot effect. In the second part, I will show the result obtained in the study of the temperature behaviours of the domain in periodically poled ferroelectrics crystals. This type of measurements, based on Bragg-Fresnel diffraction, are possible only thanks to the high degree of coherence of the beam. In the third part, I will present the results obtained in the characterization of diamonds foreseen for applications other than X-ray optical elements. (author)

New structural studies of liquid crystal by reflectivity and resonant X-ray diffraction; Nouvelles etudes structurales de cristaux liquides par reflectivite et diffraction resonante des rayons X

Energy Technology Data Exchange (ETDEWEB)

Fernandes, P

2007-04-15

This memory presents three structural studies of smectic Liquid Crystals by reflectivity and resonant diffraction of X-rays. It is divided in five chapters. In the first a short introduction to Liquid Crystals is given. In particular, the smectic phases that are the object of this study are presented. The second chapter is consecrated to the X-ray experimental techniques that were used in this work. The three last chapters present the works on which this thesis can be divided. Chapter three demonstrates on free-standing films of MHPOBC (historic liquid crystal that possesses the antiferroelectric sub-phases) the possibility to extend the technique of resonant X-ray diffraction to liquid crystals without resonant element. In the fourth chapter the structure of the B{sub 2} liquid crystal phase of bent-core molecules (or banana molecules) is elucidated by using resonant X-ray diffraction combined with polarization analysis of the diffracted beam. A model of the polarization of the resonant beam diffracted by four different structures proposed for the B{sub 2} phase is developed in this chapter. In the fifth chapter a smectic binary mixture presenting a very original critical point of phase separation is studied by X-ray reflectivity and optical microscopy. A concentration gradient in the direction perpendicular to the plane of the film seems to be induced by the free-standing film geometry. The results of a simplified model of the system are compatible with this interpretation.

Thermal expansion behavior of empressite, AgTe: A structural study by means of in situ high-temperature single-crystal X-ray diffraction

International Nuclear Information System (INIS)

Bindi, Luca

2009-01-01

The crystal structure of empressite, AgTe, a rare silver telluride, has been investigated by in situ X-ray single-crystal diffraction methods within the temperature range 298-463 K. AgTe remains orthorhombic, space group Pmnb (Pnma as standard), and shows only normal thermal expansion over the entire temperature range. The unit-cell parameters show a gradual increase with the increase of temperature. Slight adjustments in the geometry of Ag-tetrahedra and in the crystal-chemical environment of tellurium atoms occur in a continuous way without abrupt structural changes. The coefficients of thermal expansion along various axes are: α a = 1.5 x 10 -5 K -1 , α b = 3.0 x 10 -5 K -1 , α c = 2.2 x 10 -5 K -1 , and the bulk thermal expansion coefficient α V is 5.4 x 10 -5 K -1 for the temperature range 298-463 K

Multiple x-ray diffraction applied to the study of crystal impurities

International Nuclear Information System (INIS)

Cardoso, L.P.

1983-06-01

The x-ray multiple diffraction technique is used in the study of impurities concentration and localization in the crystal lattice, implemented with the fundamental observation that the impurities cannot be distributed with the same spatial group symmetry of the crystal. This fact could introduce scattered intensity in the crystal reciprocal lattice forbidden nodes. This effect was effectively observed in multiple diffraction diagrams, where a reinforcement of the scattered intensity in the pure crystal is produced, when choosing conveniently the involved reflections. The reflectivity theory was developed in the kinematic case, which take into account the scattering by the impurities atoms, and the analysis showed that, in the first approximation, the impurities can influence both in the allowed and forbidden positions for the pure crystal. (L.C.J.A.)

Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase from Leptospira interrogans

International Nuclear Information System (INIS)

Nascimento, Alessandro S.; Ferrarezi, Thiago; Catalano-Dupuy, Daniela L.; Ceccarelli, Eduardo A.; Polikarpov, Igor

2006-01-01

Crystals adequate for X-ray diffraction analysis have been prepared from L. interrogans ferredoxin-NADP + reductase. Ferredoxin-NADP + reductase (FNR) is an FAD-containing enzyme that catalyzes electron transfer between NADP(H) and ferredoxin. Here, results are reported of the recombinant expression, purification and crystallization of FNR from Leptospira interrogans, a parasitic bacterium of animals and humans. The L. interrogans FNR crystals belong to a primitive monoclinic space group and diffract to 2.4 Å resolution at a synchrotron source

Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase from Leptospira interrogans

Energy Technology Data Exchange (ETDEWEB)

Nascimento, Alessandro S.; Ferrarezi, Thiago [Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970 (Brazil); Catalano-Dupuy, Daniela L.; Ceccarelli, Eduardo A. [Facultad de Ciencias Bioquímicas y Farmacéuticas, Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario (Argentina); Polikarpov, Igor, E-mail: ipolikarpov@if.sc.usp.br [Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970 (Brazil)

2006-07-01

Crystals adequate for X-ray diffraction analysis have been prepared from L. interrogans ferredoxin-NADP{sup +} reductase. Ferredoxin-NADP{sup +} reductase (FNR) is an FAD-containing enzyme that catalyzes electron transfer between NADP(H) and ferredoxin. Here, results are reported of the recombinant expression, purification and crystallization of FNR from Leptospira interrogans, a parasitic bacterium of animals and humans. The L. interrogans FNR crystals belong to a primitive monoclinic space group and diffract to 2.4 Å resolution at a synchrotron source.

Order-disorder-reorder process in thermally treated dolomite samples: a combined powder and single-crystal X-ray diffraction study

Science.gov (United States)

Zucchini, A.; Comodi, P.; Katerinopoulou, A.; Balic-Zunic, T.; McCammon, C.; Frondini, F.

2012-04-01

A combined powder and single-crystal X-ray diffraction analysis of dolomite [CaMg(CO3)2] heated to 1,200°C at 3 GPa was made to study the order-disorder-reorder process. The order/disorder transition is inferred to start below 1,100°C, and complete disorder is attained at approximately 1,200°C. Twinned crystals characterized by high internal order were found in samples annealed over 1,100°C, and their fraction was found to increase with temperature. Evidences of twinning domains combined with probable remaining disordered portions of the structure imply that reordering processes occur during the quench. Twin domains are hereby proposed as a witness to thermally induced intra-layer-type cation disordering.

Multiple x-ray diffraction simulation and applications

International Nuclear Information System (INIS)

Costa, C.A.B.S. da.

1989-09-01

A computer program (MULTX) was implemented for simulation X-ray multiple diffraction diagrams in Renninger geometries. The program uses the X-ray multiple diffraction theory for imperfect crystals. The iterative calculation of the intensities is based on the Taylor series general term, and the primary beam power expansion is given as function of the beam x penetration in the crystal surface. This development allows to consider the simultaneous interaction of the beams involved in the multiple diffraction phenomenon. The simulated diagrams are calculated point-to-point and the tests for the Si and GaAs presented good reproduction of the experimental diagrams for different primary reflections. (L.C.J.A.)

Thermal expansion behavior of empressite, AgTe: A structural study by means of in situ high-temperature single-crystal X-ray diffraction

Energy Technology Data Exchange (ETDEWEB)

Bindi, Luca [Museo di Storia Naturale, sez. di Mineralogia, Universita di Firenze, Via La Pira 4, I-50121 Firenze (Italy)], E-mail: luca.bindi@unifi.it

2009-04-03

The crystal structure of empressite, AgTe, a rare silver telluride, has been investigated by in situ X-ray single-crystal diffraction methods within the temperature range 298-463 K. AgTe remains orthorhombic, space group Pmnb (Pnma as standard), and shows only normal thermal expansion over the entire temperature range. The unit-cell parameters show a gradual increase with the increase of temperature. Slight adjustments in the geometry of Ag-tetrahedra and in the crystal-chemical environment of tellurium atoms occur in a continuous way without abrupt structural changes. The coefficients of thermal expansion along various axes are: {alpha}{sub a} = 1.5 x 10{sup -5} K{sup -1}, {alpha}{sub b} = 3.0 x 10{sup -5} K{sup -1}, {alpha}{sub c} = 2.2 x 10{sup -5} K{sup -1}, and the bulk thermal expansion coefficient {alpha}{sub V} is 5.4 x 10{sup -5} K{sup -1} for the temperature range 298-463 K.

2-nitrobenzohydrazide as a potent urease inhibitor: synthesis, characterization and single crystal x-ray diffraction analysis

International Nuclear Information System (INIS)

Abbas, N.; Khan, I.; Hameed, S.; Batool, S.

2018-01-01

2-Nitrobenzohydrazide was efficiently synthesized in two steps by the esterification of 2-nitrobenzoic acid followed by the treatment with hydrazine hydrate in methanol. The structure of 2-nitrobenzohydrazide was established by modern spectro-analytical techniques including FTIR, 1H and 13C-NMR spectroscopy and unequivocally confirmed by single crystal X-ray diffraction data. 2-Nitrobenzohydrazide crystallized in orthorhombic space group P 21 21 21 with unit cell dimensions a = 4.9764(4) Å, b = 12.5280 (3) Å, c = 12.8512(1) Å, α = β = γ = 90°. A combination of N‒H…N and N‒H…O hydrogen bonds stabilized the crystal packing of 3. The synthesized compound 3 was assessed as urease inhibitor against Jack bean urease and the results revealed good inhibitory potency with an IC50 value of 4.25 ± 0.08 µM. This inhibition strength was 5-fold higher compared to the reference inhibitor thiourea (IC50 = 21.00 ± 0.11 µM). The molecular docking studies of the synthesized inhibitor 3 inside the active pocket of urease revealed several important binding interactions. (author)

Crystallization and preliminary X-ray diffraction analysis of a glutathione S-transferase from Xylella fastidiosa

International Nuclear Information System (INIS)

Garcia, Wanius; Travensolo, Regiane F.; Rodrigues, Nathalia C.; Muniz, João R. C.; Caruso, Célia S.; Lemos, Eliana G. M.; Araujo, Ana Paula U.; Carrilho, Emanuel

2008-01-01

Glutathione S-transferase from X. fastidiosa (xfGST) has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.23 Å. Glutathione S-transferases (GSTs) form a group of multifunctional isoenzymes that catalyze the glutathione-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GST from Xylella fastidiosa (xfGST) was overexpressed in Escherichia coli and purified by conventional affinity chromatography. In this study, the crystallization and preliminary X-ray analysis of xfGST is described. The purified protein was crystallized by the vapour-diffusion method, producing crystals that belonged to the triclinic space group P1. The unit-cell parameters were a = 47.73, b = 87.73, c = 90.74 Å, α = 63.45, β = 80.66, γ = 94.55°. xfGST crystals diffracted to 2.23 Å resolution on a rotating-anode X-ray source

Crystallization and preliminary X-ray diffraction analysis of a glutathione S-transferase from Xylella fastidiosa

Energy Technology Data Exchange (ETDEWEB)

Garcia, Wanius, E-mail: wanius@if.sc.usp.br [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Travensolo, Regiane F. [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Rodrigues, Nathalia C.; Muniz, João R. C. [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Caruso, Célia S. [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Lemos, Eliana G. M. [Laboratório de Bioquímica de Microrganismos e de Plantas, Departamento de Tecnologia, UNESP, Jaboticabal (Brazil); Araujo, Ana Paula U. [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Carrilho, Emanuel, E-mail: wanius@if.sc.usp.br [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil)

2008-02-01

Glutathione S-transferase from X. fastidiosa (xfGST) has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.23 Å. Glutathione S-transferases (GSTs) form a group of multifunctional isoenzymes that catalyze the glutathione-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GST from Xylella fastidiosa (xfGST) was overexpressed in Escherichia coli and purified by conventional affinity chromatography. In this study, the crystallization and preliminary X-ray analysis of xfGST is described. The purified protein was crystallized by the vapour-diffusion method, producing crystals that belonged to the triclinic space group P1. The unit-cell parameters were a = 47.73, b = 87.73, c = 90.74 Å, α = 63.45, β = 80.66, γ = 94.55°. xfGST crystals diffracted to 2.23 Å resolution on a rotating-anode X-ray source.

Growth of ω inclusions in Ti alloys: An X-ray diffraction study

International Nuclear Information System (INIS)

Šmilauerová, J.; Harcuba, P.; Pospíšil, J.; Matěj, Z.; Holý, V.

2013-01-01

We investigated the size and crystal structure of nanometer-sized ω inclusions in single crystals of β-Ti alloys by X-ray diffraction pole-figure measurements and reciprocal space mapping. We studied the topotactical relation of the β and ω crystal lattices, and from the positions and shapes of the diffraction maxima of the ω lattice determined the mean size of the ω inclusions and the misfit of the inclusion lattice with respect to the host lattice, as well as their changes during ageing. The lattice of the ω inclusions exhibits a large positive misfit already before ageing and the misfit is subsequently reduced during the ageing process. Using the theories of elasticity and X-ray scattering we simulated diffuse X-ray scattering around the β diffraction maxima and demonstrated that the diffuse scattering is caused mainly by local elastic strains in the β host phase around the ω inclusions

Synchrotron x-ray diffraction study of liquid surfaces

DEFF Research Database (Denmark)

Als-Nielsen, Jens Aage; Pershan, P.S.

1983-01-01

A spectrometer for X-ray diffraction and refraction studies of horizontal, free surfaces of liquids is described. As an illustration smetic-A layering at the surface of a liquid crystal is presented.......A spectrometer for X-ray diffraction and refraction studies of horizontal, free surfaces of liquids is described. As an illustration smetic-A layering at the surface of a liquid crystal is presented....

Improved X-ray diffraction from Bacillus megaterium penicillin G acylase crystals through long cryosoaking dehydration

International Nuclear Information System (INIS)

Rojviriya, Catleya; Pratumrat, Thunyaluck; Saper, Mark A.; Yuvaniyama, Jirundon

2011-01-01

Penicillin G acylase from the Gram-positive bacterium B. megaterium was crystallized and X-ray diffraction from these crystals could be substantially improved by slight dehydration through a long cryo-soak. Penicillin G acylase from Bacillus megaterium (BmPGA) is currently used in the pharmaceutical industry as an alternative to PGA from Escherichia coli (EcPGA) for the hydrolysis of penicillin G to produce 6-aminopenicillanic acid (6-APA), a penam nucleus for semisynthetic penicillins. Despite the significant differences in amino-acid sequence between PGAs from Gram-positive and Gram-negative bacteria, a representative PGA structure of Gram-positive origin has never been reported. In this study, crystallization and diffraction studies of BmPGA are described. Poor diffraction patterns with blurred spots at higher resolution were typical for BmPGA crystals cryocooled after a brief immersion in cryoprotectant solution. Overnight soaking in the same cryo-solution substantially improved both the mosaicity and resolution limit through the establishment of a new crystal-packing equilibrium. A crystal of BmPGA diffracted X-rays to 2.20 Å resolution and belonged to the monoclinic space group P2 1 with one molecule of BmPGA in the asymmetric unit

Crystallization and preliminary X-ray diffraction analysis of alanine racemase from Pseudomonas putida YZ-26

International Nuclear Information System (INIS)

Liu, Junlin; Feng, Lei; Shi, Yawei; Feng, Wei

2012-01-01

A recombinant alanine racemase from the Pseudomonas putida YZ-26, has been crystallized by the sitting-drop vapor-diffusion method and X-ray diffraction data were collected to 2.4 Å. A recombinant form of alanine racemase (Alr) from Pseudomonas putida YZ-26 has been crystallized by the sitting-drop vapour diffusion method. X-ray diffraction data were collected to 2.4 Å resolution. The crystals belong to the space group C222 1 , with unit-cell parameters a = 118.08, b = 141.86, c = 113.83 Å, and contain an Alr dimer in the asymmetric unit. The Matthews coefficient and the solvent content were calculated to be 2.8 Å 3 Da −1 and approximately 50%, respectively

Crystal structure investigations of ZrAsxSey (x>y, x+y≤2) by single crystal neutron diffraction at 300 K, 25 K and 2.3 K

International Nuclear Information System (INIS)

Niewa, Rainer; Czulucki, Andreas; Schmidt, Marcus; Auffermann, Gudrun; Cichorek, Tomasz; Meven, Martin; Pedersen, Bjoern; Steglich, Frank; Kniep, Ruediger

2010-01-01

Large single crystals of ZrAs x Se y (x>y, x+y≤2, PbFCl type of structure, space group P4/nmm) were grown by Chemical Transport. Structural details were studied by single crystal neutron diffraction techniques at various temperatures. One single crystal specimen with chemical composition ZrAs 1.595(3) Se 0.393(1) was studied at ambient temperature (R1=5.10 %, wR2=13.18 %), and a second crystal with composition ZrAs 1.420(3) Se 0.560(1) was investigated at 25 K (R1=2.70%, wR2=5.70 %) and 2.3 K (R1=2.30 %, wR2=4.70 %), respectively. The chemical compositions of the crystals under investigation were determined by wavelength dispersive X-ray spectroscopy. The quantification of trace elements was carried out by Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry. According to the crystal structure refinements the crystallographic 2a site is occupied by As, together with a significant amount of vacancies. One of the 2c sites is fully occupied by As and Se (random distribution). With respect to the fractional coordinates of the atoms, the crystal structure determinations based on the data obtained at 25.0 K and 2.3 K did not show significant deviations from ambient temperature results. The temperature dependence of the displacement parameters indicates a static displacement of As on the 2a sites (located on the (0 0 1) planes) for all temperatures. No indications for any occupation of interstitial sites or the presence of vacancies on the Zr (2a) site were found. - Graphical abstract: Large single crystals of ZrAs x Se y grown by Chemical Transport to study structural details as the As-Se order scheme by single crystal neutron diffraction.

Perfect-crystal x-ray optics to treat x-ray coherence

International Nuclear Information System (INIS)

Yamazaki, Hiroshi; Ishikawa, Tetsuya

2007-01-01

X-ray diffraction of perfect crystals, which serve as x-ray monochromator and collimator, modifies coherence properties of x-ray beams. From the time-dependent Takagi-Taupin equations that x-ray wavefields obey in crystals, the reflected wavefield is formulated as an integral transform of a general incident wavefield with temporal and spatial inhomogeneity. A reformulation of rocking-curve profiles from the field solution of the Takagi-Taupin equations allows experimental evaluation of the mutual coherence function of x-ray beam. The rigorous relationship of the coherence functions between before and after reflection clarifies how the coherence is transferred by a crystal. These results will be beneficial to developers of beamline optics for the next generation synchrotron sources. (author)

New methods of X-ray diffraction spectrometry. II

International Nuclear Information System (INIS)

Soerum, H.; Bremer, J.

1980-01-01

The construction principles for a flexible X-ray spectrometer can be equipped either with a single curved crystal or with two curved crystals are described. A few of the theoretical 4+32 possible working modes are selected for a closer investigation and examples of recorded spectra are given. It is shown in the general single-crystal case that for a wavelength close to a cut-off energy the narrow diffraction cone has an elliptic section, as predicted by the theory. The spectrometer is discussed in terms of intensity, resolution and dispersive power. A comparison with other types of spectrometer is made. (Auth.)

High-pressure single-crystal X-ray diffraction of Tl2SeO4

International Nuclear Information System (INIS)

Grzechnik, Andrzej; Breczewski, Tomasz; Friese, Karen

2008-01-01

The effect of pressure on the crystal structure of thallium selenate (Tl 2 SeO 4 ) (Pmcn, Z=4), containing the Tl + cations with electron lone pairs, has been studied with single-crystal X-ray diffraction in a diamond anvil cell up to 3.64 GPa at room temperature. No phase transition has been observed. The compressibility data are fitted by a Murnaghan equation of state with the zero-pressure bulk modulus B 0 =29(1) GPa and the unit-cell volume at ambient pressure V 0 =529.6(8) A 3 (B'=4.00). Tl 2 SeO 4 is the least compressible in the c direction, while the pressure-induced changes of the a and b lattice parameters are quite similar. These observations can be explained by different pressure effects on the nine- and 11-fold coordination polyhedra around the two non-equivalent Tl atoms. The SeO 4 2- tetrahedra are not rigid units and become more distorted. Their contribution to the compressibility is small. The effect of pressure on the isotypical oxide materials A 2 TO 4 with the β-K 2 SO 4 structure is discussed. It appears that the presence of electron lone pairs on the Tl + cation does not seem to influence the compressibility of Tl 2 SeO 4 . - Graphical abstract: Pressure dependence of normalized lattice parameters and unit-cell volumes in Tl 2 SeO 4 (Pmcn, Z=4). The solid line is the Murnaghan equation of state

Crystal diffraction lens telescope for focusing nuclear gamma rays

International Nuclear Information System (INIS)

Smither, R.K.; Fernandez, P.B.; Graber, T.; Faiz, M.

1996-08-01

A crystal diffraction lens was constructed at Argonne National Laboratory for use as a telescope to focus nuclear gamma rays. It consisted of 600 single crystals of germanium arranged in 8 concentric rings. The mounted angle of each crystal was adjusted to intercept and diffract the incoming gamma rays with an accuracy of a few arc sec. The performance of the lens was tested in two ways. In one case, the gamma rays were focused on a single medium size germanium detector. In the second case, the gamma rays were focused on the central germanium detector of a 3 x 3 matrix of small germanium detectors. The efficiency, image concentration and image quality, and shape were measured. The tests performed with the 3 x 3 matrix detector system were particularly interesting. The wanted radiation was concentrated in the central detector. The 8 other detectors were used to detect the Compton scattered radiation, and their energy was summed with coincident events in the central detector. This resulted in a detector with the efficiency of a large detector (all 9 elements) and the background of a small detector (only the central element). The use of the 3 x 3 detector matrix makes it possible to tell if the source is off axis and, if so, to tell in which direction. The crystal lens acts very much like a simple convex lens for visible light. Thus if the source is off to the left then the image will focus off to the right illuminating the detector on the right side: telling one in which direction to point the telescope. Possible applications of this type of crystal lens to balloon and satellite experiments will be discussed

The determination of the crystal structures of some uranium compounds by means of x-ray and neutron diffraction

International Nuclear Information System (INIS)

Adrian, H.W.W.

1977-10-01

In industrial uranium processing or reprocessing procedures, aqueous uranyl nitrate solutions are an intermediate product. The compounds, whose structures are reported, might prove valuable as alternative crystallization products to existing methods of extracting the uranium from solution. The compounds are obtained by the addition of hydroxylammonium to the uranyl nitrate solution and are of the general formula UO 2 (NH 2 0) 2 .xH 2 0, where x can take the values zero, two, three and four. In addition a compound of the formula UO 2 (NH 2 0) 2 .2(NH 2 CH).2H 2 0 was obtained. The UO 2 (NH 2 0) compound crystallized in a monoclinic crystal form. Crystals large enough for neutron diffraction were not obtained. The structure of the UO 2 (NH 2 0) 2 .2H 2 0 could not be solved because only disordered crystalline material was available. The structure of UO 2 (NH 2 0) 2 .3H 2 0 was solved by means of room- and low-temperature neutron diffraction. The unit cell is orthorhombic. The structure of α-UO 2 (NH 2 0) 2 .4H 2 0 was investigated by means of room-temperature x-ray and room- and low-temperature neutron diffraction. The unit cell is triclinic. This compound strongly resembles the trihydrate. The UO 2 (NH 2 0) 2 .2(NH 2 0H).2H 2 0 compound gave crystals large enough for single crystal x-ray but not neutron diffraction. The unit cell is orthorhombic. The characteristic powder patterns (indexed except for the dihydrate compound) of the above compounds are reported [af

Crystallization and preliminary X-ray diffraction analysis of the glucuronoyl esterase catalytic domain from Hypocrea jecorina

International Nuclear Information System (INIS)

Wood, S. J.; Li, X.-L.; Cotta, M. A.; Biely, P.; Duke, N. E. C.; Schiffer, M.; Pokkuluri, P. R.

2008-01-01

The catalytic domain of the glucuronoyl esterase from H. jecorina was overexpresssed, purified and crystallized in space group P2 1 2 1 2 1 . X-ray diffraction data were collected to 1.9 Å resolution. The catalytic domain of the glucuronoyl esterase from Hypocrea jecorina (anamorph Trichoderma reesei) was overexpresssed, purified and crystallized by the sitting-drop vapor-diffusion method using 1.4 M sodium/potassium phosphate pH 6.9. The crystals belonged to space group P2 1 2 1 2 1 and X-ray diffraction data were collected to 1.9 Å resolution. This is the first enzyme with glucoronoyl esterase activity to be crystallized; its structure will be valuable in lignocellulose-degradation research

Single crystal X-ray structure of the artists’ pigment zinc yellow

DEFF Research Database (Denmark)

Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold

2017-01-01

electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and powder X-ray diffraction (PXRD), showed that the synthesised products and the industrial pigment were identical. Single-crystal X-ray crystallography......The artists’ pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hitherto...... been unknown. In this work, zinc yellow was synthesised by precipitation from an aqueous solution of zinc nitrate and potassium chromate under both neutral and basic conditions, and the products were compared with the pigment used in industrial paints. Analyses by Raman microscopy (MRS), scanning...

X-ray transparent Microfluidics for Protein Crystallization and Biomineralization

Science.gov (United States)

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.

Note: Application of a pixel-array area detector to simultaneous single crystal x-ray diffraction and x-ray absorption spectroscopy measurements

International Nuclear Information System (INIS)

Sun, Cheng-Jun; Brewe, Dale L.; Heald, Steve M.; Zhang, Bangmin; Chen, Jing-Sheng; Chow, G. M.; Venkatesan, T.

2014-01-01

X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) are two main x-ray techniques in synchrotron radiation facilities. In this Note, we present an experimental setup capable of performing simultaneous XRD and XAS measurements by the application of a pixel-array area detector. For XRD, the momentum transfer in specular diffraction was measured by scanning the X-ray energy with fixed incoming and outgoing x-ray angles. By selecting a small fixed region of the detector to collect the XRD signal, the rest of the area was available for collecting the x-ray fluorescence for XAS measurements. The simultaneous measurement of XRD and X-ray absorption near edge structure for Pr 0.67 Sr 0.33 MnO 3 film was demonstrated as a proof of principle for future time-resolved pump-probe measurements. A static sample makes it easy to maintain an accurate overlap of the X-ray spot and laser pump beam

Determination of Ni(II) crystal structure by powder x-ray diffraction ...

African Journals Online (AJOL)

X-ray powder diffraction pattern was used to determine the length of the unit cell, “a”, the lattice structure type, and the number of atoms per unit cell of Ni(II) crystal. The “a” value was determined to be 23.66 ± 0.005 Å, particle size of 34.87 nm, volume 13.24 Å and Strain value ε = 9.8 x 10-3. The cell search on PXRD patterns ...

Takagi-Taupin description of x-ray dynamical diffraction from diffractive optics with large numerical aperture

International Nuclear Information System (INIS)

Yan Hanfei; Maser, Joerg; Macrander, Albert; Shen Qun; Vogt, Stefan; Stephenson, G. Brian; Kang, Hyon Chol

2007-01-01

We present a formalism of x-ray dynamical diffraction from volume diffractive optics with large numerical aperture and high aspect ratio, in an analogy to the Takagi-Taupin equations [Acta Crystallogr. 15, 1311 (1962); Bull. Soc. Fr. Mineral. Crystallogr. 87, 469 (1964)] for strained single crystals. We derive a set of basic equations for dynamical diffraction from volume diffractive optics, which enable us to study the focusing property of these optics with various grating profiles. We study volume diffractive optics that satisfy the Bragg condition to various degrees, namely, flat, tilted, and wedged geometries, and derive the curved geometries required for ultimate focusing. We show that the curved geometries satisfy both the Bragg condition everywhere and phase requirement for point focusing and effectively focus hard x rays to a scale close to the wavelength. Our calculations were made for an x-ray wavelength of 0.064 nm (19.5 keV)

X-ray topography under conditions of monochromatic spherical wave diffraction

International Nuclear Information System (INIS)

Aristov, V.V.; Polovinkina, V.I.; Ibhikawa, Tetsuya; Kiduta, Seishi.

1981-01-01

An X-ray topographic scheme was developed in which there is a large distance between the X-ray source and the specimen. A monochromatic X-ray beam with an angular divergence 6 x 10 - 5 rad obtained by double successive diffraction in the (n 1 , +n 2 ) setting was used. This scheme enables diffraction focusing of a weakly absorbed wave field onto the exit surface of the crystal to be performed. Topographs of a wedge-shaped silicon crystal were obtained. Interference effects such as focusing, anomalous and ordinary Pendelloesung effects peculiar to X-ray spherical wave diffraction were observed in the topographs with high resolution. (author)

Hard X-ray diffraction enhanced imaging only using two crystals

Institute of Scientific and Technical Information of China (English)

LI Gang; WANG Nan; WU Ziyu

2004-01-01

Different configurations for the monochromator crystals and the analyzer crystals have been used in hard X-ray diffraction enhanced imaging (DEI) methods to overcome the complex task to adjust each of them to the ideal position. Here we present a very compact DEI configuration, and preliminary results of experiments performed at the Beijing Synchrotron Radiation Facility (BSRF) using only two crystals: the first one acting as monochromator and the second one as analyzer in the Bragg geometry. Refraction contrast images characterized by high contrast and spatial resolution are obtained and compared with absorption images. Differences among these images will be outlined and discussed emphasizing the potential capabilities of this very simple layout that guarantees a high transmission efficiency.

Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

Energy Technology Data Exchange (ETDEWEB)

Abramchik, Yu. A. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Timofeev, V. I., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” (Russian Federation); Muravieva, T. I.; Esipov, R. S., E-mail: espiov@mx.ibch.ru [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” (Russian Federation)

2016-11-15

Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P12{sub 1}1 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.

Crystallization and preliminary X-ray diffraction analysis of maize aldose reductase

Energy Technology Data Exchange (ETDEWEB)

Kiyota, Eduardo [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil); Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas-SP (Brazil); Sousa, Sylvia Morais de [Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas-SP (Brazil); Santos, Marcelo Leite dos; Costa Lima, Aline da [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil); Menossi, Marcelo [Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas-SP (Brazil); Yunes, José Andrés [Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas-SP (Brazil); Aparicio, Ricardo, E-mail: aparicio@iqm.unicamp.br [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil)

2007-11-01

Preliminary X-ray diffraction studies of apo maize aldose reductase at 2.0 Å resolution are reported. Maize aldose reductase (AR) is a member of the aldo-keto reductase superfamily. In contrast to human AR, maize AR seems to prefer the conversion of sorbitol into glucose. The apoenzyme was crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 47.2, b = 54.5, c = 100.6 Å and one molecule in the asymmetric unit. Synchrotron X-ray diffraction data were collected and a final resolution limit of 2.0 Å was obtained after data reduction. Phasing was carried out by an automated molecular-replacement procedure and structural refinement is currently in progress. The refined structure is expected to shed light on the functional/enzymatic mechanism and the unusual activities of maize AR.

Crystallization and preliminary X-ray diffraction analysis of maize aldose reductase

International Nuclear Information System (INIS)

Kiyota, Eduardo; Sousa, Sylvia Morais de; Santos, Marcelo Leite dos; Costa Lima, Aline da; Menossi, Marcelo; Yunes, José Andrés; Aparicio, Ricardo

2007-01-01

Preliminary X-ray diffraction studies of apo maize aldose reductase at 2.0 Å resolution are reported. Maize aldose reductase (AR) is a member of the aldo-keto reductase superfamily. In contrast to human AR, maize AR seems to prefer the conversion of sorbitol into glucose. The apoenzyme was crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 47.2, b = 54.5, c = 100.6 Å and one molecule in the asymmetric unit. Synchrotron X-ray diffraction data were collected and a final resolution limit of 2.0 Å was obtained after data reduction. Phasing was carried out by an automated molecular-replacement procedure and structural refinement is currently in progress. The refined structure is expected to shed light on the functional/enzymatic mechanism and the unusual activities of maize AR

Crystallization and preliminary X-ray diffraction analysis of the glucuronoyl esterase catalytic domain from Hypocrea jecorina

Energy Technology Data Exchange (ETDEWEB)

Wood, S. J. [Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Li, X.-L.; Cotta, M. A. [Fermentation Biotechnology Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604 (United States); Biely, P. [Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava (Slovakia); Duke, N. E. C.; Schiffer, M.; Pokkuluri, P. R., E-mail: rajp@anl.gov [Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

2008-04-01

The catalytic domain of the glucuronoyl esterase from H. jecorina was overexpresssed, purified and crystallized in space group P2{sub 1}2{sub 1}2{sub 1}. X-ray diffraction data were collected to 1.9 Å resolution. The catalytic domain of the glucuronoyl esterase from Hypocrea jecorina (anamorph Trichoderma reesei) was overexpresssed, purified and crystallized by the sitting-drop vapor-diffusion method using 1.4 M sodium/potassium phosphate pH 6.9. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1} and X-ray diffraction data were collected to 1.9 Å resolution. This is the first enzyme with glucoronoyl esterase activity to be crystallized; its structure will be valuable in lignocellulose-degradation research.

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin.

Science.gov (United States)

Jaimohan, S M; Naresh, M D; Arumugam, V; Mandal, A B

2009-10-01

Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemoglobins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 A resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 A, beta = 109.35 degrees . Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

Glancing angle synchrotron X-ray diffraction

Energy Technology Data Exchange (ETDEWEB)

Cernik, R J [Daresbury Lab., Warrington, WA (United States)

1996-09-01

This paper describes in basic detail some of the techniques that can be used to study thin films and surfaces. These are all in the X-ray region and cover reflectivity, diffraction form polycrystalline films, textured films and single crystal films. Other effects such as fluorescence and diffuse scattering are mentioned but not discussed in detail. Two examples of the reflectivity from multilayers and the diffraction from iron oxide films are discussed. The advantages of the synchrotron for these studies is stressed and the experimental geometries that can be employed are described i detail. A brief bibliography is provided at the end to accompany this part of the 1996 Frascati school.

Glancing angle synchrotron X-ray diffraction

International Nuclear Information System (INIS)

Cernik, R.J.

1996-01-01

This paper describes in basic detail some of the techniques that can be used to study thin films and surfaces. These are all in the X-ray region and cover reflectivity, diffraction form polycrystalline films, textured films and single crystal films. Other effects such as fluorescence and diffuse scattering are mentioned but not discussed in detail. Two examples of the reflectivity from multilayers and the diffraction from iron oxide films are discussed. The advantages of the synchrotron for these studies is stressed and the experimental geometries that can be employed are described i detail. A brief bibliography is provided at the end to accompany this part of the 1996 Frascati school

X-ray characterization of curved crystals for hard x-ray astronomy

Science.gov (United States)

Buffagni, Elisa; Bonnini, Elisa; Ferrari, Claudio; Virgilli, Enrico; Frontera, Filippo

2015-05-01

Among the methods to focus photons the diffraction in crystals results as one of the most effective for high energy photons. An assembling of properly oriented crystals can form a lens able to focus x-rays at high energy via Laue diffraction in transmission geometry; this is a Laue lens. The x-ray diffraction theory provides that the maximum diffraction efficiency is achieved in ideal mosaic crystals, but real mosaic crystals show diffraction efficiencies several times lower than the ideal case due to technological problems. An alternative and convenient approach is the use of curved crystals. We have recently optimized an efficient method based on the surface damage of crystals to produce self-standing uniformly curved Si, GaAs and Ge tiles of thickness up to 2-3 mm and curvature radii R down to a few meters. We show that, for curved diffracting planes, such crystals have a diffraction efficiency nearly forty times higher than the diffraction efficiency of perfect similar flat crystals, thus very close to that of ideal mosaic crystals. Moreover, in an alternative configuration where the diffracting planes are perpendicular to the curved ones, a focusing effect occurs and will be shown. These results were obtained for several energies between 17 and 120 keV with lab sources or at high energy facilities such as LARIX at Ferrara (Italy), ESRF at Grenoble (France), and ANKA at Karlsruhe (Germany).

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the regulator AcrR from Escherichia coli

International Nuclear Information System (INIS)

Li, Ming; Qiu, Xi; Su, Chih-Chia; Long, Feng; Gu, Ruoyu; McDermott, Gerry; Yu, Edward W.

2006-01-01

The transcriptional regulator AcrR from Escherichia coli has been cloned, overexpressed, purified and crystallized and X-ray diffraction data have been collected to a resolution of 2.5 Å. This paper describes the cloning, expression, purification and preliminary X-ray data analysis of the AcrR regulatory protein. The Escherichia coli AcrR is a member of the TetR family of transcriptional regulators. It regulates the expression of the AcrAB multidrug transporter. Recombinant AcrR with a 6×His tag at the C-terminus was expressed in E. coli and purified by metal-affinity chromatography. The protein was crystallized using hanging-drop vapor diffusion. X-ray diffraction data were collected from cryocooled crystals at a synchrotron light source. The best crystal diffracted to 2.5 Å. The space group was determined to be P3 2 , with unit-cell parameters a = b = 46.61, c = 166.16 Å

Characterization of CuCl quantum dots grown in NaCl single crystals via optical measurements, X-ray diffraction, and transmission electron microscopy

Science.gov (United States)

Miyajima, Kensuke; Akatsu, Tatsuro; Itoh, Ken

2018-05-01

We evaluated the crystal size, shape, and alignment of the lattice planes of CuCl quantum dots (QDs) embedded in NaCl single crystals by optical measurements, X-ray diffraction (XRD) patterns, and transmission electron microscopy (TEM). We obtained, for the first time, an XRD pattern and TEM images for CuCl QDs in NaCl crystals. The XRD pattern showed that the lattice planes of the CuCl QDs were parallel to those of the NaCl crystals. In addition, the size of the QDs was estimated from the diffraction width. It was apparent from the TEM images that almost all CuCl QDs were polygonal, although some cubic QDs were present. The mean size and size distribution of the QDs were also obtained. The dot size obtained from optical measurements, XRD, and TEM image were almost consistent. Our new findings can help to reveal the growth mechanism of semiconductor QDs embedded in a crystallite matrix. In addition, this work will play an important role in progressing the study of optical phenomena originating from assembled semiconductor QDs.

X-Ray diffraction studies of silicon implanted with high energy ions

International Nuclear Information System (INIS)

Wieteska, K.; Wierzchowski, W.; Graeff, W.

1998-01-01

The character of lattice deformation in silicon implanted with high energy alpha-particles and protons was studied using a number of X-ray methods. The experiments included double-crystal spectrometer method as well as single crystal section and projection topography realised both with conventional and synchrotron X-ray sources. All observed diffraction patterns were reasonably explainable assuming the lattice parameter distribution proportional to the vacancy-interstitial distribution coming from the Biersack-ziegler theory. The theoretical rocking curves and distribution in back-reflection double-crystal and section topographs well corresponding to the experimental results were calculated using numerical integration of the takagi-taupin equations

X-ray diffraction in laser-irradiated epsomite crystals grown in presence of borax

International Nuclear Information System (INIS)

Zaitseva, E.V.; Portnov, V.N.; Faddeev, M.A.; Chuprunov, E.V.

1997-01-01

Relative changes in the intensities ΔI/I of the (220) and (440) X-ray diffraction reflection during laser irradiation of epsomite (MgSO 2 ·7H 2 O) crystals grown from an aqueous solution in the presence of borax (Na 2 B 4 O 7 ·10H 2 O) were measured using the CoK α , CuK α , MoK α radiations. The intensities measured depend on the real crystal structure dependent on the borax content in the solution. The dependence of ΔI/I is studied as a function of borax in the solution and X-ray-radiation wavelength

Secondary extinction in cylindrical and spherical crystals for X-ray and neutron diffraction

International Nuclear Information System (INIS)

Hu Huachen; Li Zhaohuan; Yang Bin; Shen Caiwan

2001-01-01

The distribution of the reflection power ratio for a neutron or x-ray diffracted from a cylindrical crystal immersed in an homogenous incident beam is obtained by the numerical solution of the transfer equations for the first time. The profile well reflects all the physical properties of the absorption and extinction behaviour in the crystals. A systematic investigation of the secondary extinction for cylindrical and spherical crystals was carried out based on these results

X-ray topography using the forward transmitted beam under multiple-beam diffraction conditions

Energy Technology Data Exchange (ETDEWEB)

Tsusaka, Y., E-mail: tsusaka@sci.u-hyogo.ac.jp; Takano, H. [Graduate School of Material Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Hyogo 678-1297 (Japan); Takeda, S. [SPring-8 Service Co., Ltd., 1-20-5, Kouto, Shingu, Tatsuno, Hyogo 679-5165 (Japan); Yokoyama, K.; Matsui, J. [Synchrotron Radiation Nanotechnology Center, University of Hyogo, 1-490-2, Kouto, Shingu, Tatsuno, Hyogo 679-5165 (Japan); Kagoshima, Y. [Graduate School of Material Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Hyogo 678-1297 (Japan); Synchrotron Radiation Nanotechnology Center, University of Hyogo, 1-490-2, Kouto, Shingu, Tatsuno, Hyogo 679-5165 (Japan)

2016-02-15

X-ray topographs are taken for a sapphire wafer with the [0001] surface normal, as an example, by forward transmitted synchrotron x-ray beams combined with two-dimensional electronic arrays in the x-ray detector having a spatial resolution of 1 μm. They exhibit no shape deformation and no position shift of the dislocation lines on the topographs. Since the topography is performed under multiple-beam diffraction conditions, the topographic images of a single diffraction (two-wave approximation condition) or plural diffractions (six-wave approximation condition) can be recorded without large specimen position changes. As usual Lang topographs, it is possible to determine the Burgers vector of each dislocation line. Because of high parallelism of the incoming x-rays and linear sensitivity of the electronic arrays to the incident x-rays, the present technique can be used to visualize individual dislocations in single crystals of the dislocation density as high as 1 × 10{sup 5} cm{sup −2}.

About some practical aspects of X-ray diffraction : From single crystal to powders

Energy Technology Data Exchange (ETDEWEB)

Giacovazzo, C [Bari Univ. (Italy). Dip. Geomineralogico

1996-09-01

An ideal polycrystalline material or power is an ensemble of a very large number of randomly oriented crystallites. It is shown the effect that this random orientation has on the diffraction of a specimen assumed to contain only one reciprocal lattice node. The most remarkable difference with the single-crystal case is that now must think of scattering vectors not as lying on discrete nodes of reciprocal lattice vectors, the distances from the single-crystal reciprocal lattice nodes to the origin of reciprocal space.

About some practical aspects of X-ray diffraction : From single crystal to powders

International Nuclear Information System (INIS)

Giacovazzo, C.

1996-01-01

An ideal polycrystalline material or power is an ensemble of a very large number of randomly oriented crystallites. It is shown the effect that this random orientation has on the diffraction of a specimen assumed to contain only one reciprocal lattice node. The most remarkable difference with the single-crystal case is that now must think of scattering vectors not as lying on discrete nodes of reciprocal lattice vectors, the distances from the single-crystal reciprocal lattice nodes to the origin of reciprocal space

Solid state structural investigations of the bis(chalcone) compound with single crystal X-ray crystallography, DFT, gamma-ray spectroscopy and chemical spectroscopy methods

Science.gov (United States)

Yakalı, Gül; Biçer, Abdullah; Eke, Canel; Cin, Günseli Turgut

2018-04-01

A bis(chalcone), (2E,6E)-2,6-bis((E)-3phenylallidene)cyclohexanone, was characterized by 1H NMR, 13C NMR, FTIR, UV-Vis spectroscopy, gamma-ray spectroscopy and single crystal X- ray structural analysis. The optimized molecular structure of the compound is calculated using DFT/B3LYP with 6-31G (d,p) level. The calculated geometrical parameters are in good agreement with the experimental data obtained from our reported X-ray structure. The powder and single crystal compounds were gama-irradiated using clinical electron linear accelerator and 60Co gamma-ray source, respectively. Spectral studies (1H NMR, 13C NMR, FTIR and UV-Vis) of powder chalcone compound were also investigated before and after irradiation. Depending on the irradiation notable changes were observed in spectral features powder sample. Single crystal X-ray diffraction investigation shows that both unirradiated and irradiated single crystal samples crystallizes in a orthorhombic crystal system in the centrosymmetric space group Pbcn and exhibits an C-H..O intramolecular and intermolecular hydrogen bonds. The crystal packing is stabilised by strong intermolecular bifurcate C-H..O hydrogen bonds and π…π stacking interactions. The asymmetric unit of the title compound contains one-half of a molecule. The other half of the molecule is generated with (1-x,y,-3/2-z) symmetry operator. The molecule is almost planar due to having π conjugated system of chalcones. However, irradiated single crystal compound showed significant changes lattice parameters, crystal volume and density. According to results of gamma-ray spectroscopy, radioactive elements of powder compound which are 123Sb(n,g),124Sb,57Fe(g,p),56Mn, 55Mn(g,n), and 54Mn were determined using photoactivation analysis. However, the most intensive gamma-ray energy signals are 124Sb.

Anomalous effect of high-frequency ultrasound on radiation diffraction in deformed single crystals

International Nuclear Information System (INIS)

Iolin, E.M.; Rajtman, Eh.A.; Kuvaldin, B.V.; Zolotoyabko, Eh.V.

1988-01-01

Results are presented of a theoretical and experimental study of neutron and X-ray diffraction in defromed single crystals on high-frequency ultrasonic excitation. It is demonstrated theoretically that at a frequency exceeding a certain threshold value the ultrasound violates the adiabatic conditions for the excitation point motion on the dispersion surface branches. This leads to an anomalous (compared to diffraction for a perfect crystal) dependence of the diffraction intensity on the ultrasonic wave amplitude. The experimental data for Si crystals are in good agreement with the theoretical predictions

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto

OpenAIRE

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

2010-01-01

Nattokinase, a protein found in high levels in the traditional Japanese food natto, has been reported to have high thrombolytic activity. In the present study, the crystallization of native nattokinase and the collection of X-ray diffraction date from a nattokinase crystal to a resolution of 1.74 Å are reported.

Cloning, recombinant production, crystallization and preliminary X-ray diffraction analysis of SDF2-like protein from Arabidopsis thaliana

International Nuclear Information System (INIS)

Radzimanowski, Jens; Ravaud, Stephanie; Schott, Andrea; Strahl, Sabine; Sinning, Irmgard

2009-01-01

Overexpression, purification, crystallization and preliminary X-ray diffraction of the stromal-cell-derived factor 2-like protein of Arabidopsis thaliana are reported. The crystals belonged to the space group P6 1 and diffracted to 1.95 Å resolution. The stromal-cell-derived factor 2-like protein of Arabidopsis thaliana (AtSDL) has been shown to be highly up-regulated in response to unfolded protein response (UPR) inducing reagents, suggesting that it plays a crucial role in the plant UPR pathway. AtSDL has been cloned, overexpressed, purified and crystallized using the vapour-diffusion method. Two crystal forms have been obtained under very similar conditions. The needle-shaped crystals did not diffract X-rays, while the other form diffracted to 1.95 Å resolution using a synchrotron-radiation source and belonged to the hexagonal space group P6 1 , with unit-cell parameters a = b = 96.1, c = 69.3 Å

Characterization of calcium crystals in Abelia using x-ray diffraction and electron microscopes

Science.gov (United States)

Localization, chemical composition, and morphology of calcium crystals in leaves and stems of Abelia mosanensis and A. ×grandiflora were analyzed with a variable pressure scanning electron microscope (VP-SEM) equipped with an X-ray diffraction system, low temperature SEM (LT-SEM) and a transmission ...

Adsorption structure of dimethyl ether on silicalite-1 zeolite determined using single-crystal X-ray diffraction

International Nuclear Information System (INIS)

Fujiyama, Shinjiro; Seino, Shintaro; Kamiya, Natsumi; Nishi, Koji; Yokomori, Yoshinobu

2014-01-01

The most stable sorption site of dimethyl ether on silicalite-1 is the sinusoidal channel. The configuration of guest molecules (linear or bent) plays an important role in determining where the stable sorption site is situated. The adsorption structures of dimethyl ether (DME) on silicalite-1 zeolite (MFI-type) are determined using single-crystal X-ray diffraction. The structure of low-loaded DME-silicalite-1 indicates that all DME molecules are located in the sinusoidal channel, which is the most stable sorption site based on the van der Waals interaction between DME and the framework. The configuration of guest molecules (linear or bent) plays an important role in determining where the stable sorption site is in the pore system of MFI-type zeolites. Bent molecules favor the sinusoidal channel, while linear molecules favor the straight channel. The contribution of DME–DME interactions is considerable in the high-loaded DME-silicalite-1 structure

Crystallization and preliminary X-ray diffraction studies of the putative haloalkane dehalogenase DppA from Plesiocystis pacifica SIR-I

International Nuclear Information System (INIS)

Bogdanović, Xenia; Hesseler, Martin; Palm, Gottfried J.; Bornscheuer, Uwe T.; Hinrichs, Winfried

2010-01-01

The crystallization and preliminary X-ray diffraction studies of DppA from P. pacifica SIR-I are reported. DppA from Plesiocystis pacifica SIR-I is a putative haloalkane dehalogenase (EC 3.8.1.5) and probably catalyzes the conversion of halogenated alkanes to the corresponding alcohols. The enzyme was expressed in Escherichia coli BL21 and purified to homogeneity by ammonium sulfate precipitation and reversed-phase and ion-exchange chromatography. The DppA protein was crystallized by the vapour-diffusion method and protein crystals suitable for data collection were obtained in the orthorhombic space group P2 1 2 1 2. The DppA crystal diffracted X-rays to 1.9 Å resolution using an in-house X-ray generator

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin

International Nuclear Information System (INIS)

Jaimohan, S. M.; Naresh, M. D.; Arumugam, V.; Mandal, A. B.

2009-01-01

Parakeet (Psittacula krameri) haemoglobin has been purified and crystallized under low salt buffered conditions. Preliminary analysis of the crystal that belonged to monoclinic system (C2) is reported. Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemoglobins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 Å resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 Å, β = 109.35°. Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit

Re-examination of the crystal structure of the β-pyrochlore oxide superconductor KOs 2O 6 by X-ray and convergent-beam electron diffraction analyses

Science.gov (United States)

Yamaura, Jun-Ichi; Hiroi, Zenji; Tsuda, Kenji; Izawa, Koichi; Ohishi, Yasuo; Tsutsui, Satoshi

2009-01-01

The crystal structure of the β-pyrochlore oxide superconductor KOs 2O 6 is re-examined. A single-crystal X-ray diffraction (XRD) analysis at room temperature first revealed that the compound crystallizes in a cubic structure with the centrosymmetric space group Fd3¯m, as in conventional pyrochlore oxides. Later, however, Schuck et al. claimed a different non-centrosymmetric F4¯3m structure based on their single-crystal XRD analysis. To unambiguously determine the true crystal structure of KOs 2O 6, we carried out high-resolution synchrotron powder X-ray and convergent-beam electron diffraction measurements at room temperature. The space group was determined with high reliability to be centrosymmetric Fd3¯m, not F4¯3m. This confirms the importance of the K atom location in a high-symmetry site, which causes unusually large rattling of the K atom.

X-ray diffraction and X-ray standing-wave study of the lead stearate film structure

Energy Technology Data Exchange (ETDEWEB)

Blagov, A. E.; Dyakova, Yu. A.; Kovalchuk, M. V.; Kohn, V. G.; Marchenkova, M. A.; Pisarevskiy, Yu. V.; Prosekov, P. A., E-mail: prosekov@crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2016-05-15

A new approach to the study of the structural quality of crystals is proposed. It is based on the use of X-ray standing-wave method without measuring secondary processes and considers the multiwave interaction of diffraction reflections corresponding to different harmonics of the same crystallographic reflection. A theory of multiwave X-ray diffraction is developed to calculate the rocking curves in the X-ray diffraction scheme under consideration for a long-period quasi-one-dimensional crystal. This phase-sensitive method is used to study the structure of a multilayer lead stearate film on a silicon substrate. Some specific structural features are revealed for the surface layer of the thin film, which are most likely due to the tilt of the upper layer molecules with respect to the external normal to the film surface.

Real-time observation of epitaxial crystal growth in gaseous environment using x-ray diffraction and x-ray reflectometry

International Nuclear Information System (INIS)

Kawamura, Tomoaki; Bhunia, Satyaban; Watanabe, Yoshio; Fujikawa, Seiji

2008-01-01

We made the x-ray diffractometer combined with the MOCVD growth system for the real-time observation of epitaxial growth in gaseous environment, and investigated the growth mechanism of InP crystals. Changes of the (-5/2 O) Bragg diffraction during the growth revealed that the growth starts immediately after the In source has been supplied and gradually stopped, owing to the migrating In atoms on the surface. Additionally, one can easily determine the growth modes, including 3-dimensional mode, layer-by-layer mode, and step-flow mode, by observing the change of x-ray reflectivity with various growth conditions. (author)

Crystallization and preliminary X-ray diffraction analysis of the haem-binding protein HemS from Yersinia enterocolitica

International Nuclear Information System (INIS)

Schneider, Sabine; Paoli, Massimo

2005-01-01

The haem binding protein HemS from Y. enterocolitica has been crystallized in complex with its ligand. The crystals diffracted X-rays to 2.6 Å in-house. Bacteria have evolved strategies to acquire iron from their environment. Pathogenic microbes rely on specialized proteins to ‘steal’ haem from their host and use it as an iron source. HemS is the ultimate recipient of a molecular-relay system for haem uptake in Gram-negative species, functioning as the cytosolic carrier of haem. Soluble expression and high-quality diffraction crystals were obtained for HemS from Yersinia enterocolitica. Crystals belong to the orthorhombic space group I222, with unit-cell parameters a = 74.86, b = 77.45, c = 114.09 Å, and diffract X-rays to 2.6 Å spacing in-house. Determination of the structure of the haem–HemS complex will reveal the molecular basis of haem binding

Crystallization and preliminary X-ray diffraction analysis of the haem-binding protein HemS from Yersinia enterocolitica

Energy Technology Data Exchange (ETDEWEB)

Schneider, Sabine; Paoli, Massimo, E-mail: max.paoli@nottingham.ac.uk [School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)

2005-08-01

The haem binding protein HemS from Y. enterocolitica has been crystallized in complex with its ligand. The crystals diffracted X-rays to 2.6 Å in-house. Bacteria have evolved strategies to acquire iron from their environment. Pathogenic microbes rely on specialized proteins to ‘steal’ haem from their host and use it as an iron source. HemS is the ultimate recipient of a molecular-relay system for haem uptake in Gram-negative species, functioning as the cytosolic carrier of haem. Soluble expression and high-quality diffraction crystals were obtained for HemS from Yersinia enterocolitica. Crystals belong to the orthorhombic space group I222, with unit-cell parameters a = 74.86, b = 77.45, c = 114.09 Å, and diffract X-rays to 2.6 Å spacing in-house. Determination of the structure of the haem–HemS complex will reveal the molecular basis of haem binding.

5-Arylidene derivatives of Meldrum's acid: Synthesis, structural characterization using single crystal and powder crystal X-ray diffraction, and electronic properties

Science.gov (United States)

Dey, Tanusri; Ghosh, Soumen; Ghosh, Somnath; Mukherjee, Alok Kumar

2015-07-01

Four 5-arylidene derivatives of Meldrum's acid, 5-(4-chlorobenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (2), 5-(3-hydroxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (3), 5-(3,4-dimethoxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (4) and 5-(2,4-dimethoxy benzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (5) have been synthesized and their crystal structures have been determined using single crystal X-ray diffractometry for 2, 4 and 5 and X-ray powder diffraction for 3. The nature of intermolecular interactions in 2-5 has been analyzed through Hirshfeld surfaces and 2D fingerprint plots. The DFT optimized molecular geometries in 2-5 agree closely with those obtained from the crystallographic studies. The crystal packing in 2-5 exhibits an interplay of Osbnd H⋯O, Csbnd H⋯O, Csbnd H⋯Cl and Csbnd H⋯π (arene) hydrogen bonds and π⋯π interactions, which assemble molecules into three-dimensional architecture in 2, 3 and 5 and two-dimensional framework in 4. The Hirshfeld surface analyses of 2-5, Meldrum's acid (1) and a few related 5-arylidene derivatives of Meldrum's acid retrieved from the Cambridge Structural Database (CSD) indicate that about 85% of the Hirshfeld surface area (72% in 2 where H⋯Cl contribution is about 13%) in this class of compounds are due to H⋯H, O⋯H and C⋯H contacts. The HOMO-LUMO energy gap (>2.2 eV) in 2-5 indicates a significant degree of internal charge transfer within the molecule.

Advances in thin film diffraction instrumentation by X-ray optics

International Nuclear Information System (INIS)

Haase, A.

1996-01-01

The structural characterisation of thin films requires a parallel X-ray beam of high intensity. Parallel beam geometry is commonly used in high resolution and single crystal experiments, but also in the field of X-ray diffraction for polycrystalline material (e.g. in phase, texture and stress analysis). For grazing incidence diffraction (GID), the use of small slits on the primary side and of long soller slits with a flat monochromator on the secondary side is standard. New optical elements have been introduced with polychromatic or monochromatic radiation. By means of different applications the results are compared with those of classical beam optics. X-ray fiber optics utilize total external reflection of X-rays on smooth surfaces. Effects of monochromatization are presented. In many fields of application, fiber optics may replace conventional collimators. The use of primary and secondary channel cut crystals can also produce a high parallel monochromatic X-ray beam. A parabolically bent graded multilayer produces a monochromatic parallel beam of high intensity. Compared with classical Bragg-Brentano (focussing) geometry, excellent results have been obtained, especially for samples with an irregular shape. In combination with a channel cut monochromator there is a substantial gain in intensity leading to an increase of the dynamic intensity range of rocking curves

Advances in thin film diffraction instrumentation by X-ray optics

Energy Technology Data Exchange (ETDEWEB)

Haase, A [Rich. Seifert and Co., Analytical X-ray Systems, Ahrensburg (Germany)

1996-09-01

The structural characterisation of thin films requires a parallel X-ray beam of high intensity. Parallel beam geometry is commonly used in high resolution and single crystal experiments, but also in the field of X-ray diffraction for polycrystalline material (e.g. in phase, texture and stress analysis). For grazing incidence diffraction (GID), the use of small slits on the primary side and of long soller slits with a flat monochromator on the secondary side is standard. New optical elements have been introduced with polychromatic or monochromatic radiation. By means of different applications the results are compared with those of classical beam optics. X-ray fiber optics utilize total external reflection of X-rays on smooth surfaces. Effects of monochromatization are presented. In many fields of application, fiber optics may replace conventional collimators. The use of primary and secondary channel cut crystals can also produce a high parallel monochromatic X-ray beam. A parabolically bent graded multilayer produces a monochromatic parallel beam of high intensity. Compared with classical Bragg-Brentano (focussing) geometry, excellent results have been obtained, especially for samples with an irregular shape. In combination with a channel cut monochromator there is a substantial gain in intensity leading to an increase of the dynamic intensity range of rocking curves.

X-ray diffraction studies of silicon implanted with high energy ions

Energy Technology Data Exchange (ETDEWEB)

Wieteska, K [Institute of Atomic Energy, Otwock-Swierk, (Poland); Wierzchowski, W [Institute of Electronic Materials Technology, Warsaw, (Poland); Graeff, W [Hasylab at Desy, Hamburg, (Germany)

1997-12-31

The character of lattice deformation in silicon in implanted with high energy {alpha} particles and protons was studied with a number of X-ray methods. The experiments included double crystal spectrometer method as well as single crystal section and projection topography realised both with conventional and synchrotron X-ray sources. All observed diffraction patterns were reasonably explainable assuming the lattice parameter depth distribution proportional to the vacancy-interstitial distribution coming from the Biersack-Ziegler theory. The theoretical rocking curves and density distribution in back-reflection double-crystal and section topography well corresponding to experimental results were calculated using numerical integration of the Takagi-Taupin equations. 9 figs.

A combined temperature-dependent electron and single-crystal X-ray diffraction study of the fresnoite compound Rb2V4+V25+O8

International Nuclear Information System (INIS)

Withers, R.L.; Hoeche, Thomas; Liu Yun; Esmaeilzadeh, Saeid; Keding, Ralf; Sales, Brian

2004-01-01

High-purity Rb 2 V 3 O 8 has been grown and temperature-dependent electron and single-crystal X-ray diffraction used to carefully investigate its fresnoite-type reciprocal lattice. In contrast to other recently investigated representatives of the fresnoite family of compounds, Rb 2 V 3 O 8 is not incommensurately modulated with an incommensurate basal plane primary modulation wave vector given by q∼0.3 *. A careful low-temperature electron diffraction study has, however, revealed the existence of weak incommensurate satellite reflections characterized by the primitive primary modulation wave vector q 1 ∼0.16c*. The reciprocal space positioning of these incommensurate satellite reflections, the overall (3+1)-d superspace group symmetry, as well as the shapes of the refined displacement ellipsoids determined from single-crystal XRD refinement, are all consistent with their arising from a distinct type of condensed rigid unit modes (RUMs) of distortion of the Rb 2 V 3 O 8 parent structure

Hard x-ray monochromator with milli-electron volt bandwidth for high-resolution diffraction studies of diamond crystals

Energy Technology Data Exchange (ETDEWEB)

Stoupin, Stanislav; Shvyd' ko, Yuri; Shu Deming; Khachatryan, Ruben; Xiao, Xianghui; DeCarlo, Francesco; Goetze, Kurt; Roberts, Timothy; Roehrig, Christian; Deriy, Alexey [Advanced Photon Source, Argonne National Laboratory, Illinois 60439 (United States)

2012-02-15

We report on design and performance of a high-resolution x-ray monochromator with a spectral bandwidth of {Delta}E{sub X}{approx_equal} 1.5 meV, which operates at x-ray energies in the vicinity of the backscattering (Bragg) energy E{sub H} = 13.903 keV of the (008) reflection in diamond. The monochromator is utilized for high-energy-resolution diffraction characterization of diamond crystals as elements of advanced x-ray crystal optics for synchrotrons and x-ray free-electron lasers. The monochromator and the related controls are made portable such that they can be installed and operated at any appropriate synchrotron beamline equipped with a pre-monochromator.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of Thermotoga neapolitana β-glucosidase B

Energy Technology Data Exchange (ETDEWEB)

Turner, Pernilla [Department of Biotechnology, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden); Pramhed, Anna [Department of Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden); Kanders, Erik; Hedström, Martin; Karlsson, Eva Nordberg, E-mail: eva.nordberg-karlsson@biotek.lu.se [Department of Biotechnology, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden); Logan, Derek T., E-mail: eva.nordberg-karlsson@biotek.lu.se [Department of Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden); Department of Biotechnology, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden)

2007-09-01

Here, the expression, purification, crystallization and X-ray diffraction data of a family 3 β-glucosidase from the hyperthermophilic bacterium Thermotoga neapolitana are reported. β-Glucosidases belong to families 1, 3 and 9 of the glycoside hydrolases and act on cello-oligosaccharides. Family 1 and 3 enzymes are retaining and are reported to have transglycosylation activity, which can be used to produce oligosaccharides and glycoconjugates. Family 3 enzymes are less well characterized than their family 1 homologues and to date only two crystal structures have been solved. Here, the expression, purification, crystallization and X-ray diffraction data of a family 3 β-glucosidase from the hyperthermophilic bacterium Thermotoga neapolitana are reported. Crystals of selenomethionine-substituted protein have also been grown. The crystals belong to space group C222{sub 1}, with unit-cell parameters a = 74.9, b = 127.0, c = 175.2 Å. Native data have been collected to 2.4 Å resolution and the structure has been solved to 2.7 Å using the selenomethionine MAD method. Model building and refinement of the structure are under way.

X-ray diffraction of multilayers and superlattices

International Nuclear Information System (INIS)

Bartels, W.J.; Hornstra, J.; Lobeek, D.J.W.

1986-01-01

Recursion formulae for calculating the reflected amplitude ratio of multilayers and superlattices have been derived from the Takagi-Taupin differential equations, which describe the dynamical diffraction of X-rays in deformed crystals. Calculated rocking curves of complicated layered structures, such as non-ideal superlattices on perfect crystals, are shown to be in good agreement with observed diffraction profiles. The kinematical theory can save computing time only in the case of an ideal superlattice, for which a geometric series can be used, but the reflections must be below 10% so that multiple reflections can be neglected. For a perfect crystal of arbitrary thickness the absorption at the center of the dynamical reflection is found to be proportional to the square root of the reflectivity. Sputter-deposited periodic multilayers of tungsten and carbon can be considered as an artificial crystal, for which dynamical X-ray diffraction calculations give results very similar to those of a macroscopic optical description in terms of the complex index of refraction and Fresnel reflection coefficients. (orig.)

Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus

International Nuclear Information System (INIS)

Martin, Stanton L.; Guenther, Richard H.; Sit, Tim L.; Swartz, Paul D.; Meilleur, Flora; Lommel, Steven A.; Rose, Robert B.

2010-01-01

Virions of red clover necrotic mosaic virus have been purified and crystallized. The space group was determined to be I23, with unit-cell parameter a = 377.8 Å. The crystals diffracted to 4 Å resolution. Red clover necrotic mosaic virus (RCNMV) is a species that belongs to the Tombusviridae family of plant viruses with a T = 3 icosahedral capsid. RCNMV virions were purified and were crystallized for X-ray analysis using the hanging-drop vapor-diffusion method. Self-rotation functions and systematic absences identified the space group as I23, with two virions in the unit cell. The crystals diffracted to better than 4 Å resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. The data were processed to 6 Å in the analysis presented here

Purification, crystallization and preliminary X-ray diffraction studies of UDP-N-acetylglucosamine pyrophosphorylase from Candida albicans

Energy Technology Data Exchange (ETDEWEB)

Maruyama, Daisuke; Nishitani, Yuichi; Nonaka, Tsuyoshi; Kita, Akiko [Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); Fukami, Takaaki A.; Mio, Toshiyuki; Yamada-Okabe, Hisafumi [Kamakura Research Laboratory, Chugai Pharmaceutical Co. Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530 (Japan); Yamada-Okabe, Toshiko [Department of Hygiene, School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama 236-0004 (Japan); Miki, Kunio, E-mail: miki@kuchem.kyoto-u.ac.jp [Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayocho, Sayo-gun, Hyogo 679-5148 (Japan)

2006-12-01

UDP-N-acetylglucosamine pyrophosphorylase was purified and crystallized and X-ray diffraction data were collected to 2.3 Å resolution. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is an essential enzyme in the synthesis of UDP-N-acetylglucosamine. UAP from Candida albicans was purified and crystallized by the sitting-drop vapour-diffusion method. The crystals of the substrate and product complexes both diffract X-rays to beyond 2.3 Å resolution using synchrotron radiation. The crystals of the substrate complex belong to the triclinic space group P1, with unit-cell parameters a = 47.77, b = 62.89, c = 90.60 Å, α = 90.01, β = 97.72, γ = 92.88°, whereas those of the product complex belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.95, b = 90.87, c = 94.88 Å.

Crystallization and preliminary X-ray diffraction analysis of the lytic transglycosylase MltE from Escherichia coli

International Nuclear Information System (INIS)

Artola-Recolons, Cecilia; Llarrull, Leticia I.; Lastochkin, Elena; Mobashery, Shahriar; Hermoso, Juan A.

2010-01-01

Crystals of the lytic transglycosylase MltE from E. coli were grown using the microbatch method and diffracted to a resolution of 2.1 Å. MltE from Escherichia coli (193 amino acids, 21 380 Da) is a lytic transglycosylase that initiates the first step of cell-wall recycling. This enzyme is responsible for the cleavage of the cell-wall peptidoglycan at the β-1,4-glycosidic bond between the N-acetylglucosamine and N-acetylmuramic acid units. At the end this reaction generates a disaccharide that is internalized and initiates the recycling process. To obtain insights into the biological functions of MltE, crystallization trials were performed and crystals of MltE protein that were suitable for X-ray diffraction analysis were obtained. The MltE protein of E. coli was crystallized using the hanging-drop vapour-diffusion method at 291 K. Crystals grew from a mixture consisting of 28% polyethylene glycol 4000, 0.1 M Tris pH 8.4 and 0.2 M magnesium chloride. Further optimization was performed using the microbatch technique. Single crystals were obtained that belonged to the orthorhombic space group C222 1 , with unit-cell parameters a = 123.32, b = 183.93, c = 35.29 Å, and diffracted to a resolution of 2.1 Å

Structure solution from powder neutron and x-ray diffraction data: getting the best of both worlds

International Nuclear Information System (INIS)

Hunter, B.A.

2000-01-01

Full text: Powder diffraction methods have traditionally been used in three main areas: phase identification and quantification, lattice parameter determination and structure refinement. Until recently structure solution has been the almost exclusive domain of single crystal diffraction methods, predominantly using x-rays. The increasing use of synchrotron and neutron sources, and the unrelenting advances in computing hardware and software means that powder methods are challenging single crystal methods as a practical method for structure solution, especially when single crystal method can not be applied. It is known that structural refinements from a known starting structure using combined X-ray and neutron data sets are capable of providing highly accurate structures. Likewise, using combined x-ray and neutron powder diffraction data in the structure solution process should also be a powerful technique, although to date no one is pursuing this methodology. This paper present examples of solutions to the problem. Namely we are using high resolution powder X-ray and neutron methods to solve the structures of molecular materials and minerals, then refining the structures using both sets of data. In this way we exploit the advantages of both methods while minimising the disadvantages. We present our solution for a small amino acid structure, a metalorganic and a mineral structure

Single-crystal X-ray diffraction study of SrGeO3 high-pressure perovskite phase at 100 K

Science.gov (United States)

Nakatsuka, Akihiko; Arima, Hiroshi; Ohtaka, Osamu; Fujiwara, Keiko; Yoshiasa, Akira

2017-10-01

Single-crystal X-ray diffraction study of SrGeO3 perovskite (cubic; space group Pmɜ¯m) synthesized at 6 GPa and 1223 K was conducted at a low temperature of 100 K. The residual electron density revealed the presence of the bonding electron at the center of the Ge-O bond, in accordance with our previous conclusion that the Ge-O bond is strongly covalent. From comparison with our previous structure-refinement result at 296 K, the mean square displacement (MSD) of the O atom in the direction of the Ge-O bond is suggested to exhibit no significant temperature dependence, in contrast to that in the direction perpendicular to the bond. Thus, the strong covalency of the Ge-O bond can have a large influence on the temperature dependence of thermal vibration of the O atom.

Preliminary morphological and X-ray diffraction studies of the crystals of the DNA cetyltrimethylammonium salt.

Science.gov (United States)

Osica, V D; Pyatigorskaya, T L; Polyvtsev, O F; Dembo, A T; Kliya, M O; Vasilchenko, V N; Verkin, B I; Sukharevskya, B Y

1977-04-01

Double-stranded DNA molecules (molecular weight 2.5 X 10(5) - 5 X 10(5) daltons) have been crystallized from water-salt solutions as cetyltrimethylammonium salts (CTA-DNA). Variation of crystallization conditions results in a production of different types of CTA-DNA crystals: spherulits, dendrites, needle-shaped and faceted rhombic crystals, the latter beeing up to 0.3 mm on a side. X-ray diffraction data indicate that DNA molecules in the crystals form a hexagonal lattice which parameters vary slightly with the morphological type of the crystal. Comparison of the melting curves of the DNA preparation before and after crystallization suggests that DNA molecules are partially fractionated in the course of crystallization. Crystals of the CTA-DNA-proflavine complex have also been obtained.

Peculiarities of section topograms for the multiple diffraction of X rays

Energy Technology Data Exchange (ETDEWEB)

Kohn, V. G., E-mail: kohnvict@yandex.ru [National Research Centre “Kurchatov Institute” (Russian Federation); Smirnova, I. A. [Russian Academy of Sciences, Institute of Solid State Physics (Russian Federation)

2016-07-15

The distortion of interference fringes on the section topograms of single crystal due to the multiple diffraction of X rays has been investigated. The cases of the 220 and 400 reflections in a silicon crystal in the form of a plate with a surface oriented normally to the [001] direction are considered both theoretically and experimentally. The same section topogram exhibits five cases of multiple diffraction at small azimuthal angles for the 400 reflection and MoK{sub α} radiation, while the topogram for the 220 reflection demonstrates two cases of multiple diffraction. All these cases correspond to different combinations of reciprocal lattice vectors. Exact theoretical calculations of section topograms for the aforementioned cases of multiple diffraction have been performed for the first time. The section topograms exhibit two different distortion regions. The distortions in the central region of the structure are fairly complex and depend strongly on the azimuthal angle. In the tails of the multiple diffraction region, there is a shift of two-beam interference fringes, which can be observed even with a laboratory X-ray source.

Crystallization and preliminary X-ray diffraction analysis of the middle domain of Paip1

International Nuclear Information System (INIS)

Kanaan, Ahmad Seif; Frank, Filipp; Maedler-Kron, Chelsea; Verma, Karan; Sonenberg, Nahum; Nagar, Bhushan

2009-01-01

The crystallization of the putative MIF4G domain of Paip1 is described. The crystals belonged to the monoclinic space group P2 1 and diffracted X-rays to beyond 2.2 Å resolution. The poly(A)-binding protein (PABP) simultaneously interacts with the poly(A) tail of mRNAs and the scaffolding protein eIF4G to mediate mRNA circularization, resulting in stimulation of protein translation. PABP is regulated by the PABP-interacting protein Paip1. Paip1 is thought to act as a translational activator in 5′ cap-dependent translation by interacting with PABP and the initiation factors eIF4A and eIF3. Here, the crystallization and preliminary diffraction analysis of the middle domain of Paip1 (Paip1M), which produces crystals that diffract to a resolution of 2.2 Å, are presented

X-ray diffraction from ideal mosaic crystals in external fields of certain types. I. Atomic displacements and the corresponding diffraction patterns

International Nuclear Information System (INIS)

Treushnikov, E.N.

2000-01-01

The problem of the theoretical description of X-ray diffraction from ideal mosaic crystals under the effect of various external fields has been formulated. Electric, magnetic, electromagnetic, and acoustic perturbations are considered. The atomic displacements in crystals under the effect of external fields and the types of the corresponding diffraction patterns are analyzed for various types of perturbations. The crystal classes are determined in which atomic displacements can be recorded experimentally. Diffraction patterns formed under the effect of various external factors are considered on the basis of the derived dependence of the structure factor on the characteristics of an applied force field

Variable-temperature single-crystal X-ray diffraction study of tetragonal and cubic perovskite-type barium titanate phases.

Science.gov (United States)

Nakatani, Tomotaka; Yoshiasa, Akira; Nakatsuka, Akihiko; Hiratoko, Tatsuya; Mashimo, Tsutomu; Okube, Maki; Sasaki, Satoshi

2016-02-01

A variable-temperature single-crystal X-ray diffraction study of a synthetic BaTiO3 perovskite has been performed over the temperature range 298-778 K. A transition from a tetragonal (P4mm) to a cubic (Pm3m) phase has been revealed near 413 K. In the non-centrosymmetric P4mm symmetry group, both Ti and O atoms are displaced along the c-axis in opposite directions with regard to the Ba position fixed at the origin, so that Ti(4+) and Ba(2+) cations occupy off-center positions in the TiO6 and BaO12 polyhedra, respectively. Smooth temperature-dependent changes of the atomic coordinates become discontinuous with the phase transition. Our observations imply that the cations remain off-center even in the high-temperature cubic phase. The temperature dependence of the mean-square displacements of Ti in the cubic phase includes a significant static component which means that Ti atoms are statistically distributed in the off-center positions.

Synthesis and single crystal X-ray analysis of two griseofulvin metabolites

DEFF Research Database (Denmark)

Rønnest, Mads Holger; Harris, Pernille; Gotfredsen, Charlotte Held

2010-01-01

The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis.......The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis....

X-ray conductivity of ZnSe single crystals

Energy Technology Data Exchange (ETDEWEB)

Degoda, V. Ya., E-mail: degoda@univ.kiev.ua; Podust, G. P. [Taras Shevchenko Kyiv National University, Physics Department (Ukraine)

2016-05-15

The experimental I–V and current–illuminance characteristics of the X-ray conductivity and X-ray luminescence of zinc-selenide single crystals feature a nonlinear shape. The performed theoretical analysis of the kinetics of the X-ray conductivity shows that even with the presence of shallow and deep traps for free charge carriers in a semiconductor sample, the integral characteristics of the X-ray conductivity (the current–illuminance and I–V dependences) should be linear. It is possible to assume that the nonlinearity experimentally obtained in the I–V and current–illuminance characteristics can be caused by features of the generation of free charge carriers upon X-ray irradiation, i.e., the generation of hundreds of thousands of free charge carriers of opposite sign in a local region with a diameter of <1 μm and Coulomb interaction between the free charge carriers of opposite signs.

Submicron X-ray diffraction

International Nuclear Information System (INIS)

MacDowell, Alastair; Celestre, Richard; Tamura, Nobumichi; Spolenak, Ralph; Valek, Bryan; Brown, Walter; Bravman, John; Padmore, Howard; Batterman, Boris; Patel, Jamshed

2000-01-01

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

High resolution X-ray diffraction studies on unirradiated

Indian Academy of Sciences (India)

High-resolution X-ray diffraction technique, employing a three-crystal monochromator–collimator combination is used to study the irradiation induced defects in flux grown Sr-hexaferrite crystals irradiated with 50 MeV Li3+ ion beams at room temperature with a fluence value of 1 × 1014 ions/cm2. The diffraction curves of the ...

Single order soft X-ray diffraction with quasi-random radius pinhole array spectroscopic photon sieves

International Nuclear Information System (INIS)

Zhang Qiang-Qiang; Wei Lai; Yang Zu-Hua; Qian Feng; Fan Quan-Ping; Zhang Bo; Gu Yu-Qiu; Cao Lei-Feng

2014-01-01

A novel single order diffraction grating in the soft X-ray region, called quasi-random radius pinhole array spectroscopic photon sieves (QRSPS), is proposed in this paper. This new grating is composed of pinholes on a substrate, whose radii are quasi-random, while their centers are regular. Analysis proves that its transmittance function across the grating bar is similar to that of sinusoidal transmission gratings. Simulation results show that the QRSPS can suppress higher-order diffraction effectively. And the QRSPS would still retain its characteristic of single order diffraction when we take the effect of X-ray penetration into account. These properties indicate that the QRSPS can be used in the soft X-ray spectra measurement. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

The phase problem and perspectives of surface X-ray diffraction

International Nuclear Information System (INIS)

Tajiri, Hiroo; Takahashi, Toshio

2009-01-01

The emergence of synchrotron radiation sources has accelerated the application of diffraction techniques to surface sciences. Surface X-ray diffraction has become the state-of-the-art technique for determining ordered structures of atoms on crystal surfaces. We introduce surface X-ray diffraction briefly from the historical point of view and describe the concept that not only determine constellation of surface atoms but also view surface atoms as image. The progress in experimental and theoretical studies of surface X-ray diffraction including crystallographic direct methods is reviewed. (author)

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

Science.gov (United States)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

High-resolution X-ray diffraction studies of multilayers

DEFF Research Database (Denmark)

Christensen, Finn Erland; Hornstrup, Allan; Schnopper, H. W.

1988-01-01

High-resolution X-ray diffraction studies of the perfection of state-of-the-art multilayers are presented. Data were obtained using a triple-axis perfect-crystal X-ray diffractometer. Measurements reveal large-scale figure errors in the substrate. A high-resolution triple-axis set up is required...

Expression, purification, crystallization and preliminary X-ray diffraction analysis of Arabidopsis thaliana cyclophilin 38 (AtCyp38)

International Nuclear Information System (INIS)

Vasudevan, Dileep; Gopalan, Gayathri; He, Zengyong; Luan, Sheng; Swaminathan, Kunchithapadam

2005-01-01

Crystallization of Arabidopsis thaliana cyclophilin 38. The crystal diffracts X-rays to 2.5 Å resolution. AtCyp38 is one of the highly divergent multidomain cyclophilins from Arabidopsis thaliana. A recombinant form of AtCyp38 (residues 83–437) was expressed in Escherichia coli and purified to homogeneity. The protein was crystallized using the vapour-batch technique with PEG 6000 and t-butanol as precipitants. Crystals of recombinant AtCyp38 diffracted X-rays to better than 2.5 Å resolution at 95 K using a synchrotron-radiation source. The crystal belongs to the C-centred orthorhombic space group C222 1 , with unit-cell parameters a = 58.2, b = 95.9, c = 167.5 Å, and contains one molecule in the asymmetric unit. The selenomethionine derivative of the AtCyp38 protein was overexpressed, purified and crystallized in the same space group and data were collected to 3.5 Å at the NSLS synchrotron. The structure is being solved by the MAD method

A program for the derivation of crystal unit cell parameters from X-ray powder diffraction measurements

International Nuclear Information System (INIS)

Ferguson, I.F.; Rogerson, A.H.

1984-01-01

The program, FIRESTAR, determines the dimensions of a crystallographic unit cell from a set of X-ray powder diffraction measurements corresponding to a set of Bragg reflections, provided that the crystal system applicable is known and the Bragg reflections have been indexed. The program includes a range of possible extrapolation functions, and the data may be weighted. Provision is made for detecting and rejecting a single 'bad' measurement, and then rejecting measurements which lie outside an error limit set in the input data. (orig.)

Rapid X-ray crystal structure analysis in few second measurements using microstrip gas chamber

CERN Document Server

Ochi, A; Tanimori, T; Ohashi, Y; Toyokawa, H; Nishi, Y; Nishi, Y; Nagayoshi, T; Koishi, S

2001-01-01

X-ray crystal structure analysis using microstrip gas chamber was successfully carried out in a measurement time within a few seconds. The continuous rotation photograph method, in which most of the diffraction peaks can be obtained within one continuous rotation of the sample crystal (without stopping or oscillation), was applied for this measurement. As an example, the structure of a single crystal of ammonium bitartrate (r=1 mm, spherical) was measured. Diffraction spots from the sample, which were sufficient to obtain crystal structure, were successfully obtained by taking only 2 s measurements with a commercially available laboratory X-ray source.

Polarisation resonance in X-ray diffraction

International Nuclear Information System (INIS)

Goodman, P.; Paterson, D.; Matheson, S.

1994-01-01

The study of crystal structures by means of dynamic X-ray diffraction has placed a challenge to theoreticians to revise the X-ray diffraction theory based on Maxwell's equation. In this paper the feasibility of using 'polarisation resonance' as a tool in the determination of absolute configuration for asymmetric structures is investigated. Two (left- and right-handed), σ + and σ- , circular polarization states for 3-beam conditions are considered. Moreover, extending interaction into the 3 rd. dimension (normal to the beam) opens the possibility of absolute configuration determination of asymmetric structures in 3 dimensions. The computational scheme used is shown in terms of scattering diagrams. 7 refs., 1 tab., 6 figs

Characterization of monoclinic crystals in tablets by pattern-fitting procedure using X-ray powder diffraction data.

Science.gov (United States)

Yamamura, Shigeo; Momose, Yasunori

2003-06-18

The purpose of this study is to characterize the monoclinic crystals in tablets by using X-ray powder diffraction data and to evaluate the deformation feature of crystals during compression. The monoclinic crystals of acetaminophen and benzoic acid were used as the samples. The observed X-ray diffraction intensities were fitted to the analytic expression, and the fitting parameters, such as the lattice parameters, the peak-width parameters, the preferred orientation parameter and peak asymmetric parameter were optimized by a non-linear least-squares procedure. The Gauss and March distribution functions were used to correct the preferred orientation of crystallites in the tablet. The March function performed better in correcting the modification of diffraction intensity by preferred orientation of crystallites, suggesting that the crystallites in the tablets had fiber texture with axial orientation. Although a broadening of diffraction peaks was observed in acetaminophen tablets with an increase of compression pressure, little broadening was observed in the benzoic tablets. These results suggest that "acetaminophen is a material consolidating by fragmentation of crystalline particles and benzoic acid is a material consolidating by plastic deformation then occurred rearrangement of molecules during compression". A pattern-fitting procedure is the superior method for characterizing the crystalline drugs of monoclinic crystals in the tablets, as well as orthorhombic isoniazid and mannitol crystals reported in the previous paper.

Ultrafast coherent diffractive imaging of nanoparticles using X-ray free-electron laser radiation

International Nuclear Information System (INIS)

Kassemeyer, Stephan

2014-01-01

Coherent diffractive imaging with X-ray free-electron lasers (X-FEL) promises high-resolution structure determination of single microscopic particles without the need for crystallization. The diffraction signal of small samples can be very weak, a difficulty that can not be countered by merely increasing the number of photons because the sample would be damaged by a high absorbed radiation dose. Traditional X-ray crystallography avoids this problem by bringing many sample particles into a periodic arrangement, which amplifies the individual signals while distributing the absorbed dose. Depending on the sample, however, crystallization can be very difficult or even impossible. This thesis presents algorithms for a new imaging approach using X-FEL radiation that works with single, non-crystalline sample particles. X-FELs can deliver X-rays with a peak brilliance many orders of magnitude higher than conventional X-ray sources, compensating for their weak interaction cross sections. At the same time, FELs can produce ultra-short pulses down to a few femtoseconds. In this way it is possible to perform ultra-fast imaging, essentially ''freezing'' the atomic positions in time and terminating the imaging process before the sample is destroyed by the absorbed radiation. This thesis primarily focuses on the three-dimensional reconstruction of single (and not necessarily crystalline) particles using coherent diffractive imaging at X-FELs: in order to extract three-dimensional information from scattering data, two-dimensional diffraction patterns from many different viewing angles must be combined. Therefore, the diffraction signal of many identical sample copies in random orientations is measured. The main result of this work is a globally optimal algorithm that can recover the sample orientations solely based on the diffraction signal, enabling three-dimensional imaging for arbitrary samples. The problem of finding three-dimensional orientations is

Syntheses and crystal structure determination by X-ray powder diffraction of new compounds of Benzovesamicol

International Nuclear Information System (INIS)

Rukiah, M.; Assaad, Th.

2012-06-01

The compound 2,2,2-Trifluoro-N-(1a,2,7,7 a-tetra-hydronaphtho[2,3-b]oxiren-3-yl)- acetamide, C 1 2H 1 0F 3 NO 2 , an important precursor in the preparation of benzovesamicol analogues for the diagnosis of Alzheimers disease, was prepared by the epoxidation of 5,8-dihydronaphthalene-1-amine using 3-chloroperoxybenzoic acid. The structure was determined by X-ray powder diffraction, multinuclear NMR spectroscopy and FT-IR spectroscopy. A pair of molecules form intermolecular N- H...O hydrogen bonds, involving the amino and oxirene groups, to produce a dimer.The two racemic compounds (2RS,3RS)-5-amino-3-(4-phenylpiperazin-1-yl)-1,2,3,4 tetrahydronaphthalene-2-ol, C 2 0H 2 5N 3 O, (I) and (2RS,3RS)-5-amino-3-[4-(3- methoxyphenyl)piperazin-1-yl]-1,2,3,4-tetrahydronaphthalene-2-ol, C 2 1H 2 7N 3 O 2 , (II) important benzovesamicol analogues for the diagnosis of Alzheimer's disease, have been synthesized and characterized by FT-IR, and 1 H and 13 C NMR spectroscopic analyses. The crystal structures were analyses using powder diffraction as no suitable single crystal were obtained. The two compounds are racemic mixtures of enantiomers which crystallize in the monoclinic system in a centrosymmetric space group (P21/c). Crystallography, in particular powder X-ray diffraction, was pivotal in revealing that the enantio-resolution did not succeed. In two compounds, the piperazine ring has a chair conformation, while the cyclohexene ring assumes a half-chair conformation. In (I) the crystal packing is mediated by weak contacts, principally by complementary intermolecular N--H...O hydrogen bonds that connect successive molecules into a chain. Further stabilization is provided by weak C--H...N contacts and by a weak intermolecular C--H...π interaction. While in (II), the crystal packing is dominated by intermolecular O--H...N hydrogen bonding which links molecules along the c direction. (authors)

Ionothermal synthesis of β-NH4AlF4 and the determination by single crystal X-ray diffraction of its room temperature and low temperature phases

International Nuclear Information System (INIS)

Parnham, Emily R.; Slawin, Alex M.Z.; Morris, Russell E.

2007-01-01

β-NH 4 AlF 4 has been synthesised ionothermally using 1-ethyl-3-methylimidazolium hexafluorophosphate as solvent and template provider. β-NH 4 AlF 4 crystals were produced which were suitable for single crystal X-ray diffraction analysis. A phase transition occurs between room temperature (298 K) and low temperature (93 K) data collections. At 298 K the space group=I4/mcm (no. 140), α=11.642(5), c=12.661(5) A, Z=2 (10NH 4 AlF 4 ), wR(F 2 )=0.1278, R(F)=0.0453. At 93 K the space group=P4 2 /ncm (no. 138), α=11.616(3), c=12.677(3) A, Z=2 (10NH 4 AlF 4 ), wR(F 2 )=0.1387, R(F)=0.0443. The single crystal X-ray diffraction study of β-NH 4 AlF 4 shows the presence of two different polymorphs at low and room temperature, indicative of a phase transition. The [AlF 4/2 F 2 ] - layers are undisturbed except for a small tilting of the AlF 6 octahedra in the c-axis direction. -Ionothermal synthesis, the use of an ionic liquid as the solvent in materials preparation, has been used to prepare β-NH 4 AlF 4 , and structural characterisation indicates that there are two versions of the structure, a low temperature primitive phase at 93 K and a high temperature body-centered phase at 298 K

Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coli

International Nuclear Information System (INIS)

Hor, Lilian; Dobson, Renwick C. J.; Dogovski, Con; Hutton, Craig A.; Perugini, Matthew A.

2009-01-01

Diaminopimelate (DAP) epimerase, an enzyme in the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the cloning, expression, purification, crystallization and preliminary diffraction analysis of DAP epimerase from E. coli are reported. Diaminopimelate (DAP) epimerase (EC 5.1.1.7) catalyzes the penultimate step of lysine biosynthesis in bacteria and plants, converting l,l-diaminopimelate to meso-diaminopimelate. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DAP epimerase from Escherichia coli are presented. Crystals were obtained in space group P4 1 2 1 2 and diffracted to 2.0 Å resolution, with unit-cell parameters a = b = 89.4, c = 179.6 Å. Molecular replacement was conducted using Bacillus anthracis DAP epimerase as a search model and showed the presence of two molecules in the asymmetric unit, with an initial R free of 0.456 and R work of 0.416

Purification, crystallization and preliminary X-ray diffraction analysis of human Gadd45γ

International Nuclear Information System (INIS)

Zhang, Wenzheng; Zhao, Mingzhuo; Li, Jianhui; Li, Xuemei; Zeng, ZongHao; Rao, Zihe

2008-01-01

The human Gadd45γ protein has been crystallized as a prelude towards determination of its three-dimensional structure by X-ray crystallography. Gadd45, MyD118 and CR6 (also termed Gadd45α, Gadd45β and Gadd45γ, respectively) comprise a family of proteins that play important roles in negative growth control, maintenance of genomic stability, DNA repair, cell-cycle control and apoptosis. Recombinant human Gadd45γ and its selenomethionine derivative were expressed in an Escherichia coli expression system and purified; they were then crystallized using the hanging-drop vapour-diffusion method. Diffraction-quality crystals were grown at 291 K using PEG 3350 as precipitant. Using synchrotron radiation, the best diffraction data were collected to 2.3 Å resolution for native crystals at 100 K; selenomethionyl derivative data were collected to 3.3 Å resolution. All the crystals belonged to space group I2 1 3, with approximate unit-cell parameters a = b = c = 126 Å

Structural phase transitions in Bi[sub 2]V[sub 1[minus]x]Ge[sub x]O[sub 5. 5[minus]x/2] (x = 0. 2, 0. 4, and 0. 6) single crystals: X-ray crystallographic study

Energy Technology Data Exchange (ETDEWEB)

Sooryanarayana, K.; Guru Row, T.N.; Varma, K.B.R. (Indian Inst. of Science, Bangalore (India))

1999-02-01

Single crystals of Bi[sub 2]V[sub 1[minus]x]Ge[sub x]O[sub 5.5[minus]x/2] (x = 0.2, 0.4, and 0.6) were grown by slow cooling of melts. Bismuth vanadate transforms from an orthorhombic to a tetragonal structure and subsequently to an orthorhombic system when the Ge[sup 4+] concentration was varied from x = 0.2 to x = 0.6. All of these compositions crystallized in polar space groups (Aba2, F4mm, and Fmm2 for x = 0.2, 0.4, and 0.6, respectively). The structures were fully determined by single crystal X-ray diffraction studies.

Crystallization Kinetics of Nanocrystalline Materials by Combined X-ray Diffraction and Differential Scanning Calorimetry Experiments

Czech Academy of Sciences Publication Activity Database

Gil-González, E.; Perejón, A.; Sánchez-Jiménez, P. E.; Medina-Carrasco, S.; Kupčík, Jaroslav; Šubrt, Jan; Criado, J. M.; Pérez-Maqueda, L. A.

2018-01-01

Roč. 18, č. 5 (2018), s. 3107-3116 ISSN 1528-7483 Institutional support: RVO:61388980 Keywords : nanocrysalline alloys * combined X ray diffraction * crystallization kinetics Subject RIV: CA - Inorganic Chemistry OBOR OECD: Inorganic and nuclear chemistry Impact factor: 4.055, year: 2016

Geometrical and wave-optical effects on the performance of a bent-crystal dispersive X-ray spectrometer

International Nuclear Information System (INIS)

Sutter, J.P.; Amboage, M.; Hayama, S.; Diaz-Moreno, S.

2010-01-01

The X-ray focusing properties of a bent single crystal diffracting in Bragg geometry are discussed. First, it is assumed that a polychromatic point source is focused to a point image. The elliptical arc that the crystal must trace and the aberrations caused by bending the crystal cylindrically are derived from the ray paths. For a source of finite size, the magnification is found to vary over the crystal's length, so that rays of different wavelength produce images of different size. More realistic treatments of penetration and diffraction are performed with spherical monochromatic incident waves, using Takagi-Taupin calculations to create the diffracted wave and the Fresnel integral to trace the diffracted wave's evolution. Such 'wave-optical' calculations on a symmetric Si (1 1 1) crystal with 7 keV X-rays predict beam sizes different from those found in ray traces. Optimal sample and detector placement therefore requires wave effects to be considered.

Source assemblage types for cratonic diamonds from X-ray synchrotron diffraction

Science.gov (United States)

Nestola, F.; Alvaro, M.; Casati, M. N.; Wilhelm, H.; Kleppe, A. K.; Jephcoat, A. P.; Domeneghetti, M. C.; Harris, J. W.

2016-11-01

Three single crystals of clinopyroxene trapped within three different gem-quality diamonds from the Udachnaya kimberlite (Siberia, Russia) were analysed in situ by single-crystal synchrotron X-ray diffraction in order to obtain information on their chemical composition and infer source assemblage type. A non-destructive approach was used with high-energy (≈ 60 keV; λ ≈ 0.206 Å) at I15, the extreme-conditions beamline at Diamond Light Source. A dedicated protocol was used to center the mineral inclusions located deep inside the diamonds in the X-ray beam. Our results reveal that two of the inclusions can be associated with peridotitic paragenesis whereas the third is eclogitic. This study also demonstrates that this non-destructive experimental approach is extremely efficient in evaluating the origin of minerals trapped in their diamond hosts.

Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

Energy Technology Data Exchange (ETDEWEB)

Abramchik, Yu. A. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Timofeev, V. I., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation); Muravieva, T. I.; Sinitsyna, E. V.; Esipov, R. S., E-mail: esipov@mx.ibch.ru [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation)

2017-01-15

Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus (T. th HB27) has high thermal stability and shows maximum activity at 75°Ð¡, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.

Escherichia coli tRNAArg acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis

International Nuclear Information System (INIS)

Eichert, André; Schreiber, Angela; Fürste, Jens P.; Perbandt, Markus; Betzel, Christian; Erdmann, Volker A.; Förster, Charlotte

2009-01-01

Various E. coli tRNA Arg acceptor-stem microhelix isoacceptors have been crystallized and investigated by high-resolution X-ray diffraction analysis. The aminoacylation of tRNA is a crucial step in cellular protein biosynthesis. Recognition of the cognate tRNA by the correct aminoacyl-tRNA synthetase is ensured by tRNA identity elements. In tRNA Arg , the identity elements consist of the anticodon, parts of the D-loop and the discriminator base. The minor groove of the aminoacyl stem interacts with the arginyl-tRNA synthetase. As a consequence of the redundancy of the genetic code, six tRNA Arg isoacceptors exist. In the present work, three different Escherichia coli tRNA Arg acceptor-stem helices were crystallized. Two of them, the tRNA Arg microhelices RR-1660 and RR-1662, were examined by X-ray diffraction analysis and diffracted to 1.7 and 1.8 Å resolution, respectively. The tRNA Arg RR-1660 helix crystallized in space group P1, with unit-cell parameters a = 26.28, b = 28.92, c = 29.00 Å, α = 105.74, β = 99.01, γ = 97.44°, whereas the tRNA Arg RR-1662 helix crystallized in space group C2, with unit-cell parameters a = 33.18, b = 46.16, c = 26.04 Å, β = 101.50°

A more general expression for the average X-ray diffraction intensity of crystals with an incommensurate one-dimensional modulation

International Nuclear Information System (INIS)

Lam, E.J.W.; Beurskens, P.T.; Smaalen, S. van

1994-01-01

Statistical methods are used to derive an expression for the average X-ray diffraction intensity, as a function of (sinθ)/λ, of crystals with an incommensurate one-dimensional modulation. Displacive and density modulations are considered, as well as a combination of these two. The atomic modulation functions are given by truncated Fourier series that may contain higher-order harmonics. The resulting expression for the average X-ray diffraction intensity is valid for main reflections and low-order satellite reflections. The modulation of individual atoms is taken into account by the introduction of overall modulation amplitudes. The accuracy of this expression for the average X-ray diffraction intensity is illustrated by comparison with model structures. A definition is presented for normalized structure factors of crystals with an incommensurate one-dimensional modulation that can be used in direct-methods procedures for solving the phase problem in X-ray crystallography. A numerical fitting procedure is described that can extract a scale factor, an overall temperature parameter and overall modulation amplitudes from experimental reflection intensities. (orig.)

Crystallization and X-ray diffraction studies of arginine kinase from the white Pacific shrimp Litopenaeus vannamei

International Nuclear Information System (INIS)

Lopez-Zavala, Alonso A.; Sotelo-Mundo, Rogerio R.; Garcia-Orozco, Karina D.; Isac-Martinez, Felipe; Brieba, Luis G.; Rudiño-Piñera, Enrique

2012-01-01

The crystallization and preliminary X-ray diffraction analysis at 1.25 Å resolution of free-ligand arginine kinase from the Pacific whiteleg shrimp Litopenaeus vannamei are reported. Crystals belong to space group P2 1 2 1 2 1 , phases were determined by molecular replacement and refinement was performed with Phenix. Crystals of an unligated monomeric arginine kinase from the Pacific whiteleg shrimp Litopenaeus vannamei (LvAK) were successfully obtained using the microbatch method. Crystallization conditions and preliminary X-ray diffraction analysis to 1.25 Å resolution are reported. Data were collected at 100 K on NSLS beamline X6A. The crystals belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 56.5, b = 70.2, c = 81.7 Å. One monomer per asymmetric unit was found, with a Matthews coefficient (V M ) of 2.05 Å 3 Da −1 and 40% solvent content. Initial phases were determined by molecular replacement using a homology model of LvAK as the search model. Refinement was performed with PHENIX, with final R work and R free values of 0.15 and 0.19, respectively. Biological analysis of the structure is currently in progress

Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

International Nuclear Information System (INIS)

Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima; Guimaraes, Luciana; Vieira Filho, Sidney A.

2012-01-01

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Guimaraes, Luciana [Universidade Federal de Sao Joao Del-Rei (UFSJ), MG (Brazil). Dept. de Ciencias Naturais; Vieira Filho, Sidney A., E-mail: bibo@ef.ufop.br [Universidade Federal de Ouro Preto (UFOP), MG (Brazil). Dept. de Farmacia

2012-07-01

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

Science.gov (United States)

Vasilieva, A. V.; Grigoryeva, N. A.; Mistonov, A. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Lukashin, A. V.; Tretyakov, Yu D.; Petukhov, A. V.; Byelov, D.; Chernyshov, D.; Okorokov, A. I.; Bouwman, W. G.; Grigoriev, S. V.

2010-10-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a0 = 650 ± 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length Ltran is 2.4 ± 0.1 μm, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length Llong is 3.4 ± 0.2 μm, and the structure mosaic is of order of 10°.

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

International Nuclear Information System (INIS)

Vasilieva, A V; Okorokov, A I; Grigoriev, S V; Grigoryeva, N A; Mistonov, A A; Sapoletova, N A; Napolskii, K S; Eliseev, A A; Lukashin, A V; Tretyakov, Yu D; Petukhov, A V; Byelov, D; Chernyshov, D; Bouwman, W G

2010-01-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a 0 = 650 ± 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length L tran is 2.4 ± 0.1 μm, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length L long is 3.4 ± 0.2 μm, and the structure mosaic is of order of 10 0 .

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

Energy Technology Data Exchange (ETDEWEB)

Vasilieva, A V; Okorokov, A I; Grigoriev, S V [Petersburg Nuclear Physics Institute, Gatchina, 188350, St. Petersburg (Russian Federation); Grigoryeva, N A; Mistonov, A A [Department of Physics, St. Petersburg State University, 198504, St. Petersburg (Russian Federation); Sapoletova, N A; Napolskii, K S; Eliseev, A A; Lukashin, A V; Tretyakov, Yu D [Department of Materials Science, Moscow State University, 119899, Moscow (Russian Federation); Petukhov, A V; Byelov, D [Debye Institute, Utrecht University, 3584 CH Utrecht (Netherlands); Chernyshov, D [SNBL European Synchrotron Radiation Facility (ESRF), 38043 Grenoble (France); Bouwman, W G, E-mail: vasilieva@lns.pnpi.spb.r [Delft Technical University, 2629 JB Delft (Netherlands)

2010-10-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a{sub 0} = 650 {+-} 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length L{sub tran} is 2.4 {+-} 0.1 {mu}m, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length L{sub long} is 3.4 {+-} 0.2 {mu}m, and the structure mosaic is of order of 10{sup 0}.

Crystallization and preliminary X-ray diffraction analysis of the fructofuranosidase from Schwanniomyces occidentalis

International Nuclear Information System (INIS)

Polo, Aitana; Álvaro-Benito, Miguel; Fernández-Lobato, María; Sanz-Aparicio, Julia

2009-01-01

The invertase from Schwanniomyces occidentalis has been expressed in Saccharomyces cerevisiae, purified and crystallized. The wild-type enzyme was also purified and crystallized and diffraction data were collected to 2.9 Å resolution. Schwanniomyces occidentalis invertase is an extracellular enzyme that releases β-fructose from the nonreducing termini of various β-d-fructofuranoside substrates. Its ability to produce 6-kestose by transglycosylation makes this enzyme an interesting research target for applications in industrial biotechnology. The enzyme has been expressed in Saccharomyces cerevisiae. Recombinant and wild-type forms, which showed different glycosylation patterns, were crystallized by vapour-diffusion methods. Although crystallization trials were conducted on both forms of the protein, crystals suitable for X-ray crystallographic analyses were only obtained from the wild-type enzyme. The crystals belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 105.78, b = 119.49, c = 137.68 Å. A diffraction data set was collected using a synchrotron source. Self-rotation function and sedimentation-velocity experiments suggested that the enzyme was dimeric with twofold symmetry

Self-standing quasi-mosaic crystals for focusing hard X-rays

International Nuclear Information System (INIS)

Camattari, Riccardo; Guidi, Vincenzo; Bellucci, Valerio; Neri, Ilaria; Frontera, Filippo; Jentschel, Michael

2013-01-01

A quasi mosaic bent crystal for high-resolution diffraction of X and γ rays has been realized. A net curvature was imprinted to the crystal thanks to a series of superficial grooves to keep the curvature without external devices. The crystal highlights very high diffraction efficiency due to quasi mosaic curvature. Quasi mosaic crystals of this kind are proposed for the realization of a high-resolution focusing Laue lens for hard X-rays.

X-ray diffraction measurements to determine longitudinal and transverse lattice deformation in shocked LiF

International Nuclear Information System (INIS)

Rigg, P.A.; Gupta, Y.M.

2000-01-01

Experimental methods using both single and multiple x-ray diffraction were developed to determine real time, lattice deformation in directions parallel and perpendicular to shock wave propagation in single crystals subjected to plate impact loading. Initial experiments used single diffraction to monitor the interplanar spacing change, parallel to the shock propagation direction, in LiF crystals shocked along the [111] and [100] directions. These measurements, in combination with the macroscopic volume compression, were used to determine the state of compression of the unit cell. Subsequent development of a multiple diffraction technique permitted simultaneous determination of both the longitudinal and transverse lattice deformations. The present results showed that shock compression, below 4 GPa, along the [111] orientation--which results in macroscopic elastic deformation - produced one-dimensional unit cell compression. In contrast, shock compression along the [100] orientation - which results in macroscopic elastic-plastic deformation--produced isotropic unit cell compression. The implications of the present results and the ability to make quantitative x-ray diffraction measurements under shock loading are discussed

Nanosecond X-ray detector based on high resistivity ZnO single crystal semiconductor

Energy Technology Data Exchange (ETDEWEB)

Zhao, Xiaolong; He, Yongning, E-mail: yongning@mail.xjtu.edu.cn; Peng, Wenbo; Huang, Zhiyong; Qi, Xiaomeng; Pan, Zijian; Zhang, Wenting [School of Electronic and Information Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Chen, Liang; Liu, Jinliang; Zhang, Zhongbing; Ouyang, Xiaoping [Radiation Detection Research Center, Northwest Institute of Nuclear Technology, Xi' an 710024 (China)

2016-04-25

The pulse radiation detectors are sorely needed in the fields of nuclear reaction monitoring, material analysis, astronomy study, spacecraft navigation, and space communication. In this work, we demonstrate a nanosecond X-ray detector based on ZnO single crystal semiconductor, which emerges as a promising compound-semiconductor radiation detection material for its high radiation tolerance and advanced large-size bulk crystal growth technique. The resistivity of the ZnO single crystal is as high as 10{sup 13} Ω cm due to the compensation of the donor defects (V{sub O}) and acceptor defects (V{sub Zn} and O{sub i}) after high temperature annealing in oxygen. The photoconductive X-ray detector was fabricated using the high resistivity ZnO single crystal. The rise time and fall time of the detector to a 10 ps pulse electron beam are 0.8 ns and 3.3 ns, respectively, indicating great potential for ultrafast X-ray detection applications.

Intergrown new zeolite beta polymorphs with interconnected 12-ring channels solved by combining electron crystallography and single-crystal X-ray diffraction

KAUST Repository

Yu, Zhengbao

2012-10-09

Two new polymorphs of zeolite beta, denoted as SU-78A and SU-78B, were synthesized by employing dicyclohexylammonium hydroxides as organic structure-directing agents. The structure was solved by combining transmission electron microscopy and single-crystal X-ray diffraction. SU-78 is an intergrowth of SU-78A and SU-78B and contains interconnected 12-ring channels in three directions. The two polymorphs are built from the same building layer, similar to that for the zeolite beta family. The layer stacking in SU-78, however, is different from those in zeolite beta polymorph A, B, and C, showing new zeolite framework topologies. SU-78 is thermally stable up to 600 °C. © 2012 American Chemical Society.

Observation of parametric X-ray radiation in an anomalous diffraction region

Energy Technology Data Exchange (ETDEWEB)

Alexeyev, V.I., E-mail: vial@x4u.lebedev.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation); Eliseyev, A.N., E-mail: elisseev@pluton.lpi.troitsk.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation); Irribarra, E., E-mail: esteban.irribarra@epn.edu.ec [Escuela Politécnica Nacional, Ladrón de Guevara E11-253, Quito (Ecuador); Kishin, I.A., E-mail: ivan.kishin@mail.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation); Kubankin, A.S., E-mail: kubankin@bsu.edu.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation); Nazhmudinov, R.M., E-mail: fizeg@bk.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation)

2016-08-19

A new possibility to expand the energy region of diffraction processes based on the interaction of relativistic charged particles with crystalline structures is presented. Diffracted photons related to parametric X-ray radiation produced by relativistic electrons are detected below the low energy threshold for the X-ray diffraction mechanism in crystalline structures for the first time. The measurements were performed during the interaction of 7 MeV electrons with a textured polycrystalline tungsten foil and a highly oriented pyrolytic graphite crystal. The experiment results are in good agreement with a developed model based on the PXR kinematical theory. The developed experimental approach can be applied to separate the contributions of real and virtual photons to the total diffracted radiation generated during the interaction of relativistic charged particles with crystalline targets. - Highlights: • Parametric X-ray radiation below the low energy threshold for diffraction of free X-rays. • Experimental separation of the contributions from different radiation mechanisms. • PXR from relativistic electrons in mosaic crystals and textured polycrystlas.

Single crystal growth and structure refinements of CsMxTe2-xO6 (M = Al, Ga, Ge, In) pyrochlores

International Nuclear Information System (INIS)

Siritanon, Theeranun; Sleight, A.W.; Subramanian, M.A.

2011-01-01

Graphical abstract: Single crystals of CsM x Te 2-x O 6 pyrochlores with M = Al, Ga, Ge, and In have been grown and structure refinements indicate deviations from ideal stoichiometry presumably related to mixed valency of tellurium. Highlights: → Single crystals of CsM x Te 2-x O 6 pyrochlores with M = Al, Ga, Ge, and In have been grown. → Structure refinements from single crystal X-ray diffraction data confirm e structure. → Deviations from ideal stoichiometry suggest mixed valency of tellurium and hence conductivity. -- Abstract: Single crystals of CsM x Te 2-x O 6 pyrochlores with M = Al, Ga, Ge, and In have been grown from a TeO 2 flux. Structure refinements from single crystal X-ray diffraction data are reported. These results are used to discuss deviations from ideal stoichiometry that result in electronic conductivity presumably related to mixed valency of tellurium.

X-ray diffraction study of thermally and stress-induced phase transformations in single crystalline Ni-Mn-Ga alloys

International Nuclear Information System (INIS)

Martynov, V.V.

1995-01-01

Using in-situ single crystal X-ray diffraction methods, thermally- and stress-induced crystal structure evolution was investigated in two Ni-Mn-Ga Heusler-type alloys. For the 51at.%Ni-24at.%Mn-25at.%Ga alloy it was found that application of external stress in a temperature range ∼20 C above the M s at first causes intensity changes of X-ray diffuse scattering peaks in β-phase. Further stressing results in stress-induced phase transformations and under the appropriate conditions three successive martensitic transformations (one is parent-to-martensite and two are martensite-to-martensite transformations) can be stress induced. Of these only the parent-to-martensite transformation can be thermally-induced. Two successive structural transformations (thermally-induced parent-to-martensite and stress-induced martensite-to-martensite transformations) were found in 52at.%Ni-25at.%Mn-23at.%Ga alloy. Crystal structure, lattice parameters, type of modulation, and the length of modulation period for all martensites were identified. (orig.)

Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein

International Nuclear Information System (INIS)

Liu, Yueyong; Xu, Yanhui; Zhu, Jieqing; Qiu, Bingsheng; Rao, Zihe; Gao, George F.; Tien, Po

2005-01-01

Single crystals of the central structure domains from mumps virus F protein have been obtained by the hanging-drop vapour-diffusion method. A diffraction data set has been collected to 2.2 Å resolution. Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in the mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 Å resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 Å, β = 98.4°. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion

Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design

International Nuclear Information System (INIS)

MacElrevey, Celeste; Wedekind, Joseph E.

2005-01-01

Well diffracting decamer crystals of the hepatitis delta virus RNA-editing site were prepared, but exhibited merohedral twinning and base averaging owing to duplex symmetry. A longer asymmetric construct that includes additional flanking RNA sequences has been crystallized that does not appear to exhibit these defects. RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ‘structure-based’ readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 Å resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 × 1 internal loops yielded crystals in the primitive tetragonal space group P4 1 2 1 2 or P4 3 2 1 2. X-ray diffraction data were collected to 2.8 Å resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 Å. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported

Sensitivity of triple-crystal X-ray diffractometers to microdefects in silicon

International Nuclear Information System (INIS)

Molodkin, V.B.; Olikhovskii, S.I.; Len, E.G.; Kislovskii, E.N.; Kladko, V.P.; Reshetnyk, O.V.; Vladimirova, T.P.; Sheludchenko, B.V.

2009-01-01

The dynamical theory, which describes both diffraction profiles and reciprocal space maps measured from imperfect crystals with account for instrumental factors of triple-crystal diffractometer (TCD), has been developed for adequate quantitative characterization of microdefects. Analytical expressions for coherent and diffuse scattering (DS) intensities measured by TCD in the Bragg diffraction geometry have been derived by using the generalized statistical dynamical theory of X-ray scattering in real single crystals with randomly distributed defects. The DS intensity distributions from single crystals containing clusters and dislocation loops have been described by explicit analytical expressions. Particularly, these expressions take into account anisotropy of displacement fields around defects with discrete orientations. Characteristics of microdefect structures in silicon single crystals grown by Czochralsky- and float-zone methods have been determined by analyzing the measured TCD profiles and reciprocal space maps. The sensitivities of reciprocal space maps and diffraction profiles to defect characteristics have been compared. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

An X-ray wave theory for heavily distorted crystals. 1

International Nuclear Information System (INIS)

Ohkawa, T.; Hashimoto, H.

1985-01-01

An X-ray diffraction theory is developed of monochromatic waves having spherical wave front, which is applicable to an interpretation of divergent X-ray diffraction images of crystals containing arbitral types of strain field. The theory is divided into two parts. In part I, Takagi's theory is expanded by introducing amplitude and phase correction functions and a new improved representation for the X-ray diffraction theory is given. In part II dispersion surfaces in heavily distorted crystals are discussed, and in the discussion the resonance shift functions are introduced. These formulations can lead to a complete understanding of the extinction phenomena. (author)

X-ray Microprobe for Fluorescence and Diffraction Analysis

International Nuclear Information System (INIS)

Ice, G.E.

2005-01-01

X-ray diffraction (see unit 1.1) and x-ray excited fluorescence analysis are powerful techniques for the nondestructive measurement of crystal structure and chemical composition. X-ray fluorescence analysis is inherently nondestructive with orders of magnitude lower power deposited for the same detectable limit as with fluorescence excited by charged particle probes (Sparks, 1980). X-ray diffraction analysis is sensitive to crystal structure with orders-of-magnitude greater sensitivity to crystallographic strain than electron probes (Rebonato, et al. 1989). When a small-area x-ray microbeam is used as the probe, chemical composition (Z>14), crystal structure, crystalline texture, and crystalline strain distributions can be determined. These distributions can be studied both at the surface of the sample and deep within the sample (Fig. 1). Current state-of-the-art can achieve an ∼1 mm-D x-ray microprobe and an ∼0.1 mm-D x-ray microprobe has been demonstrated (Bilderback, et al., 1994). Despite their great chemical and crystallographic sensitivities, x-ray microprobe techniques have until recently been restricted by inefficient x-ray focusing optics and weak x-ray sources; x-ray microbeam analysis was largely superseded by electron techniques in the 50's. However, interest in x-ray microprobe techniques has now been revived (Howells, et al., 1983; Ice and Sparks, 1984; Chevallier, et al., 1997; Riekel 1992; Thompson, el al., 1992; and Making and Using... 1997) by the development of efficient x-ray focusing optics and ultra-high intensity synchrotron x-ray sources (Buras and Tazzari, 1984; Shenoy, et al., 1988). These advances have increased the achievable microbeam flux by more than 11 orders of magnitude (Fig. 2) (Ice, 1997); the flux in a tunable 1 mm-D beam on a 'so called' 3rd-generation synchrotron source such as the APS can exceed the flux in a fixed-energy mm2 beam on a conventional source. These advances make x-ray microfluorescence and x-ray

Single crystal X-ray structure of the artists' pigment zinc yellow

Science.gov (United States)

Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold; Sanyova, Jana; Bendix, Jesper

2017-08-01

The artists' pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hitherto been unknown. In this work, zinc yellow was synthesised by precipitation from an aqueous solution of zinc nitrate and potassium chromate under both neutral and basic conditions, and the products were compared with the pigment used in industrial paints. Analyses by Raman microscopy (MRS), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and powder X-ray diffraction (PXRD), showed that the synthesised products and the industrial pigment were identical. Single-crystal X-ray crystallography determined the structure of zinc yellow as KZn2(CrO4)2(H2O)(OH) or as KZn2(CrO4)2(H3O2) emphasizing the μ-H3O2- moiety. Notably, the zinc yellow is isostructural to the recently structurally characterized cadmium analog and both belong to the natrochalcite structure type.

X-ray diffraction diagnostic design for the National Ignition Facility

Science.gov (United States)

Ahmed, Maryum F.; House, Allen; Smith, R. F.; Ayers, Jay; Lamb, Zachary S.; Swift, David W.

2013-09-01

This paper describes the design considerations for Target Diffraction In-Situ (TARDIS), an x-ray diffraction diagnostic at the National Ignition Facility. A crystal sample is ramp-compressed to peak pressures between 10 and 30 Mbar and, during a pressure hold period, is probed with quasi-monochromatic x-rays emanating from a backlighter source foil. The crystal spectrography diffraction lines are recorded onto image plates. The crystal sample, filter, and image plates are packaged into one assembly, allowing for accurate and repeatable target to image plate registration. Unconverted laser light impinges upon the device, generating debris, the effects of which have been mitigated. Dimpled blast shields, high strength steel alloy, and high-z tungsten are used to shield and protect the image plates. A tapered opening was designed to provide adequate thickness of shielding materials without blocking the drive beams or x-ray source from reaching the crystal target. The high strength steel unit serves as a mount for the crystal target and x-ray source foil. A tungsten body contains the imaging components. Inside this sub-assembly, there are three image plates: a 160 degree field of view curved plate directly opposite the target opening and two flat plates for the top and bottom. A polycarbonate frame, coated with the appropriate filter material and embedded with registration features for image plate location, is inserted into the diagnostic body. The target assembly is metrologized and then the diagnostic assembly is attached.

X-ray diffraction analysis of LiCu2O2 crystals with additives of silver atoms

International Nuclear Information System (INIS)

Sirotinkin, V. P.; Bush, A. A.; Kamentsev, K. E.; Dau, H. S.; Yakovlev, K. A.; Tishchenko, E. A.

2015-01-01

Silver-containing LiCu 2 O 2 crystals up to 4 × 8 × 8 mm in size were grown by the crystallization of 80(1-x)CuO · 20 x AgNO 3 · 20Li 2 CO 3 (0 ≤ x ≤ 0.5) mixture melt. According to the X-ray spectral and Rietveld X-ray diffraction data, the maximum amount of silver incorporated in the LiCu 2 O 2 structure is about 4 at % relative to the copper content. It was established that silver atoms occupy statistically crystallographic positions of lithium atoms. The incorporation of silver atoms is accompanied by a noticeable increase in parameter c of the LiCu 2 O 2 rhombic unit cell, a slight increase in parameter a, and a slight decrease in parameter b

Crystallization and preliminary X-ray diffraction analysis of a tRNASer acceptor-stem microhelix

International Nuclear Information System (INIS)

Förster, Charlotte; Krauss, Norbert; Brauer, Arnd B. E.; Szkaradkiewicz, Karol; Brode, Svenja; Hennig, Klaus; Fürste, Jens P.; Perbandt, Markus; Betzel, Christian; Erdmann, Volker A.

2006-01-01

In order to investigate tRNA identity elements, an elongator tRNA Ser acceptor-stem helix was crystallized and a data set was collected to 1.8 Å resolution aiming at a comparison with the corresponding region in suppressor tRNA Sec . In order to understand elongator tRNA Ser and suppressor tRNA Sec identity elements, the respective acceptor-stem helices have been synthesized and crystallized in order to analyse and compare their structures in detail at high resolution. The synthesis, crystallization and preliminary X-ray diffraction results for a seven-base-pair tRNA Ser acceptor-stem helix are presented here. Diffraction data were collected to 1.8 Å, applying synchrotron radiation and cryogenic cooling. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 36.14, b = 38.96, c = 30.81 Å, β = 110.69°

Crystal structure analysis of LaMnO_3 with x-ray diffraction technique using the Rietveld method

International Nuclear Information System (INIS)

Engkir Sukirman; Wisnu Ari Adi; Yustinus Purwamargapratala

2010-01-01

Crystal structure analysis of LaMnO_3 using the Rietveld method has been carried out. The LaMnO_3 sample was synthesized with high energy mechanical milling from the raw materials of La_2O_3 and MnO_2 with the appropriate mol ratio. Milling were performed for 10 hours, pelletized and hereinafter sintered at 1350 °C for 6 hours. The sample characterizations covered the crystal structure and electric-magnetic properties of the materials by X-ray diffraction technique using the Rietveld method and the four point probe, respectively. The Rietveld refinement results based on the X-rays diffraction data indicate that the sample of LaMnO_3 is single phase with the crystal system: orthorhombic, the space group: Pnma No. 62 and the lattice parameters: a = 55.4405(9) Å; b = 7.717(1) Å dan c = 5.537(1) Å. The material owns Magnetic Resonance (MR) respond of 7 %, the mean value of crystallite size, D = 17 nm and lattice strain, e = - 0.5 %. So, the material go through a compressive strain, and according to the Nanda's strain model, it becomes a type G antiferromagnetic insulator. Because the insulator properties of the material does not change although being hit by the external magnetic field, hence the MR respond is only caused by the order of electron spin. Therefore at room temperature, LaMnO_3_._0 just exhibits a small MR respond. (author)

Crystallization and preliminary X-ray analysis of isomaltase from Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Yamamoto, Keizo; Miyake, Hideo; Kusunoki, Masami; Osaki, Shigeyoshi

2008-01-01

The crystallization and preliminary X-ray analysis of isomaltase is reported. Isomaltase from Saccharomyces cerevisiae is an oligo-1,6-glucosidase that preferentially hydrolyzes isomaltose, with little activity towards isomaltotriose or longer oligosaccharides. An amino-acid sequence analysis of the isomaltase revealed that it belongs to glucoside hydrolase family 13. Recombinant isomaltase was purified and crystallized by the hanging-drop vapour-diffusion method with PEG 3350 as the precipitant. The crystals belonged to space group C2, with unit-cell parameters a = 95.67, b = 115.42, c = 61.77 Å, β = 91.17°. X-ray diffraction data were collected to 1.35 Å resolution from a single crystal on a synchrotron-radiation source

A spectrometer for X-ray energy-dispersive diffraction using synchrotron radiation

International Nuclear Information System (INIS)

Buras, B.; Gerward, L.; Staun Olsen, J.; Steenstrup, S.

1981-10-01

The paper describes a white-beam X-ray energy dispersive diffractometer using the synchroton radiation from the DORIS ESR. The following features of the instrument are discussed: Horizontal or vertical scattering plane, collimators, sample environment, remote control of gonimeter, data acquisition, energy-sensitive detectors using small-area and large-area detector crystals, modes of operation, powder and single crystal diffraction. An example is given from a high-pressure study of YbH 2 using a diamond anvil cell. (orig./HP)

X-ray crystallography

Science.gov (United States)

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.

Nano structured materials studied by coherent X-ray diffraction

International Nuclear Information System (INIS)

Gulden, Johannes

2013-03-01

Structure determination with X-rays in crystallography is a rapidly evolving field. Crystallographic methods for structure determination are based on the assumptions about the crystallinity of the sample. It is vital to understand the structure of possible defects in the crystal, because they can influence the structure determination. All conventional methods to characterize defects require a modelling through simulated data. No direct methods exist to image the core of defects in crystals. Here a new method is proposed, which will enable to visualize the individual scatterers around and at defects in crystals. The method is based on coherent X-ray scattering. X-rays are perfectly suited since they can penetrate thick samples and buried structures can be investigated Recent developments increased the coherent flux of X-Ray sources such as synchrotrons by orders of magnitude. As a result, the use of the coherent properties of X-rays is emerging as a new aspect of X-ray science. New upcoming and operating X-ray laser sources will accelerate this trend. One new method which has the capacity to recover structural information from the coherently scattered photons is Coherent X-ray Diffraction Imaging (CXDI). The main focus of this thesis is the investigation of the structure and the dynamics of colloidal crystals. Colloidal crystals can be used as a model for atomic crystals in order to understand the growth and defect structure. Despite the large interest in these structures, many details are still unknown.Therefore, it is vital to develop new approaches to measure the core of defects in colloidal crystals. After an introduction into the basics of the field of coherent X-ray scattering, this thesis introduces a novel method, Small Angle Bragg Coherent Diffractive Imaging, (SAB-CDI). This new measurement technique which besides the relevance to colloidal crystals can be applied to a large variety of nano structured materials. To verify the experimental possibilities the

Nano structured materials studied by coherent X-ray diffraction

Energy Technology Data Exchange (ETDEWEB)

Gulden, Johannes

2013-03-15

Structure determination with X-rays in crystallography is a rapidly evolving field. Crystallographic methods for structure determination are based on the assumptions about the crystallinity of the sample. It is vital to understand the structure of possible defects in the crystal, because they can influence the structure determination. All conventional methods to characterize defects require a modelling through simulated data. No direct methods exist to image the core of defects in crystals. Here a new method is proposed, which will enable to visualize the individual scatterers around and at defects in crystals. The method is based on coherent X-ray scattering. X-rays are perfectly suited since they can penetrate thick samples and buried structures can be investigated Recent developments increased the coherent flux of X-Ray sources such as synchrotrons by orders of magnitude. As a result, the use of the coherent properties of X-rays is emerging as a new aspect of X-ray science. New upcoming and operating X-ray laser sources will accelerate this trend. One new method which has the capacity to recover structural information from the coherently scattered photons is Coherent X-ray Diffraction Imaging (CXDI). The main focus of this thesis is the investigation of the structure and the dynamics of colloidal crystals. Colloidal crystals can be used as a model for atomic crystals in order to understand the growth and defect structure. Despite the large interest in these structures, many details are still unknown.Therefore, it is vital to develop new approaches to measure the core of defects in colloidal crystals. After an introduction into the basics of the field of coherent X-ray scattering, this thesis introduces a novel method, Small Angle Bragg Coherent Diffractive Imaging, (SAB-CDI). This new measurement technique which besides the relevance to colloidal crystals can be applied to a large variety of nano structured materials. To verify the experimental possibilities the

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

International Nuclear Information System (INIS)

Cheung, Eugene Y.; David, Sarah E.; Harris, Kenneth D.M.; Conway, Barbara R.; Timmins, Peter

2007-01-01

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H 2 NC(CH 3 ) 3- n (CH 2 OH) n , with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family (n=0, 1, 2), but significantly contrasting structural properties for the member with n=3. - Graphical abstract: Structural properties of a family of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine are discussed and rationalized

Controlled molecules for X-ray diffraction experiments at free-electron lasers

International Nuclear Information System (INIS)

Stern, Stephan

2013-12-01

X-ray diffractive imaging is at the very heart of materials science and has been utilized for decades to solve unknown molecular structures. Nowadays, it serves as the key method of structural biology to solve molecular structures of large biological molecules comprising several thousand or even millions of atoms. However, X-ray diffraction from isolated molecules is very weak. Therefore, the regular and periodic arrangement of a huge number of identical copies of a certain molecule of interest within a crystal lattice has been a necessary condition in order to exploit Bragg diffraction of X-rays. This results in a huge increase in scattered signal and a strongly improved signal-to-noise ratio compared to diffraction from non-crystalline samples. The major bottleneck of structural biology is that many of biologically interesting molecules refuse to form crystals of sufficient size to be used at synchrotron X-ray lightsources. However, novel X-ray free-electron lasers (XFELs), which became operational very recently, promise to address this issue. X-ray pulses provided by XFELs are many orders of magnitude more intense than X-ray pulses from a synchrotron source and at the same time as short as only several tens of femtoseconds. Combined with wavelengths in the nm-pm range, XFELs are well-suited to study ultrafast atomic and molecular dynamics. Additionally, the ultrashort pulses can be utilized to circumvent the damage threshold which set a limit to the incident intensity in X-ray diffraction experiments before. At XFELs, though eventually destroying the investigated sample, no significant sample deterioration happens on the ultrashort timescale of the XFEL pulse and the measured diffraction pattern is due to an (almost) unharmed sample. In the framework of this thesis, the approach of utilizing the highly intense XFEL pulses for X-ray diffraction of weakly-scattering non-crystalline samples was taken to the limit of small isolated molecules. X-ray diffraction was

Controlled molecules for X-ray diffraction experiments at free-electron lasers

Energy Technology Data Exchange (ETDEWEB)

Stern, Stephan

2013-12-15

X-ray diffractive imaging is at the very heart of materials science and has been utilized for decades to solve unknown molecular structures. Nowadays, it serves as the key method of structural biology to solve molecular structures of large biological molecules comprising several thousand or even millions of atoms. However, X-ray diffraction from isolated molecules is very weak. Therefore, the regular and periodic arrangement of a huge number of identical copies of a certain molecule of interest within a crystal lattice has been a necessary condition in order to exploit Bragg diffraction of X-rays. This results in a huge increase in scattered signal and a strongly improved signal-to-noise ratio compared to diffraction from non-crystalline samples. The major bottleneck of structural biology is that many of biologically interesting molecules refuse to form crystals of sufficient size to be used at synchrotron X-ray lightsources. However, novel X-ray free-electron lasers (XFELs), which became operational very recently, promise to address this issue. X-ray pulses provided by XFELs are many orders of magnitude more intense than X-ray pulses from a synchrotron source and at the same time as short as only several tens of femtoseconds. Combined with wavelengths in the nm-pm range, XFELs are well-suited to study ultrafast atomic and molecular dynamics. Additionally, the ultrashort pulses can be utilized to circumvent the damage threshold which set a limit to the incident intensity in X-ray diffraction experiments before. At XFELs, though eventually destroying the investigated sample, no significant sample deterioration happens on the ultrashort timescale of the XFEL pulse and the measured diffraction pattern is due to an (almost) unharmed sample. In the framework of this thesis, the approach of utilizing the highly intense XFEL pulses for X-ray diffraction of weakly-scattering non-crystalline samples was taken to the limit of small isolated molecules. X-ray diffraction was

Single-particle coherent diffractive imaging with a soft x-ray free electron laser: towards soot aerosol morphology

Science.gov (United States)

Bogan, Michael J.; Starodub, Dmitri; Hampton, Christina Y.; Sierra, Raymond G.

2010-10-01

The first of its kind, the Free electron LASer facility in Hamburg, FLASH, produces soft x-ray pulses with unprecedented properties (10 fs, 6.8-47 nm, 1012 photons per pulse, 20 µm diameter). One of the seminal FLASH experiments is single-pulse coherent x-ray diffractive imaging (CXDI). CXDI utilizes the ultrafast and ultrabright pulses to overcome resolution limitations in x-ray microscopy imposed by x-ray-induced damage to the sample by 'diffracting before destroying' the sample on sub-picosecond timescales. For many lensless imaging algorithms used for CXDI it is convenient when the data satisfy an oversampling constraint that requires the sample to be an isolated object, i.e. an individual 'free-standing' portion of disordered matter delivered to the centre of the x-ray focus. By definition, this type of matter is an aerosol. This paper will describe the role of aerosol science methodologies used for the validation of the 'diffract before destroy' hypothesis and the execution of the first single-particle CXDI experiments being developed for biological imaging. FLASH CXDI now enables the highest resolution imaging of single micron-sized or smaller airborne particulate matter to date while preserving the native substrate-free state of the aerosol. Electron microscopy offers higher resolution for single-particle analysis but the aerosol must be captured on a substrate, potentially modifying the particle morphology. Thus, FLASH is poised to contribute significant advancements in our knowledge of aerosol morphology and dynamics. As an example, we simulate CXDI of combustion particle (soot) morphology and introduce the concept of extracting radius of gyration of fractal aggregates from single-pulse x-ray diffraction data. Future upgrades to FLASH will enable higher spatially and temporally resolved single-particle aerosol dynamics studies, filling a critical technological need in aerosol science and nanotechnology. Many of the methodologies described for FLASH will

Single-particle coherent diffractive imaging with a soft x-ray free electron laser: towards soot aerosol morphology

International Nuclear Information System (INIS)

Bogan, Michael J; Starodub, Dmitri; Hampton, Christina Y; Sierra, Raymond G

2010-01-01

The first of its kind, the Free electron LASer facility in Hamburg, FLASH, produces soft x-ray pulses with unprecedented properties (10 fs, 6.8-47 nm, 10 12 photons per pulse, 20 μm diameter). One of the seminal FLASH experiments is single-pulse coherent x-ray diffractive imaging (CXDI). CXDI utilizes the ultrafast and ultrabright pulses to overcome resolution limitations in x-ray microscopy imposed by x-ray-induced damage to the sample by 'diffracting before destroying' the sample on sub-picosecond timescales. For many lensless imaging algorithms used for CXDI it is convenient when the data satisfy an oversampling constraint that requires the sample to be an isolated object, i.e. an individual 'free-standing' portion of disordered matter delivered to the centre of the x-ray focus. By definition, this type of matter is an aerosol. This paper will describe the role of aerosol science methodologies used for the validation of the 'diffract before destroy' hypothesis and the execution of the first single-particle CXDI experiments being developed for biological imaging. FLASH CXDI now enables the highest resolution imaging of single micron-sized or smaller airborne particulate matter to date while preserving the native substrate-free state of the aerosol. Electron microscopy offers higher resolution for single-particle analysis but the aerosol must be captured on a substrate, potentially modifying the particle morphology. Thus, FLASH is poised to contribute significant advancements in our knowledge of aerosol morphology and dynamics. As an example, we simulate CXDI of combustion particle (soot) morphology and introduce the concept of extracting radius of gyration of fractal aggregates from single-pulse x-ray diffraction data. Future upgrades to FLASH will enable higher spatially and temporally resolved single-particle aerosol dynamics studies, filling a critical technological need in aerosol science and nanotechnology. Many of the methodologies described for FLASH will

Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I

International Nuclear Information System (INIS)

Enderle, Mathias; McCarthy, Andrew; Paithankar, Karthik Shivaji; Grininger, Martin

2015-01-01

Bacterial and fungal type I fatty-acid synthases (FAS I) are evolutionarily connected, as bacterial FAS I is considered to be the ancestor of fungal FAS I. In this work, the production, crystallization and X-ray diffraction data analysis of a bacterial FAS I are reported. While a deep understanding of the fungal and mammalian multi-enzyme type I fatty-acid synthases (FAS I) has been achieved in recent years, the bacterial FAS I family, which is narrowly distributed within the Actinomycetales genera Mycobacterium, Corynebacterium and Nocardia, is still poorly understood. This is of particular relevance for two reasons: (i) although homologous to fungal FAS I, cryo-electron microscopic studies have shown that bacterial FAS I has unique structural and functional properties, and (ii) M. tuberculosis FAS I is a drug target for the therapeutic treatment of tuberculosis (TB) and therefore is of extraordinary importance as a drug target. Crystals of FAS I from C. efficiens, a homologue of M. tuberculosis FAS I, were produced and diffracted X-rays to about 4.5 Å resolution

Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I

Energy Technology Data Exchange (ETDEWEB)

Enderle, Mathias [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany); McCarthy, Andrew [EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9 (France); Paithankar, Karthik Shivaji, E-mail: paithankar@em.uni-frankfurt.de [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Grininger, Martin, E-mail: paithankar@em.uni-frankfurt.de [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany)

2015-10-23

Bacterial and fungal type I fatty-acid synthases (FAS I) are evolutionarily connected, as bacterial FAS I is considered to be the ancestor of fungal FAS I. In this work, the production, crystallization and X-ray diffraction data analysis of a bacterial FAS I are reported. While a deep understanding of the fungal and mammalian multi-enzyme type I fatty-acid synthases (FAS I) has been achieved in recent years, the bacterial FAS I family, which is narrowly distributed within the Actinomycetales genera Mycobacterium, Corynebacterium and Nocardia, is still poorly understood. This is of particular relevance for two reasons: (i) although homologous to fungal FAS I, cryo-electron microscopic studies have shown that bacterial FAS I has unique structural and functional properties, and (ii) M. tuberculosis FAS I is a drug target for the therapeutic treatment of tuberculosis (TB) and therefore is of extraordinary importance as a drug target. Crystals of FAS I from C. efficiens, a homologue of M. tuberculosis FAS I, were produced and diffracted X-rays to about 4.5 Å resolution.

Dynamical theoretical model of the high-resolution double-crystal x-ray diffractometry of imperfect single crystals with microdefects

International Nuclear Information System (INIS)

Molodkin, V. B.; Olikhovskii, S. I.; Kislovskii, E. N.; Vladimirova, T. P.; Skakunova, E. S.; Seredenko, R. F.; Sheludchenko, B. V.

2008-01-01

The dynamical diffraction model has been developed for the quantitative description of rocking curves (RCs) measured in the Bragg diffraction geometry from single crystals containing homogeneously distributed microdefects of several types and with arbitrary sizes. The analytical expressions for coherent and diffuse RC components, which take self-consistently multiple-scattering effects into account and depend explicitly on microdefect characteristics (radius, concentration, strength, etc.), have been derived with taking into account the instrumental factors. The developed model has been applied to determine the characteristics of oxygen precipitates and dislocation loops in silicon crystals grown by Czochralsky and float-zone methods using RCs measured by the high-resolution double-crystal x-ray diffractometer. It has been shown, particularly, that completely dynamical consideration of Huang as well as Stockes-Wilson diffuse scattering (DS) in both diffuse RC component and coefficient of extinction of coherent RC component due to DS, together with taking asymmetry and thermal DS effects into account, provides the possibility to distinguish contributions into RC from defects of different types, which have equal or commensurable effective radii

Nd-doped Lu3Al5O12 single-crystal scintillator for X-ray imaging

International Nuclear Information System (INIS)

Sugiyama, Makoto; Fujimoto, Yutaka; Yanagida, Takayuki; Totsuka, Daisuke; Chani, Valery; Yokota, Yuui; Yoshikawa, Akira

2013-01-01

The optical and scintillation properties of Nd-doped Lu 3 Al 5 O 12 (Nd:LuAG) crystals grown by the Czochralski (Cz) method were examined under X-ray excitation. Their applicability for X-ray imaging was also inspected. The radioluminescence spectrum induced by X-rays showed a broad host emission and sharp Nd 3+ 4f–4f emission peaks in the UV to visible wavelengths. The light output current of the Nd:LuAG was 85% of that of a standard CdWO 4 X-ray scintillator. The afterglow value measured 20 ms after X-ray irradiation was 1.5%. An X-ray radiographic image was successfully obtained using the Nd:LuAG scintillator coupled with the charge coupled device (CCD) photodetector. -- Highlights: ► The Nd:LuAG single crystal was produced to perform X-ray imaging test. ► The sample exhibited the 85% light output current of the standard CdWO 4 . ► The afterglow intensity of the sample was very high compared with the CdWO 4 . ► The X-ray radiographic image was obtained from the Nd:LuAG single crystal

Crystallization and preliminary X-ray diffraction analysis of two extracytoplasmic solute receptors of the DctP family from Bordetella pertussis

International Nuclear Information System (INIS)

Rucktooa, Prakash; Huvent, Isabelle; Antoine, Rudy; Lecher, Sophie; Jacob-Dubuisson, Françoise; Villeret, Vincent; Bompard, Coralie

2006-01-01

Sample preparation, crystallization and preliminary X-ray analysis are reported for two B. pertussis extracytoplasmic solute receptors. DctP6 and DctP7 are two Bordetella pertussis proteins which belong to the extracytoplasmic solute receptors (ESR) superfamily. ESRs are involved in the transport of substrates from the periplasm to the cytosol of Gram-negative bacteria. DctP6 and DctP7 have been crystallized and diffraction data were collected using a synchrotron-radiation source. DctP6 crystallized in space group P4 1 2 1 2, with unit-cell parameters a = 108.39, b = 108.39, c = 63.09 Å, while selenomethionyl-derivatized DctP7 crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 64.87, b = 149.83, c = 170.65 Å. The three-dimensional structure of DctP7 will be determined by single-wavelength anomalous diffraction, while the DctP6 structure will be solved by molecular-replacement methods

Determination of crystal structures with large known fragments directly from measured X-ray powder diffraction intensities

International Nuclear Information System (INIS)

Rius, J.; Miravitlles, C.

1988-01-01

A strategy for the determination of crystal structures with large known fragments directly from measured X-ray powder diffraction intensities is presented. It is based on the automated full-symmetry Patterson search method described by Rius and Miravitlles where the Fourier coefficients of the observed Patterson function are modified to allow the use of powder diffraction intensity data. Its application to two structures, one with simulated and one with experimental data, is shown. (orig.)

Time and space domain separation of pulsed X-ray beams diffracted from vibrating crystals

Energy Technology Data Exchange (ETDEWEB)

Nosik, V. L., E-mail: v-nosik@yandex.ru, E-mail: nosik@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” (Russian Federation)

2016-11-15

It is known that a set of additional reflections (satellites) may arise on rocking curves in the case of X-ray diffraction in the Bragg geometry from crystals where high-frequency ultrasonic vibrations are excited. It is shown that, under certain conditions, the pulse wave fields of the satellites and main reflection may be intersected in space (playing the role of pump and probe beams) and in time (forming interference superlattices).

Intensity of diffracted X-rays from biomolecules with radiation damage caused by strong X-ray pulses

International Nuclear Information System (INIS)

Kai, Takeshi; Tokuhisa, Atsushi; Moribayashi, Kengo; Fukuda, Yuji; Kono, Hidetoshi; Go, Nobuhiro

2014-01-01

In order to realize the coherent X-ray diffractive imaging of single biomolecules, the diffraction intensities, per effective pixel of a single biomolecule with radiation damage, caused by irradiation using a strong coherent X-ray pulse, were examined. A parameter survey was carried out for various experimental conditions, using a developed simulation program that considers the effect of electric field ionization, which was slightly reported on in previous studies. The two simple relationships among the parameters were identified as follows: (1) the diffraction intensity of a biomolecule slightly increases with the incident X-ray energy; and that (2) the diffraction intensity is approximately proportional to the target radius, when the radius is longer than 400 Å, since the upper limit of the incident intensity for damage to the biomolecules marginally changes with respect to the target radius. (author)

Crystallization and X-ray diffraction analysis of an ‘all-locked’ nucleic acid duplex derived from a tRNASer microhelix

International Nuclear Information System (INIS)

Behling, Katja; Eichert, André; Fürste, Jens P.; Betzel, Christian; Erdmann, Volker A.; Förster, Charlotte

2009-01-01

A completely ‘all-locked’ nucleic acid duplex was designed from an E. coli tRNA Ser microhelix. The helix consists exclusively of LNA building blocks and was crystallized. The crystals diffracted to 1.9 Å resolution. Modified nucleic acids are of great interest with respect to their nuclease resistance and enhanced thermostability. In therapeutical and diagnostic applications, such molecules can substitute for labile natural nucleic acids that are targeted against particular diseases or applied in gene therapy. The so-called ‘locked nucleic acids’ contain modified sugar moieties such as 2′-O,4′-C-methylene-bridged β-d-ribofuranose and are known to be very stable nucleic acid derivatives. The structure of locked nucleic acids in single or multiple LNA-substituted natural nucleic acids and in LNA–DNA or LNA–RNA heteroduplexes has been well investigated, but the X-ray structure of an ‘all-locked’ nucleic acid double helix has not been described to date. Here, the crystallization and X-ray diffraction data analysis of an ‘all-locked’ nucleic acid helix, which was designed as an LNA originating from a tRNA Ser microhelix RNA structure, is presented. The crystals belonged to space group C2, with unit-cell parameters a = 77.91, b = 40.74, c = 30.06 Å, β = 91.02°. A high-resolution and a low-resolution data set were recorded, with the high-resolution data showing diffraction to 1.9 Å resolution. The crystals contained two double helices per asymmetric unit, with a Matthews coefficient of 2.48 Å 3 Da −1 and a solvent content of 66.49% for the merged data

Observation of sagittal X-ray diffraction by surface acoustic waves in Bragg geometry.

Science.gov (United States)

Vadilonga, Simone; Zizak, Ivo; Roshchupkin, Dmitry; Evgenii, Emelin; Petsiuk, Andrei; Leitenberger, Wolfram; Erko, Alexei

2017-04-01

X-ray Bragg diffraction in sagittal geometry on a Y-cut langasite crystal (La 3 Ga 5 SiO 14 ) modulated by Λ = 3 µm Rayleigh surface acoustic waves was studied at the BESSY II synchrotron radiation facility. Owing to the crystal lattice modulation by the surface acoustic wave diffraction, satellites appear. Their intensity and angular separation depend on the amplitude and wavelength of the ultrasonic superlattice. Experimental results are compared with the corresponding theoretical model that exploits the kinematical diffraction theory. This experiment shows that the propagation of the surface acoustic waves creates a dynamical diffraction grating on the crystal surface, and this can be used for space-time modulation of an X-ray beam.

Computer simulations of X-ray six-beam diffraction in a perfect silicon crystal. I

Czech Academy of Sciences Publication Activity Database

Kohn, V.G.; Khikhlukha, Danila

2016-01-01

Roč. 72, May (2016), s. 349-356 ISSN 2053-2733 R&D Projects: GA MŠk EF15_008/0000162; GA MŠk ED1.1.00/02.0061 Grant - others:ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162; ELI Beamlines(XE) CZ.1.05/1.1.00/02.0061 Institutional support: RVO:68378271 Keywords : X-ray diffraction * silicon crystal * six-beam diffraction * section topography * computer simulations Subject RIV: BL - Plasma and Gas Discharge Physics OBOR OECD: Fluids and plasma physics (including surface physics) Impact factor: 5.725, year: 2016

Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Trypanosoma brucei gambiense glycerol kinase

International Nuclear Information System (INIS)

Balogun, Emmanuel Oluwadare; Inaoka, Daniel Ken; Kido, Yasutoshi; Shiba, Tomoo; Nara, Takeshi; Aoki, Takashi; Honma, Teruki; Tanaka, Akiko; Inoue, Masayuki; Matsuoka, Shigeru; Michels, Paul A. M.; Harada, Shigeharu; Kita, Kiyoshi

2010-01-01

Glycerol kinase from human African trypanosomes has been purified and crystallized for X-ray structure analysis. In the bloodstream forms of human trypanosomes, glycerol kinase (GK; EC 2.7.1.30) is one of the nine glycosomally compartmentalized enzymes that are essential for energy metabolism. In this study, a recombinant Trypanosoma brucei gambiense GK (rTbgGK) with an N-terminal cleavable His 6 tag was overexpressed, purified to homogeneity and crystallized by the sitting-drop vapour-diffusion method using PEG 400 as a precipitant. A complete X-ray diffraction data set to 2.75 Å resolution indicated that the crystals belonged to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 63.84, b = 121.50, c = 154.59 Å. The presence of two rTbgGK molecules in the asymmetric unit gives a Matthews coefficient (V M ) of 2.5 Å 3 Da −1 , corresponding to 50% solvent content

Control of synchrotron x-ray diffraction by means of standing acoustic waves

International Nuclear Information System (INIS)

Zolotoyabko, E.; Quintana, J.P.

2004-01-01

Synchrotron x-ray diffraction measurements in quartz crystals of different thickness excited by standing acoustic waves were carried out at the Advanced Photon Source of Argonne National Laboratory. We demonstrated the ability to significantly modify the quartz rocking curves for 20-25 keV x rays by changing the shear wave parameters in the frequency range between 15 and 105 MHz. Dynamic deformation introduced into the crystal lattice by acoustic waves resulted in a remarkable broadening of the rocking curves. The broadening effect strongly depends on the strength of the ultrasound, which can be easily regulated by changing the acoustic amplitude or frequency near the resonance. The maximum rocking curve broadening reached 17 times, which corresponds to the wavelength band, Δλ/λ=4x10 -3 , when used as a monochromator or analyzer for 20-25 keV x rays. The initial rocking curve shape is restored by sweeping the acoustic frequency within a 50-100 kHz range near the resonance. The tunable broadening effect allows effective manipulation of x-ray intensities in time domain. Time-resolved x-ray diffraction measurements under a 19.6 MHz acoustic wave excitation were performed by synchronizing the acoustic wave and x-ray burst periodicity. We used the fact that twice per period the standing wave produces a zero net deformation across the crystal thickness. By introducing an oscillating delay to the acoustic excitation, we were able to effectively change the phase of the acoustic wave relative to the x-ray burst periodicity. The x-ray diffraction intensity was strongly affected by tuning the timing of the x-ray arrivals to the minimum or maximum acoustic deformation. A deep modulation of x rays was observed in a wide frequency range between 0.1 Hz and 1 MHz, which certifies that acoustically excited quartz crystals can potentially be used as slow and fast x-ray modulators with high duty cycle

Characterization, crystallization and preliminary X-ray analysis of the adhesive domain of SdrE from Staphylococcus aureus

International Nuclear Information System (INIS)

Xiang, Hua; Gao, Fangfang; Wang, Dacheng; Liu, Jing; Hu, Jia; Zhang, Liqing; Li, Shentao; Deng, Xuming

2010-01-01

The adhesive domain of SdrE from Staphylococcus aureus was recombinantly expressed in Escherichia coli and crystallized. X-ray diffraction data were collected to 1.8 Å resolution. The adhesive domain of SdrE from Staphylococcus aureus was recombinantly expressed in Escherichia coli. The purified protein was identified by SDS–PAGE and MALDI–TOF MS. The protein was crystallized using the vapour-diffusion method in hanging-drop mode with PEG 8000 as the primary precipitating agent. X-ray diffraction data were collected to 1.8 Å resolution from a single crystal of the protein. Preliminary X-ray analysis indicated that the crystal belonged to space group P1, with unit-cell parameters a = 40.714, b = 66.355, c = 80.827 Å, α = 111.19, β = 93.99, γ = 104.39°

X-ray diffraction and chemical bonding

International Nuclear Information System (INIS)

Bats, J.W.

1976-01-01

Chemical bonds are investigated in sulfamic acid (H 3 N-SO 3 ), sodium sulfonlate dihydrate (H 2 NC 6 H 4 SO 3 Na.2H 2 O), 2,5-dimercaptothiadiazole (HS-C 2 N 2 S-SH), sodium cyanide dihydrate (NaCN.2H 2 O), sodium thiocyanate (NaSCN) and ammonium thiocyanate (NH 4 SCN) by X-ray diffraction, and if necessary completed with neutron diffraction. Crystal structures and electron densities are determined together with bond length and angles. Also the effects of thermal motion are discussed

Inspection of single CdSe nanowires by use of micro-focused X-ray diffraction

Energy Technology Data Exchange (ETDEWEB)

Kurtulus, Oezguel [Dogus University, Istanbul (Turkey); Li, Zhen [University of Queensland, Brisbane (Australia); Arezki, Bahia; Biermanns, Andreas; Pietsch, Ullrich [University of Siegen (Germany)

2010-07-01

The morphology of CdSe nanowires (NW) can easily be controlled by various growth methods. In this study, CdSe NWs are prepared by solution-liquid-solid (SLS) approach providing needle-shaped wires of about 60nm in diameter and several microns in length. To make X-ray single NW inspection possible, the NWs were dispersed in toluene and hexadecylamine, homogenized by centrifugation and finally spin-coated on silicon substrate. SEM images revealed that the NWs are randomly oriented with length axis parallel to the substrate. However, at selected areas, the distance between neighboured NWs is in the order of one micron. These samples were investigated by X-ray diffraction using a 300 nm x 600 nm micro-focus at beamline ID1 of ESRF. Diffraction from 110W/2-20ZB basal plane was selected for single nanowire inspection. In order to measure various single objects subsequently, the sample was laterally scanned through the beam keeping the diffraction angle fixed. It was observed that the individual NWs differ slightly in peak position and peak width. From powder diffraction, it is known that NWs consist of an admixture of a wurtzite (W) and zinc-blende (ZB) structure units and the coherent illumination of sample by the micro-focus enables to visualize these zinc-blende and wurzite units separated by stacking faults.

Crystallization and preliminary X-ray diffraction analysis of the putative aldose 1-epimerase YeaD from Escherichia coli

International Nuclear Information System (INIS)

You, Weijie; Qiu, Xiaoting; Zhang, Yujie; Ma, Jinming; Gao, Yongxiang; Zhang, Xiao; Niu, Liwen; Teng, Maikun

2010-01-01

The putative aldose 1-epimerase YeaD from Escherichia coli was crystallized and diffraction data were collected to a resolution of 1.9 Å. Escherichia coli YeaD (ecYeaD) is suggested to be a member of the galactose mutarotase-like superfamily. Galactose mutarotase is an enzyme that converts α-galactose to β-galactose. The known structures of these galactose mutarotase-like proteins are similar to those of galactose mutarotases, with the catalytic residues being conserved, but there are some differences between them in the substrate-binding pocket. In order to reveal the specificity of ecYeaD, a three-dimensional structure is essential. Full-length ecYeaD with an additional 6×His tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 4000 as a precipitant at 283 K. An X-ray diffraction data set was collected to a resolution of 1.9 Å from a single flash-cooled crystal that belonged to space group P2 1 2 1 2 1

The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum

International Nuclear Information System (INIS)

Dobson, Renwick C. J.; Atkinson, Sarah C.; Gorman, Michael A.; Newman, Janet M.; Parker, Michael W.; Perugini, Matthew A.

2008-01-01

Dihydrodipicolinate synthase (DHDPS), an enzyme in the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the expression, purification, crystallization and preliminary diffraction analysis of DHDPS from C. botulinum are reported. In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. This enzyme, which is part of the diaminopimelate pathway leading to lysine, couples (S)-aspartate-β-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from Clostridium botulinum, an important bacterial pathogen, are presented. The enzyme was crystallized in a number of forms, predominantly using PEG precipitants, with the best crystal diffracting to beyond 1.9 Å resolution and displaying P4 2 2 1 2 symmetry. The unit-cell parameters were a = b = 92.9, c = 60.4 Å. The crystal volume per protein weight (V M ) was 2.07 Å 3 Da −1 , with an estimated solvent content of 41%. The structure of the enzyme will help guide the design of novel therapeutics against the C. botulinum pathogen

Crystallization and preliminary X-ray diffraction analysis of the MIF4G domain of DAP5

International Nuclear Information System (INIS)

Frank, Filipp; Virgili, Geneviève; Sonenberg, Nahum; Nagar, Bhushan

2009-01-01

The MIF4G domain of DAP5 was crystallized in two distinct crystal forms. Diffraction patterns have been analyzed and preliminary analysis, including molecular replacement, is presented here. Death-associated protein 5 (DAP5) is a member of the eIF4G family of scaffolding proteins that mediate cap-independent translation initiation by recruiting the translational machinery to internal ribosomal entry sites (IRESs) on mRNA. The MIF4G domain of DAP5 directly interacts with the eukaryotic initiation factors eIF4A and eIF3 and enhances the translation of several viral and cellular IRESs. Here, the crystallization and preliminary X-ray diffraction analysis of the MIF4G domain of DAP5 is presented

Influence of the crystal-surface unevenness on the angular spread of an x-ray diffracted beam

International Nuclear Information System (INIS)

Hrda, JaromIra; Potlovskiy, Kirill; Hrdy, JaromIr; Slechtova, Venceslava

2005-01-01

One of the factors influencing the focus size in diffractive-refractive optics is the quality of diffracting surface. If the surface is uneven, as it is when the silicon crystal surface is only etched, then the diffraction at each point of the surface is a combination of an asymmetric and inclined diffraction (general asymmetric diffraction). This somewhat deviates and spreads the diffracted beam. The integration over the surface hit by an incident beam gives the angular spread of the diffracted beam. It is shown theoretically that in some cases (highly asymmetric, highly inclined cut) the etched surface may create the spread of the diffracted beam such that it causes a significant broadening of the focus. In this case a mechanical-chemical polishing is necessary. This has been verified by us earlier in a preliminary experiment with synchrotron radiation. In this work the new experiment with the same crystals is performed using double crystal (+, -) arrangement and a laboratory x-ray source (CuKα radiation). We compared two samples; one of them is mechanically-chemically (MC) polished and thus the diffracting surface is almost perfect; the other is only etched. This experiment allows a better comparison of the result with the theory. The difference between the measured rocking curve widths for the etched and MC polished crystals (10'') roughly agrees with theory (7''), which supports the correctness of the theoretical approach

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

International Nuclear Information System (INIS)

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

2013-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Warren, Anna J. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Armour, Wes [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Oxford e-Research Centre, 7 Keble Road, Oxford OX1 3QG (United Kingdom); Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Horrell, Sam [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); University of Liverpool, Liverpool L69 3BX (United Kingdom); McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

2013-07-01

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

Two-dimensional x-ray diffraction

CERN Document Server

He, Bob B

2009-01-01

Written by one of the pioneers of 2D X-Ray Diffraction, this useful guide covers the fundamentals, experimental methods and applications of two-dimensional x-ray diffraction, including geometry convention, x-ray source and optics, two-dimensional detectors, diffraction data interpretation, and configurations for various applications, such as phase identification, texture, stress, microstructure analysis, crystallinity, thin film analysis and combinatorial screening. Experimental examples in materials research, pharmaceuticals, and forensics are also given. This presents a key resource to resea

Transistor properties of exfoliated single crystals of 2 H -Mo (Se1-xT ex ) 2(0 ≤x ≤1 )

Science.gov (United States)

Uesugi, Eri; Miao, Xiao; Ota, Hiromi; Goto, Hidenori; Kubozono, Yoshihiro

2017-06-01

Field-effect transistors (FETs) were fabricated using exfoliated single crystals of Mo (Se1-xT ex) 2 with an x range of 0 to 1, and the transistor properties fully investigated at 295 K in four-terminal measurement mode. The chemical composition and crystal structure of exfoliated single crystals were identified by energy-dispersive x-ray spectroscopy (EDX), single-crystal x-ray diffraction, and Raman scattering, suggesting the 2 H - structure in all Mo (Se1-xT ex) 2 . The lattice constants of a and c increase monotonically with increasing x , indicating the substitution of Se by Te. When x 0.4 . In contrast, the polarity of a thick single-crystal Mo (Se1-xT ex) 2 FET did not change despite an increase in x . The change of polarity in a thin single-crystal FET was well explained by the variation of electronic structure. The absence of such change in the thick single-crystal FET can be reasonably interpreted based on the large bulk conduction due to naturally accumulated electrons. The μ value in the thin single-crystal FET showed a parabolic variation, with a minimum μ at around x =0.4 , which probably originates from the disorder of the single crystal caused by the partial replacement of Se by Te, i.e., a disorder that may be due to ionic size difference of Se and Te.

Purification, crystallization, small-angle X-ray scattering and preliminary X-ray diffraction analysis of the SH2 domain of the Csk-homologous kinase

International Nuclear Information System (INIS)

Gunn, Natalie J.; Gorman, Michael A.; Dobson, Renwick C. J.; Parker, Michael W.; Mulhern, Terrence D.

2011-01-01

The Src-homology 2 (SH2) domain of Csk-family protein tyrosine kinases acts as a conformational switch to regulate their catalytic activity, which in turn promotes the inhibition of their proto-oncogenic targets, the Src-family kinases. Here, the expression, purification, small-angle X-ray scattering and preliminary diffraction analysis of the SH2 domain of the Csk-homologous kinase is reported. The C-terminal Src kinase (Csk) and Csk-homologous kinase (CHK) are endogenous inhibitors of the proto-oncogenic Src family of protein tyrosine kinases (SFKs). Phosphotyrosyl peptide binding to their Src-homology 2 (SH2) domains activates Csk and CHK, enhancing their ability to suppress SFK signalling; however, the detailed mechanistic basis of this activation event is unclear. The CHK SH2 was expressed in Escherichia coli and the purified protein was characterized as monomeric by synchrotron small-angle X-ray scattering in-line with size-exclusion chromatography. The CHK SH2 crystallized in 0.2 M sodium bromide, 0.1 M bis-Tris propane pH 6.5 and 20% polyethylene glycol 3350 and the best crystals diffracted to ∼1.6 Å resolution. The crystals belonged to space group P2, with unit-cell parameters a = 25.8, b = 34.6, c = 63.2 Å, β = 99.4°

Preliminary small-angle X-ray scattering and X-ray diffraction studies of the BTB domain of lola protein from Drosophila melanogaster

Science.gov (United States)

Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Dorovatovskii, P. V.; Popov, V. O.

2017-11-01

The Drosophila genome has several dozens of transcription factors (TTK group) containing BTB domains assembled into octamers. The LOLA protein belongs to this family. The purification, crystallization, and preliminary X-ray diffraction and small-angle X-ray scattering (SAXS) studies of the BTB domain of this protein are reported. The crystallization conditions were found by the vapor-diffusion technique. A very low diffraction resolution (8.7 Å resolution) of the crystals was insufficient for the determination of the threedimensional structure of the BTB domain. The SAXS study demonstrated that the BTB domain of the LOLA protein exists as an octamer in solution.

X-ray-excited optical luminescence of protein crystals: a new tool for studying radiation damage during diffraction data collection.

Science.gov (United States)

Owen, Robin L; Yorke, Briony A; Pearson, Arwen R

2012-05-01

During X-ray irradiation protein crystals radiate energy in the form of small amounts of visible light. This is known as X-ray-excited optical luminescence (XEOL). The XEOL of several proteins and their constituent amino acids has been characterized using the microspectrophotometers at the Swiss Light Source and Diamond Light Source. XEOL arises primarily from aromatic amino acids, but the effects of local environment and quenching within a crystal mean that the XEOL spectrum of a crystal is not the simple sum of the spectra of its constituent parts. Upon repeated exposure to X-rays XEOL spectra decay non-uniformly, suggesting that XEOL is sensitive to site-specific radiation damage. However, rates of XEOL decay were found not to correlate to decays in diffracting power, making XEOL of limited use as a metric for radiation damage to protein crystals. © 2012 International Union of Crystallography

Basic of X-ray diffraction

International Nuclear Information System (INIS)

Giacovazzo, C.

1996-01-01

The basic concepts of X-ray diffraction may be more easily understood if it is made preliminary use of a mathematical background. In these pages the authors will first define the delta function and its use for the representation of a lattice. Then the concepts of Fourier transform and convolution are given. At the end of this talk one should realize that a crystal is the convolution of the lattice with a function representing the content of the unit cell

Basic of X-ray diffraction

Energy Technology Data Exchange (ETDEWEB)

Giacovazzo, C [Bari Univ. (Italy). Dip. Geomineralogico

1996-09-01

The basic concepts of X-ray diffraction may be more easily understood if it is made preliminary use of a mathematical background. In these pages the authors will first define the delta function and its use for the representation of a lattice. Then the concepts of Fourier transform and convolution are given. At the end of this talk one should realize that a crystal is the convolution of the lattice with a function representing the content of the unit cell.

X-ray diffraction topography observations of the core in Bi12SiO20 crystals doped with Mn

International Nuclear Information System (INIS)

Milenov, T.I.; Botev, P.A.; Rafailov, P.M.; Gospodinov, M.M.

2004-01-01

The core region in a bismuth silicate--Bi 12 SiO 20 (BSO) crystal doped with Mn was examined by X-ray double-crystal diffraction topography. Specific features were observed in the topographies as lines and contrast differences that point to defects occupying the central part of the crystal. We discuss the nature of these defects and propose an explanation in terms of stacking faults arranged in different structures

Discovery and development of x-ray diffraction

Science.gov (United States)

Jeong, Yeuncheol; Yin, Ming; Datta, Timir

2013-03-01

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

Pressure-induced crystallization and phase transformation of amorphous selenium: Raman spectroscopy and x-ray diffraction studies

International Nuclear Information System (INIS)

Yang Kaifeng; Cui Qiliang; Hou Yuanyuan; Liu Bingbing; Zhou Qiang; Hu Jingzhu; Mao, H-K; Zou Guangtian

2007-01-01

High-pressure Raman spectroscopy studies have been carried out on amorphous Se (a-Se) at room temperature in a diamond anvil cell with an 830 nm exciting line. Raman evidence for the pressure-induced crystallization of a-Se and the coexistence of the unknown high-pressure phase with the hexagonal phase is presented for the first time. Further experimental proof of high-pressure angle-dispersive x-ray diffraction studies for a-Se indicates that the unknown high-pressure phase is also a mixture phase of the tetragonal I4 1 /acd and Se IV structure. Our Raman and x-ray diffraction results suggest that hexagonal Se I undergoes a direct transition to triclinic Se III at about 19 GPa, which is in good agreement with the theoretical prediction

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyoxalase I from Leishmania infantum

International Nuclear Information System (INIS)

Barata, Lídia; Sousa Silva, Marta; Schuldt, Linda; Costa, Gonçalo da; Tomás, Ana M.; Ferreira, António E. N.; Weiss, Manfred S.; Ponces Freire, Ana; Cordeiro, Carlos

2010-01-01

Glyoxalase I from L. infantum was cloned, overexpressed in E. coli, purified and crystallized. Glyoxalase I (GLO1) is the first of the two glyoxalase-pathway enzymes. It catalyzes the formation of S-d-lactoyltrypanothione from the non-enzymatically formed hemithioacetal of methylglyoxal and reduced trypanothione. In order to understand its substrate binding and catalytic mechanism, GLO1 from Leishmania infantum was cloned, overexpressed in Escherichia coli, purified and crystallized. Two crystal forms were obtained: a cube-shaped form and a rod-shaped form. While the cube-shaped form did not diffract X-rays at all, the rod-shaped form exhibited diffraction to about 2.0 Å resolution. The crystals belonged to space group P2 1 2 1 2, with unit-cell parameters a = 130.03, b = 148.51, c = 50.63 Å and three dimers of the enzyme per asymmetric unit

Crystallization and X-ray diffraction analysis of human CLEC5A (MDL-1), a dengue virus receptor

International Nuclear Information System (INIS)

Watson, Aleksandra A.; O’Callaghan, Christopher A.

2009-01-01

Recombinant human CLEC5A was crystallized in the trigonal space group P3 1 and X-ray diffraction data were collected to 1.56 Å resolution. The human C-type lectin-like protein CLEC5A (also known as MDL-1) is expressed on the surface of myeloid cells and plays a critical role in dengue-virus-induced disease by signalling through the transmembrane adaptor protein DAP12. The C-type lectin-like domain of CLEC5A was expressed in Escherichia coli, refolded and purified. Recombinant CLEC5A crystals were grown by sitting-drop vapour diffusion using polyethylene glycol 6000 as a precipitant. After optimization, crystals were grown which diffracted to 1.56 Å using synchrotron radiation. The results presented in this paper suggest that crystals producing diffraction of this quality will be suitable for structural determination of human CLEC5A

X-ray diffraction imaging of material microstructures

KAUST Repository

Varga, Laszlo

2016-10-20

Various examples are provided for x-ray imaging of the microstructure of materials. In one example, a system for non-destructive material testing includes an x-ray source configured to generate a beam spot on a test item; a grid detector configured to receive x- rays diffracted from the test object; and a computing device configured to determine a microstructure image based at least in part upon a diffraction pattern of the x-rays diffracted from the test object. In another example, a method for determining a microstructure of a material includes illuminating a beam spot on the material with a beam of incident x-rays; detecting, with a grid detector, x-rays diffracted from the material; and determining, by a computing device, a microstructure image based at least in part upon a diffraction pattern of the x-rays diffracted from the material.

Acemetacin cocrystal structures by powder X-ray diffraction

Science.gov (United States)

Bolla, Geetha

2017-01-01

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p-aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthon R 3 2(9)R 2 2(8)R 3 2(9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study. PMID:28512568

Acemetacin cocrystal structures by powder X-ray diffraction

Directory of Open Access Journals (Sweden)

Geetha Bolla

2017-05-01

Full Text Available Cocrystals of acemetacin drug (ACM with nicotinamide (NAM, p-aminobenzoic acid (PABA, valerolactam (VLM and 2-pyridone (2HP were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthon R32(9R22(8R32(9 with three different syn amides (VLM, 2HP and caprolactam. The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I or syn (type II. ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O...H, N...H, Cl...H and C...H interactions. The physicochemical properties of these cocrystals are under study.

Modern trends in x-ray powder diffraction

International Nuclear Information System (INIS)

Goebel, H.E.; Snyder, R.L.

1985-01-01

The revival of interest in X-ray powder diffraction, being quoted as a metamorphosis from the 'ugly duckling' to a 'beautiful swan', can be attributed to a number of modern developments in instrumentation and evaluation software. They result in faster data collection, improved accuracy and resolution, and better detectability of minor phases. The ease of data evaluation on small computers coupled direct to the instrument allows convenient execution of previously tedious and time-consuming off-line tasks like qualitative and quantitative analysis, characterization of microcrystalline properties, indexing, and lattice-constant refinements, as well as structure refinements or even exploration of new crystal structures. Powder diffraction has also progressed from an isolated analytical laboratory method to an in situ technique for analysing solid-state reactions or for the on-stream control of industrial processes. The paper surveys these developments and their real and potential applications, and tries to emphasize new trends that are regarded as important steps for the further progress of X-ray powder diffraction

A geometrical approach for semi-automated crystal centering and in situ X-ray diffraction data collection

International Nuclear Information System (INIS)

Mohammad Yaser Heidari Khajepour; Ferrer, Jean-Luc; Lebrette, Hugo; Vernede, Xavier; Rogues, Pierrick

2013-01-01

High-throughput protein crystallography projects pushed forward the development of automated crystallization platforms that are now commonly used. This created an urgent need for adapted and automated equipment for crystal analysis. However, first these crystals have to be harvested, cryo-protected and flash-cooled, operations that can fail or negatively impact on the crystal. In situ X-ray diffraction analysis has become a valid alternative to these operations, and a growing number of users apply it for crystal screening and to solve structures. Nevertheless, even this shortcut may require a significant amount of beam time. In this in situ high-throughput approach, the centering of crystals relative to the beam represents the bottleneck in the analysis process. In this article, a new method to accelerate this process, by recording accurately the local geometry coordinates for each crystal in the crystallization plate, is presented. Subsequently, the crystallization plate can be presented to the X-ray beam by an automated plate-handling device, such as a six-axis robot arm, for an automated crystal centering in the beam, in situ screening or data collection. Here the preliminary results of such a semi-automated pipeline are reported for two distinct test proteins. (authors)

Purification, crystallization and X-ray diffraction analysis of human dynamin-related protein 1 GTPase-GED fusion protein

International Nuclear Information System (INIS)

Klinglmayr, Eva; Wenger, Julia; Mayr, Sandra; Bossy-Wetzel, Ella; Puehringer, Sandra

2012-01-01

The crystallization and initial diffraction analysis of human Drp1 GTPase-GED fusion protein are reported. The mechano-enzyme dynamin-related protein 1 plays an important role in mitochondrial fission and is implicated in cell physiology. Dysregulation of Drp1 is associated with abnormal mitochondrial dynamics and neuronal damage. Drp1 shares structural and functional similarities with dynamin 1 with respect to domain organization, ability to self-assemble into spiral-like oligomers and GTP-cycle-dependent membrane scission. Structural studies of human dynamin-1 have greatly improved the understanding of this prototypical member of the dynamin superfamily. However, high-resolution structural information for full-length human Drp1 covering the GTPase domain, the middle domain and the GTPase effector domain (GED) is still lacking. In order to obtain mechanistic insights into the catalytic activity, a nucleotide-free GTPase-GED fusion protein of human Drp1 was expressed, purified and crystallized. Initial X-ray diffraction experiments yielded data to 2.67 Å resolution. The hexagonal-shaped crystals belonged to space group P2 1 2 1 2, with unit-cell parameters a = 53.59, b = 151.65, c = 43.53 Å, one molecule per asymmetric unit and a solvent content of 42%. Expression of selenomethionine-labelled protein is currently in progress. Here, the expression, purification, crystallization and X-ray diffraction analysis of the Drp1 GTPase-GED fusion protein are presented, which form a basis for more detailed structural and biophysical analysis

Trajectory method in the theory of Laue diffraction of X rays in crystals: II. Effect of total reflection at bending deformation

International Nuclear Information System (INIS)

Kohn, V. G.

2008-01-01

The effect of total reflection (switching) of a spherical X-ray wave in the case of Laue diffraction in a crystal with bending deformation is analyzed by the trajectory method. Qualitative analytical description and computation of the spatial structure of the reflected beam for large and small distances between the spherical-wave source and the crystal are performed. The mechanism of much more efficient reflection of an X-ray beam by a deformed crystal in comparison with a perfect crystal is clearly demonstrated. It is also shown that the trajectory method is very convenient for description of the total reflection phenomenon.

Trajectory method in the theory of Laue diffraction of X rays in crystals: II. Effect of total reflection at bending deformation

International Nuclear Information System (INIS)

Kohn, V. G.

2008-01-01

The effect of total reflection (switching) of a spherical X-ray wave in the case of Laue diffraction in a crystal with bending deformation is analyzed by the trajectory method. Qualitative analytical description and computation of the spatial structure of the reflected beam for large and small distances between the spherical-wave source and the crystal are performed. The mechanism of much more efficient reflection of an X-ray beam by a deformed crystal in comparison with a perfect crystal is clearly demonstrated. It is also shown that the trajectory method is very convenient for description of the total reflection phenomenon

Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

Science.gov (United States)

Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

2015-02-02

Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A universal treatment of X-ray and neutron diffraction in crystals. II. Extinction

International Nuclear Information System (INIS)

Hu Huachen

1997-01-01

For pt.I see ibid., p.484-92, 1997. Based on the formalism for calculating the integrated reflection power ratio of a plane mosaic crystal by using three dimensionless parameters exact and universal expressions for the secondary-extinction factors in X-ray and neutron crystallography are developed that can be applied to reflections of all possible values of extinction factor, reflection symmetry and the absorption-to-scattering cross-section ratio of the crystal. The representation by three parameters gives a clear and definite physical meaning to the concept of extinction. The theory has been extended to treat the extinction of a spherical crystal, and the striking difference in the evaluated secondary-extinction factor between the equivalent single-plate and the exact method in the spherical-crystal treatment under θ B = 0 is explained. As a demonstration of the feasibility of using these expressions, the diffraction data for LiF and MgO crystal plates measured by Lawrence [Acta Cryst. (1972), A28, 400-404; (1973), A29, 208-210] are reanalyzed by this method. All the reflections including the strongest ones (Y o down to 0.026) are reanalyzed simultaneously with single-valued particle size and mosaic spread as fitting parameters and allowing for primary extinction if necessary. The results (R factor = 0.014 and 0.053 for LiF and MgO, respectively) are unprecedentedly good. Furthermore, in disagreement with Lawrence, the extinction of LiF is found to be of secondary type and in the case of MgO both primary and secondary extinction should be considered. The analysis also shows that the formula Y ∝ Y p Y s is valid only for very weak extinctions and that the Hamilton-Darwin equations are valid in a range much broader than previously anticipated. (orig.)

Crystallization and preliminary X-ray diffraction analysis of two extracytoplasmic solute receptors of the DctP family from Bordetella pertussis

Energy Technology Data Exchange (ETDEWEB)

Rucktooa, Prakash; Huvent, Isabelle [UMR8161 CNRS Institut de Biologie de Lille, Laboratoire de Cristallographie Macromoléculaire, 1 Rue du Professeur Calmette, BP 447, 59021 Lille CEDEX (France); IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); Antoine, Rudy; Lecher, Sophie; Jacob-Dubuisson, Françoise, E-mail: francoise.jacob@ibl.fr [IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); INSERM-U629, Lille (France); Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); Villeret, Vincent, E-mail: francoise.jacob@ibl.fr; Bompard, Coralie [UMR8161 CNRS Institut de Biologie de Lille, Laboratoire de Cristallographie Macromoléculaire, 1 Rue du Professeur Calmette, BP 447, 59021 Lille CEDEX (France); IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France)

2006-10-01

Sample preparation, crystallization and preliminary X-ray analysis are reported for two B. pertussis extracytoplasmic solute receptors. DctP6 and DctP7 are two Bordetella pertussis proteins which belong to the extracytoplasmic solute receptors (ESR) superfamily. ESRs are involved in the transport of substrates from the periplasm to the cytosol of Gram-negative bacteria. DctP6 and DctP7 have been crystallized and diffraction data were collected using a synchrotron-radiation source. DctP6 crystallized in space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = 108.39, b = 108.39, c = 63.09 Å, while selenomethionyl-derivatized DctP7 crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 64.87, b = 149.83, c = 170.65 Å. The three-dimensional structure of DctP7 will be determined by single-wavelength anomalous diffraction, while the DctP6 structure will be solved by molecular-replacement methods.

Time-Resolved Soft X-ray Diffraction Reveals Transient Structural Distortions of Ternary Liquid Crystals

Directory of Open Access Journals (Sweden)

Klaus Mann

2009-11-01

Full Text Available Home-based soft X-ray time-resolved scattering experiments with nanosecond time resolution (10 ns and nanometer spatial resolution were carried out at a table top soft X-ray plasma source (2.2–5.2 nm. The investigated system was the lyotropic liquid crystal C16E7/paraffin/glycerol/formamide/IR 5. Usually, major changes in physical, chemical, and/or optical properties of the sample occur as a result of structural changes and shrinking morphology. Here, these effects occur as a consequence of the energy absorption in the sample upon optical laser excitation in the IR regime. The liquid crystal shows changes in the structural response within few hundred nanoseconds showing a time decay of 182 ns. A decrease of the Bragg peak diffracted intensity of 30% and a coherent macroscopic movement of the Bragg reflection are found as a response to the optical pump. The Bragg reflection movement is established to be isotropic and diffusion controlled (1 μs. Structural processes are analyzed in the Patterson analysis framework of the time-varying diffraction peaks revealing that the inter-lamellar distance increases by 2.7 Å resulting in an elongation of the coherently expanding lamella crystallite. The present studies emphasize the possibility of applying TR-SXRD techniques for studying the mechanical dynamics of nanosystems.

Modern X-ray difraction. X-ray diffractometry for material scientists, physicists, and chemicists

International Nuclear Information System (INIS)

Spiess, L.; Schwarzer, R.; Behnken, H.; Teichert, G.

2005-01-01

The book yields a comprehensive survey over the applications of X-ray diffraction in fields like material techniques, metallurgy, electrotechniques, machine engineering, as well as micro- and nanotechniques. The necessary fundamental knowledge on X-ray diffraction are mediated foundedly and illustratively. Thereby new techniques and evaluation procedures are presented as well as well known methods. The content: Production and properties of X radiation, diffraction of X radiation, hardware for X-ray diffraction, methods of X-ray diffraction, lattice-constant determination, phase analysis, X-ray profile analysis, crystal structure analysis, X-ray radiographic stress analysis, X-ray radiographic texture analysis, crystal orientation determination, pecularities at thin films, small angle scattering

Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics.

Science.gov (United States)

Stoupin, Stanislav; Antipov, Sergey; Butler, James E; Kolyadin, Alexander V; Katrusha, Andrey

2016-09-01

Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configuration and data analysis using rocking-curve topography. The variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.

Molybdenum cell for x-ray diffraction measurements of fluid alkali metals at high temperatures and high pressures

Science.gov (United States)

Matsuda, Kazuhiro; Tamura, Kozaburo; Katoh, Masahiro; Inui, Masanori

2004-03-01

We have developed a sample cell for x-ray diffraction measurements of fluid alkali metals at high temperatures and high pressures. All parts of the cell are made of molybdenum which is resistant to the chemical corrosion of alkali metals. Single crystalline molybdenum disks electrolytically thinned down to 40 μm were used as the walls of the cell through which x rays pass. The crystal orientation of the disks was controlled in order to reduce the background from the cell. All parts of the cell were assembled and brazed together using a high-temperature Ru-Mo alloy. Energy dispersive x-ray diffraction measurements have been successfully carried out for fluid rubidium up to 1973 K and 16.2 MPa. The obtained S(Q) demonstrates the applicability of the molybdenum cell to x-ray diffraction measurements of fluid alkali metals at high temperatures and high pressures.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* carbohydrate-binding protein of the human rotavirus strain Wa

International Nuclear Information System (INIS)

Kraschnefski, Mark J.; Scott, Stacy A.; Holloway, Gavan; Coulson, Barbara S.; Itzstein, Mark von; Blanchard, Helen

2005-01-01

The carbohydrate-binding component (VP8* 64–223 ) of the human Wa rotavirus spike protein has been overexpressed in E. coli, purified and crystallized in two different crystal forms. X-ray diffraction data have been collected that have enabled determination of the Wa VP8* 64–223 structure by molecular replacement. Rotaviruses exhibit host-specificity and the first crystallographic information on a rotavirus strain that infects humans is reported here. Recognition and attachment to host cells, leading to invasion and infection, is critically linked to the function of the outer capsid spike protein of the rotavirus particle. In some strains the VP8* component of the spike protein is implicated in recognition and binding of sialic-acid-containing cell-surface carbohydrates, thereby enabling infection by the virus. The cloning, expression, purification, crystallization and initial X-ray diffraction analysis of the VP8* core from human Wa rotavirus is reported. Two crystal forms (trigonal P3 2 21 and monoclinic P2 1 ) have been obtained and X-ray diffraction data have been collected, enabling determination of the VP8* 64–223 structure by molecular replacement

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* carbohydrate-binding protein of the human rotavirus strain Wa

Energy Technology Data Exchange (ETDEWEB)

Kraschnefski, Mark J.; Scott, Stacy A. [Institute for Glycomics, Griffith University (Gold Coast Campus), PMB 50 Gold Coast Mail Centre, Queensland 9726 (Australia); Holloway, Gavan; Coulson, Barbara S.; Itzstein, Mark von [Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010 (Australia); Blanchard, Helen, E-mail: h.blanchard@griffith.edu.au [Institute for Glycomics, Griffith University (Gold Coast Campus), PMB 50 Gold Coast Mail Centre, Queensland 9726 (Australia)

2005-11-01

The carbohydrate-binding component (VP8*{sub 64–223}) of the human Wa rotavirus spike protein has been overexpressed in E. coli, purified and crystallized in two different crystal forms. X-ray diffraction data have been collected that have enabled determination of the Wa VP8*{sub 64–223} structure by molecular replacement. Rotaviruses exhibit host-specificity and the first crystallographic information on a rotavirus strain that infects humans is reported here. Recognition and attachment to host cells, leading to invasion and infection, is critically linked to the function of the outer capsid spike protein of the rotavirus particle. In some strains the VP8* component of the spike protein is implicated in recognition and binding of sialic-acid-containing cell-surface carbohydrates, thereby enabling infection by the virus. The cloning, expression, purification, crystallization and initial X-ray diffraction analysis of the VP8* core from human Wa rotavirus is reported. Two crystal forms (trigonal P3{sub 2}21 and monoclinic P2{sub 1}) have been obtained and X-ray diffraction data have been collected, enabling determination of the VP8*{sub 64–223} structure by molecular replacement.

Diffraction enhanced kinetic depth X-ray imaging

Science.gov (United States)

Dicken, A.

An increasing number of fields would benefit from a single analytical probe that can characterise bulk objects that vary in morphology and/or material composition. These fields include security screening, medicine and material science. In this study the X-ray region is shown to be an effective probe for the characterisation of materials. The most prominent analytical techniques that utilise X-radiation are reviewed. The study then focuses on methods of amalgamating the three dimensional power of kinetic depth X-ray (KDFX) imaging with the materials discrimination of angular dispersive X-ray diffraction (ADXRD), thus providing KDEX with a much needed material specific counterpart. A knowledge of the sample position is essential for the correct interpretation of diffraction signatures. Two different sensor geometries (i.e. circumferential and linear) that are able to collect end interpret multiple unknown material diffraction patterns and attribute them to their respective loci within an inspection volume are investigated. The circumferential and linear detector geometries are hypothesised, simulated and then tested in an experimental setting with the later demonstrating a greater ability at discerning between mixed diffraction patterns produced by differing materials. Factors known to confound the linear diffraction method such as sample thickness and radiation energy have been explored and quantified with a possible means of mitigation being identified (i.e. via increasing the sample to detector distance). A series of diffraction patterns (following the linear diffraction approach) were obtained from a single phantom object that was simultaneously interrogated via KDEX imaging. Areas containing diffraction signatures matched from a threat library have been highlighted in the KDEX imagery via colour encoding and match index is inferred by intensity. This union is the first example of its kind and is called diffraction enhanced KDEX imagery. Finally an additional

single crystal growth, x-ray structure analysis, optical band gap

African Journals Online (AJOL)

2015-09-01

Sep 1, 2015 ... Hg...Hgand Cl...Cl interactions are stabilizing the structures in 3D pattern. UV-vis absorption spectra illustrate the change in opticalband gap from 3.01eVto 3.42eV on replacing the metal halide group.Raman and Hyper-Raman tensors calculations were performed based on single crystal X-ray data and the ...

X-ray diffraction characteristics of curved monochromators for sychrotron radiation

International Nuclear Information System (INIS)

Boeuf, A.; Rustichelli, F.; Mazkedian, S.; Puliti, P.; Melone, S.

1978-01-01

A theoretical study is presented concerning the diffraction characteristics of curved monochromators for X-ray synchrotron radiation used at the laboratories of Hamburg, Orsay and Stanford. The investigation was performed by extending to the X-ray case a simple model recently developed and fruitfully employed to describe the neutron diffraction properties of curved monochromators. Several diffraction patterns were obtained corresponding to different monochromator materials (Ge, Si) used by the different laboratories, for different reflecting planes (111), (220), asymmetry angles, X-ray wave-lengths (Mo Kα, Cu Kα, Cr Kα) and curvature radii. The results are discussed in physical terms and their implications on the design of curved monochromators for synchrotron radiation are presented. In particular, the study shows that all the monochromators used in the different laboratories should behave practically as perfect crystals and therefore should have a very low integrated reflectivity corresponding to an optimized wavelength passband Δlambda/lambda approximately 10 -4 . The gain that can be obtained by increasing the curvature, by introducing a gradient in the lattice spacing or by any other kind of imperfection is quite limited and much lower than the desirable value. The adopted model can help in obtaining a possible moderate gain in intensity by also taking into consideration other parameters, such as crystal material, reflecting plane, asymmetry of the reflection and X-ray wavelength. (Auth.)

Crystallization of uridine phosphorylase from Shewanella oneidensis MR-1 in the laboratory and under microgravity and preliminary X-ray diffraction analysis

International Nuclear Information System (INIS)

Safonova, Tatyana N.; Mordkovich, Nadezhda N.; Polyakov, Konstantin M.; Manuvera, Valentin A.; Veiko, Vladimir P.; Popov, Vladimir O.

2012-01-01

High-quality crystals of uridine phosphorylase from Shewanella oneidensis were grown under microgravity conditions. X-ray diffraction data were collected to a resolution of 0.95 Å. Uridine phosphorylase (UDP, EC 2.4.2.3), a key enzyme in the pyrimidine salvage pathway, catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. The gene expression of UDP from Shewanella oneidensis MR-1 was performed in the recipient strain Escherichia coli. The UDP protein was crystallized on earth (in the free form and in complex with uridine as the substrate) by the hanging-drop vapour-diffusion method at 296 K and under microgravity conditions (in the free form) aboard the Russian Segment of the International Space Station by the capillary counter-diffusion method. The data sets were collected to a resolution of 1.9 Å from crystals of the free form grown on earth, 1.6 Å from crystals of the complex with uridine and 0.95 Å from crystals of the free form grown under microgravity. All crystals belong to the space group P2 1 and have similar unit-cell parameters. The crystal of uridine phosphorylase grown under microgravity diffracted to ultra-high resolution and gave high-quality X-ray diffraction data

A new theory for X-ray diffraction.

Science.gov (United States)

Fewster, Paul F

2014-05-01

This article proposes a new theory of X-ray scattering that has particular relevance to powder diffraction. The underlying concept of this theory is that the scattering from a crystal or crystallite is distributed throughout space: this leads to the effect that enhanced scatter can be observed at the `Bragg position' even if the `Bragg condition' is not satisfied. The scatter from a single crystal or crystallite, in any fixed orientation, has the fascinating property of contributing simultaneously to many `Bragg positions'. It also explains why diffraction peaks are obtained from samples with very few crystallites, which cannot be explained with the conventional theory. The intensity ratios for an Si powder sample are predicted with greater accuracy and the temperature factors are more realistic. Another consequence is that this new theory predicts a reliability in the intensity measurements which agrees much more closely with experimental observations compared to conventional theory that is based on `Bragg-type' scatter. The role of dynamical effects (extinction etc.) is discussed and how they are suppressed with diffuse scattering. An alternative explanation for the Lorentz factor is presented that is more general and based on the capture volume in diffraction space. This theory, when applied to the scattering from powders, will evaluate the full scattering profile, including peak widths and the `background'. The theory should provide an increased understanding of the reliability of powder diffraction measurements, and may also have wider implications for the analysis of powder diffraction data, by increasing the accuracy of intensities predicted from structural models.

Surface-treated self-standing curved crystals as high-efficiency elements for X- and γ-ray optics: theory and experiment.

Science.gov (United States)

Bonnini, Elisa; Buffagni, Elisa; Zappettini, Andrea; Doyle, Stephen; Ferrari, Claudio

2015-06-01

The efficiency of a Laue lens for X- and γ-ray focusing in the energy range 60-600 keV is closely linked to the diffraction efficiency of the single crystals composing the lens. A powerful focusing system is crucial for applications like medical imaging and X-ray astronomy where wide beams must be focused. Mosaic crystals with a high density, such as Cu or Au, and bent crystals with curved diffracting planes (CDPs) are considered for the realization of a focusing system for γ-rays, owing to their high diffraction efficiency in a predetermined angular range. In this work, a comparison of the efficiency of CDP crystals and Cu and Au mosaic crystals was performed on the basis of the theory of X-ray diffraction. Si, GaAs and Ge CDP crystals with optimized thicknesses and moderate radii of curvature of several tens of metres demonstrate comparable or superior performance with respect to the higher atomic number mosaic crystals generally used. In order to increase the efficiency of the lens further, a stack of several CDP crystals is proposed as an optical element. CDP crystals were obtained by a surface-damage method, and a stack of two surface-damaged bent Si crystals was prepared and tested. Rocking curves of the stack were performed with synchrotron radiation at 19 keV to check the lattice alignment: they exhibited only one diffraction peak.

Grain orientation mapping of passivated aluminum interconnect lines with X-ray micro-diffraction

International Nuclear Information System (INIS)

Chang, C.H.; Patel, J.R.; MacDowell, A.A.; Padmore, H.A.; Thompson, A.C.

1998-01-01

A micro x-ray diffraction facility is under development at the Advanced Light Source. Spot sizes are typically about 1-microm size generated by means of grazing incidence Kirkpatrick-Baez focusing mirrors. Photon energy is either white of energy range 6--14 keV or monochromatic generated from a pair of channel cut crystals. Laue diffraction pattern from a single grain in a passivated 2-microm wide bamboo structured Aluminum interconnect line has been recorded. Acquisition times are of the order of seconds. The Laue pattern has allowed the determination of the crystallographic orientation of individual grains along the line length. The experimental and analysis procedure used is described, as is the latest grain orientation result. The impact of x-ray micro-diffraction and its possible future direction are discussed in the context of other developments in the area of electromigration, and other technological problems

Grain orientation mapping of passivated aluminum interconnect lines by x-ray micro-diffraction

International Nuclear Information System (INIS)

Chang, C. H.; Patel, J. R.; MacDowell, A. A.; Padmore, H. A.; Thompson, A. C.

1998-01-01

A micro x-ray diffraction facility is under development at the Advanced Light Source. Spot sizes are typically about 1-μm size generated by means of grazing incidence Kirkpatrick-Baez focusing mirrors. Photon energy is either white of energy range 6-14 keV or monochromatic generated from a pair of channel cut crystals. Laue diffraction pattern from a single grain in a passivated 2-μm wide bamboo structured Aluminum interconnect line has been recorded. Acquisition times are of the order of seconds. The Laue pattern has allowed the determination of the crystallographic orientation of individual grains along the line length. The experimental and analysis procedure used is described, as is the latest grain orientation result. The impact of x-ray micro-diffraction and its possible future direction are discussed in the context of other developments in the area of electromigration, and other technological problems

Single crystal neutron diffraction study of SrFeOsub(3-x)(x=0. 1)

Energy Technology Data Exchange (ETDEWEB)

Oda, H; Yamaguchi, Y; Takei, H; Watanabe, H [Tohoku Univ., Sendai (Japan). Research Inst. for Iron, Steel and Other Metals

1977-01-01

Neutron diffraction study was carried out on single crystals of the perovskite oxide SrFeOsub(3-x)(x=0.1). SrFeOsub(3-x)(x=0.1) has a proper screw spin structure with the propagation vector parallel to (111) direction and its Neel temperature is 118 K. The electron configuration of Fe/sup 4 +/(3d/sup 4/) ion is close to the low-spin state (tsub(2g)sup(4)) and the oxygen ion has the unpaired electron with the magnetic moment of 0.3..mu..sub(B) antiparallel to the vector sum of the magnetic moments of two iron ions lying on the neighbouring planes perpendicular to the screw axis. The absolute value of the propagation vector is almost constant. 0.130x..sqrt..3.2..pi../a A/sup -1/, at temperatures below 50 K, while it decreases gradually at higher temperatures reaching 0.118x..sqrt..3.2..pi../a A/sup -1/ at Tsub(N).

Crystallization and preliminary X-ray diffraction analysis of salutaridine reductase from the opium poppy Papaver somniferum

International Nuclear Information System (INIS)

Higashi, Yasuhiro; Smith, Thomas J.; Jez, Joseph M.; Kutchan, Toni M.

2010-01-01

Recombinant P. somniferum salutaridine reductase (SalR) was purified and crystallized with NADPH using the hanging-drop vapor-diffusion method. Crystals of the SalR–NADPH complex diffracted X-rays to a resolution of 1.9 Å. The opium poppy Papaver somniferum is the source of the narcotic analgesics morphine and codeine. Salutaridine reductase (SalR; EC 1.1.1.248) reduces the C-7 keto group of salutaridine to the C-7 (S)-hydroxyl group of salutaridinol in the biosynthetic pathway that leads to morphine in the opium poppy plant. P. somniferum SalR was overproduced in Escherichia coli and purified using cobalt-affinity and size-exclusion chromatography. Hexagonal crystals belonging to space group P6 4 22 or P6 2 22 were obtained using ammonium sulfate as precipitant and diffracted to a resolution of 1.9 Å

X-ray Laue diffraction with allowance for second derivatives of amplitudes in dynamical diffraction equations

International Nuclear Information System (INIS)

Balyan, M.K.

2014-01-01

Asymmetrical Laue diffraction in a perfect crystal with a plane entrance surface is considered. The second derivatives of amplitudes in the direction, perpendicular to diffraction plane in the dynamical diffraction equations are taken into account. Using the corresponding Green function a general form for the amplitude of diffracted wave in the crystal is derived. The sizes of the source in both directions as well as the source of crystal distance and non-monochromaticity of the radiation incident on the crystal are taken into account. On the basis of obtained expression the coherent properties of the field depending on the sizes of the source and on the width of the spectrum of the incident radiation are analyzed. Taking into account the second derivatives of amplitudes with respect to the direction, perpendicular to the diffraction plane, the time dependent propagation equations for an X-ray pulse in a perfect crystal are given

Production, purification, crystallization and preliminary X-ray diffraction studies of the nucleoside diphosphate kinase b from Leishmania major

International Nuclear Information System (INIS)

Tonoli, Celisa Caldana Costa; Vieira, Plinio Salmazo; Ward, Richard John; Arni, Raghuvir Krishnaswamy; Oliveira, Arthur Henrique Cavalcante de; Murakami, Mario Tyago

2009-01-01

Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the nucleoside diphosphate kinase b from Leishmania major are reported. The crystals belonged to the trigonal space group P3 2 21 and diffracted to 2.18 Å resolution. Nucleoside diphosphate kinases (NDKs; EC 2.7.4.6) play an essential role in the synthesis of nucleotides from intermediates in the salvage pathway in all parasitic trypanosomatids and their structural studies will be instrumental in shedding light on the biochemical machinery involved in the parasite life cycle and host–parasite interactions. In this work, NDKb from Leishmania major was overexpressed in Escherichia coli, purified to homogeneity and crystallized using the sitting-drop vapour-diffusion method. The NDK crystal diffracted to 2.2 Å resolution and belonged to the trigonal crystal system, with unit-cell parameters a = 114.2, c = 93.9 Å. Translation-function calculations yielded an unambiguous solution in the enantiomorphic space group P3 2 21

Lattice collapse and quenching of magnetism in CaFe2As2 under pressure: A single-crystal neutron and x-ray diffraction investigation

International Nuclear Information System (INIS)

Goldman, A.I.; Kreyssig, A.; Prokes, K.; Pratt, D.K.; Argyriou, D.N.; Lynn, J.W.; Nandi, S.; Kimber, S.A.J.; Chen, Y.; Lee, Y.B.; Samolyuk, G.; Leao, J.B.; Poulton, S.J.; Bud'ko, S.L.; Ni, N.; Canfield, P.C.; Harmon, B.N.; McQueeney, R.J.

2009-01-01

Single-crystal neutron and high-energy x-ray diffraction measurements have identified the phase lines corresponding to transitions among the ambient-pressure paramagnetic tetragonal (T), the antiferromagnetic orthorhombic (O), and the nonmagnetic collapsed tetragonal (cT) phases of CaFe 2 As 2 . We find no evidence of additional structures for pressures of up to 2.5 GPa (at 300 K). Both the T-cT and O-cT transitions exhibit significant hysteresis effects, and we demonstrate that coexistence of the O and cT phases can occur if a nonhydrostatic component of pressure is present. Measurements of the magnetic diffraction peaks show no change in the magnetic structure or ordered moment as a function of pressure in the O phase, and we find no evidence of magnetic ordering in the cT phase. Band-structure calculations show that the transition into the cT phase results in a strong decrease in the iron 3d density of states at the Fermi energy, consistent with a loss of the magnetic moment.

X-ray diffraction study of lithium hydrazinium sulfate and lithium ammonium sulfate crystals under a static electric field

International Nuclear Information System (INIS)

Sebastian, M.T.; Becker, R.A.; Klapper, H.

1991-01-01

X-ray diffraction studies are made on proton-conducting polar lithium hydrazinium sulfate and ferroelectric lithium ammonium sulfate. The X-ray rocking curves recorded with in situ electric field along the polar b axis of lithium hydrazinium sulfate (direction of proton conductivity) show a strong enhancement of the 0k0 diffraction intensity. The corresponding 0k0 X-ray topographs reveal extinction contrast consisting of striations parallel to the polar axis. They disappear when the electric field is switched off. The effect is very strong in 0k0 but invisible in h0l reflections. It is present only if the electric field is parallel to the polar axis b. This unusual X-ray topographic contrast is correlated with the proton conduction. It is supposed that, under electric field, an inhomogeneous charge distribution develops, distorting the crystal lattice. Similar experiments on lithium ammonium sulfate also show contrast variations, but of quite different behaviour than before. In this case they result from changes of the ferroelectric domain configuration under electric field. (orig.)

Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment

International Nuclear Information System (INIS)

Sugiyama, Shigeru; Nomura, Yusuke; Sakamoto, Taiichi; Kitatani, Tomoya; Kobayashi, Asako; Miyakawa, Shin; Takahashi, Yoshinori; Adachi, Hiroaki; Takano, Kazufumi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Nakamura, Yoshikazu; Matsumura, Hiroyoshi

2008-01-01

An RNA aptamer in complex with the human IgG Fc fragment have been crystallized. The stirring technique with a rotary shaker was used to improve the crystals and to ensure that they were of high quality and single, resulting in crystals that diffracted to 2.2 Å resolution. Aptamers, which are folded DNA or RNA molecules, bind to target molecules with high affinity and specificity. An RNA aptamer specific for the Fc fragment of human immunoglobulin G (IgG) has recently been identified and it has been demonstrated that an optimized 24-nucleotide RNA aptamer binds to the Fc fragment of human IgG and not to other species. In order to clarify the structural basis of the high specificity of the RNA aptamer, it was crystallized in complex with the Fc fragment of human IgG1. Preliminary X-ray diffraction studies revealed that the crystals belonged to the orthorhombic space group P2 1 2 1 2, with unit-cell parameters a = 83.7, b = 107.2, c = 79.0 Å. A data set has been collected to 2.2 Å resolution

Quantitative analysis of crystalline pharmaceuticals in tablets by pattern-fitting procedure using X-ray diffraction pattern.

Science.gov (United States)

Takehira, Rieko; Momose, Yasunori; Yamamura, Shigeo

2010-10-15

A pattern-fitting procedure using an X-ray diffraction pattern was applied to the quantitative analysis of binary system of crystalline pharmaceuticals in tablets. Orthorhombic crystals of isoniazid (INH) and mannitol (MAN) were used for the analysis. Tablets were prepared under various compression pressures using a direct compression method with various compositions of INH and MAN. Assuming that X-ray diffraction pattern of INH-MAN system consists of diffraction intensities from respective crystals, observed diffraction intensities were fitted to analytic expression based on X-ray diffraction theory and separated into two intensities from INH and MAN crystals by a nonlinear least-squares procedure. After separation, the contents of INH were determined by using the optimized normalization constants for INH and MAN. The correction parameter including all the factors that are beyond experimental control was required for quantitative analysis without calibration curve. The pattern-fitting procedure made it possible to determine crystalline phases in the range of 10-90% (w/w) of the INH contents. Further, certain characteristics of the crystals in the tablets, such as the preferred orientation, size of crystallite, and lattice disorder were determined simultaneously. This method can be adopted to analyze compounds whose crystal structures are known. It is a potentially powerful tool for the quantitative phase analysis and characterization of crystals in tablets and powders using X-ray diffraction patterns. Copyright 2010 Elsevier B.V. All rights reserved.

X-ray diffraction study of KTP (KTiOPO4) crystals under a static electric field

International Nuclear Information System (INIS)

Sebastian, M.T.; Klapper, H.; Bolt, R.J.

1992-01-01

X-ray diffraction studies are made on ion-conducting potassium titanyl phosphate (KTP) crystals with in situ DC electric field along different crystallographic directions. The X-ray rocking curves recorded with an electric field along the polar b axis (which is the direction of ion conduction) show a strong enhancement of the 040 reflection intensity (reflecting planes normal to the b axis) whereas the h0l reflections (reflecting planes parallel to the polar axis) do not show any intensity change. For an electric field normal to the polar axis no intensity change, either in 040 or in h0l reflections occurs. This observation is supplemented by X-ray topography. The 040 X-ray topographs recorded with in situ electric field along b exhibit strong extinction contrast in the form of striations parallel to the polar (ion-conduction) axis. The 040 intensity increase and the striation contrast are attributed to lattice deformation by the space-charge polarization due to the movement of the K + ions under the influence of the electric field. (orig.)

Indentation Size Effects in Single Crystal Copper as Revealed by Synchrotron X-ray Microdiffraction

Energy Technology Data Exchange (ETDEWEB)

Feng, G.; Budiman, A. S.; Nix, W. D.; Tamura, N.; Patel, J. R.

2007-11-19

The indentation size effect (ISE) has been observed in numerous nanoindentation studies on crystalline materials; it is found that the hardness increases dramatically with decreasing indentation size - a 'smaller is stronger' phenomenon. Some have attributed the ISE to the existence of strain gradients and the geometrically necessary dislocations (GNDs). Since the GND density is directly related to the local lattice curvature, the Scanning X-ray Microdiffraction ({mu}SXRD) technique, which can quantitatively measure relative lattice rotations through the streaking of Laue diffractions, can used to study the strain gradients. The synchrotron {mu}SXRD technique we use - which was developed at the Advanced Light Source (ALS), Berkeley Lab - allows for probing the local plastic behavior of crystals with sub-micrometer resolution. Using this technique, we studied the local plasticity for indentations of different depths in a Cu single crystal. Broadening of Laue diffractions (streaking) was observed, showing local crystal lattice rotation due to the indentation-induced plastic deformation. A quantitative analysis of the streaking allows us to estimate the average GND density in the indentation plastic zones. The size dependence of the hardness, as found by nanoindentation, will be described, and its correlation to the observed lattice rotations will be discussed.

Trapezoidal diffraction grating beam splitters in single crystal diamond

Science.gov (United States)

Kiss, Marcell; Graziosi, Teodoro; Quack, Niels

2018-02-01

Single Crystal Diamond has been recognized as a prime material for optical components in high power applications due to low absorption and high thermal conductivity. However, diamond microstructuring remains challenging. Here, we report on the fabrication and characterization of optical diffraction gratings exhibiting a symmetric trapezoidal profile etched into a single crystal diamond substrate. The optimized grating geometry diffracts the transmitted optical power into precisely defined proportions, performing as an effective beam splitter. We fabricate our gratings in commercially available single crystal CVD diamond plates (2.6mm x 2.6mm x 0.3mm). Using a sputter deposited hard mask and patterning by contact lithography, the diamond is etched in an inductively coupled oxygen plasma with zero platen power. The etch process effectively reveals the characteristic {111} diamond crystal planes, creating a precisely defined angled (54.7°) profile. SEM and AFM measurements of the fabricated gratings evidence the trapezoidal shape with a pitch of 3.82μm, depth of 170 nm and duty cycle of 35.5%. Optical characterization is performed in transmission using a 650nm laser source perpendicular to the sample. The recorded transmitted optical power as function of detector rotation angle shows a distribution of 21.1% in the 0th order and 23.6% in each +/-1st order (16.1% reflected, 16.6% in higher orders). To our knowledge, this is the first demonstration of diffraction gratings with trapezoidal profile in single crystal diamond. The fabrication process will enable beam splitter gratings of custom defined optical power distribution profiles, while antireflection coatings can increase the efficiency.

Evaluation of single crystal coefficients from mechanical and x-ray elastic constants of the polycrystal

International Nuclear Information System (INIS)

Hauk, V.; Kockelmann, H.

1979-01-01

Methods of calculation are developed for determination of single crystal elastic compliance or stiffness constants of cubic and hexagonal materials from mechanical and X-ray elastic constants of polycrystals. The calculations are applied to pure, cubic iron and hexagonal WC. There are no single crystal constants in the literature for WC, because no single crystals suitable for measurement are available. (orig.) [de

X-ray microbeam measurements of individual dislocation cell elastic strains in deformed single-crystal copper

Energy Technology Data Exchange (ETDEWEB)

Levine, Lyle E. [National Institute of Standards and Technology (NIST); Larson, Ben C [ORNL; Yang, Wenge [Carnegie Institution of Washington; Kassner, Michael E. [University of Southern California; Tischler, Jonathan Zachary [ORNL; Delos-Reyes, Michael A. [University of Southern California; Fields, Richard J. [National Institute of Standards and Technology (NIST); Liu, Wenjun [Argonne National Laboratory (ANL)

2006-01-01

The distribution of elastic strains (and thus stresses) at the sub-micrometer length scale within deformed metal single crystals has surprisingly broad implications for our understanding of important physical phenomena. These include the evolution of the complex dislocation structures that govern mechanical behavior within individual grains [1-4], the transport of dislocations through such structures [5-7], changes in mechanical properties that occur during reverse loading [8-10] (e.g. sheet metal forming), and the analyses of diffraction line profiles for microstructural studies of these phenomena [11-17]. We present the first direct, spatially-resolved measurements of the elastic strains within individual dislocation cells in copper single crystals deformed in tension and compression along <100> axes. Broad distributions of elastic strains are found, with profound implications for theories of dislocation structure evolution [4,18], dislocation transport [5-7], and the extraction of dislocation parameters from X-ray line profiles [11-17,19].

Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments

Science.gov (United States)

Baba, Seiki; Hoshino, Takeshi; Ito, Len; Kumasaka, Takashi

2013-01-01

Protein crystals are fragile, and it is sometimes difficult to find conditions suitable for handling and cryocooling the crystals before conducting X-ray diffraction experiments. To overcome this issue, a protein crystal-mounting method has been developed that involves a water-soluble polymer and controlled humid air that can adjust the moisture content of a mounted crystal. By coating crystals with polymer glue and exposing them to controlled humid air, the crystals were stable at room temperature and were cryocooled under optimized humidity. Moreover, the glue-coated crystals reproducibly showed gradual transformations of their lattice constants in response to a change in humidity; thus, using this method, a series of isomorphous crystals can be prepared. This technique is valuable when working on fragile protein crystals, including membrane proteins, and will also be useful for multi-crystal data collection. PMID:23999307

Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2

International Nuclear Information System (INIS)

Ascher, David B.; Polekhina, Galina; Parker, Michael W.

2012-01-01

The luminal domain of human endoplasmic reticulum aminopeptidase 2 has been expressed, purified and crystallized. The crystals belonged to the orthorhombic space group P2 1 2 1 2 and diffracted anisotropically to 3.3 Å resolution in the best direction on an in-house source. Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a critical enzyme involved in the final processing of MHC class I antigens. Peptide trimming by ERAP2 and the other members of the oxytocinase subfamily is essential to customize longer precursor peptides in order to fit them to the correct length required for presentation on major histocompatibility complex class I molecules. While recent structures of ERAP1 have provided an understanding of the ‘molecular-ruler’ mechanism of substrate selection, little is known about the complementary activities of its homologue ERAP2 despite their sharing 49% sequence identity. In order to gain insights into the structure–function relationship of the oxytocinase subfamily, and in particular ERAP2, the luminal region of human ERAP2 has been crystallized in the presence of the inhibitor bestatin. The crystals belonged to an orthorhombic space group and diffracted anisotropically to 3.3 Å resolution in the best direction on an in-house X-ray source. A molecular-replacement solution suggested that the enzyme has adopted the closed state as has been observed in other inhibitor-bound aminopeptidase structures

X-ray diffraction analysis of LiCu{sub 2}O{sub 2} crystals with additives of silver atoms

Energy Technology Data Exchange (ETDEWEB)

Sirotinkin, V. P., E-mail: irotinkin.vladimir@mail.ru; Bush, A. A.; Kamentsev, K. E. [Moscow State Technical University of Radio Engineering, Electronics, and Automation (Russian Federation); Dau, H. S. [People’s Friendship University of Russia (Russian Federation); Yakovlev, K. A. [Moscow State Technical University of Radio Engineering, Electronics, and Automation (Russian Federation); Tishchenko, E. A. [People’s Friendship University of Russia (Russian Federation)

2015-09-15

Silver-containing LiCu{sub 2}O{sub 2} crystals up to 4 × 8 × 8 mm in size were grown by the crystallization of 80(1-x)CuO · 20{sub x}AgNO{sub 3} · 20Li{sub 2}CO{sub 3} (0 ≤ x ≤ 0.5) mixture melt. According to the X-ray spectral and Rietveld X-ray diffraction data, the maximum amount of silver incorporated in the LiCu{sub 2}O{sub 2} structure is about 4 at % relative to the copper content. It was established that silver atoms occupy statistically crystallographic positions of lithium atoms. The incorporation of silver atoms is accompanied by a noticeable increase in parameter c of the LiCu{sub 2}O{sub 2} rhombic unit cell, a slight increase in parameter a, and a slight decrease in parameter b.

Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of an inositol monophosphatase family protein (SAS2203) from Staphylococcus aureus MSSA476

International Nuclear Information System (INIS)

Bhattacharyya, Sudipta; Dutta, Debajyoti; Ghosh, Ananta Kumar; Das, Amit Kumar

2011-01-01

The cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of an inositol monophosphatase family protein (SAS2203) from S. aureus MSSA476 is reported. The gene product of the sas2203 ORF of Staphylococcus aureus MSSA476 encodes a 30 kDa molecular-weight protein with a high sequence resemblance (29% identity) to tetrameric inositol monophosphatase from Thermotoga maritima. The protein was cloned, expressed, purified to homogeneity and crystallized. Crystals appeared in several conditions and good diffraction-quality crystals were obtained from 0.2 M Li 2 SO 4 , 20% PEG 3350, 0.1 M HEPES pH 7.0 using the sitting-drop vapour-diffusion method. A complete diffraction data set was collected to 2.6 Å resolution using a Rigaku MicroMax-007 HF Cu Kα X-ray generator and a Rigaku R-AXIS IV ++ detector. The diffraction data were consistent with the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 49.98, b = 68.35, c = 143.79 Å, α = β = γ = 90°, and the crystal contained two molecules in the asymmetric unit

High-pressure X-ray diffraction of L-ALANINE crystal

DEFF Research Database (Denmark)

Olsen, J.S.; Gerward, Leif; Souza, A.G.

2006-01-01

L-ALANINE has been studied by X-ray diffraction at ambient temperature and pressure up to 10.3 GPa. The material is found to transform to a tetragonal structure between 2 and 3 GPa. and to a monoclinic structure between 8 and 10 GPa. The experimental bulk modulus is 25(5) GPa for the orthorhombic...

Crystallization and preliminary X-ray diffraction analysis of HML, a lectin from the red marine alga Hypnea musciformis

International Nuclear Information System (INIS)

Nagano, Celso S.; Gallego del Sol, Francisca; Cavada, Benildo S.; Nascimento, Kyria Santiago Do; Nunes, Eudismar Vale; Sampaio, Alexandre H.; Calvete, Juan J.

2005-01-01

The crystallization and preliminary X-ray diffraction analysis of a red marine alga lectin isolated from H. musciformis is reported. HML, a lectin from the red marine alga Hypnea musciformis, defines a novel lectin family. Orthorhombic crystals of HML belonging to space group P2 1 2 1 2 1 grew within three weeks at 293 K using the hanging-drop vapour-diffusion method. A complete data set was collected at 2.4 Å resolution. HML is the first marine alga lectin to be crystallized

Determination of crystal structures by x-ray diffraction: applications to a lanthanide complex and a natural organic compound

International Nuclear Information System (INIS)

Miranda, J.M. de.

1986-01-01

The study fir determining crystal structures of the Ho (ReO sub(4)) sub(3) 4 TDTD 3 H sub(2) O complex and the natural organic compound C sub(14) H sub(16) O sub(6) by X-ray diffraction are presented. The experimental equipments are described in details. (M.C.K.)

Extinction correction in white X-ray and neutron diffraction

International Nuclear Information System (INIS)

Tomiyoshi, S.; Yamada, M.; Watanabe, H.

1980-01-01

Extinction effects in white-beam X-ray and neutron diffraction are considered. In white-beam diffraction, a small deviation of the wavelength from the Bragg condition Δlambda is a variable which represents the line profile of the diffraction peaks, so that by using the new parameter Δlambda the theory is converted to one in white-beam diffraction. It is shown that for a convex crystal, primary extinction agrees with the results calculated already for monochromatic diffraction. The same relation is shown to hold in secondary extinction. It is concluded that extinction theory derived for monochromatic diffraction is applicable without any modification in white-beam diffraction. (Auth.)

Expression, purification, crystallization and preliminary X-ray diffraction analysis of the TonB-dependent haem outer membrane transporter ShuA from Shigella dysenteriae

International Nuclear Information System (INIS)

Brillet, Karl; Meksem, Ahmed; Thompson, Andrew; Cobessi, David

2009-01-01

ShuA from S. dysenteriae was crystallized in several crystallization conditions containing detergents. Adding heavy atoms during crystallization strongly improved the crystal quality and the resolution limits. Diffraction data were collected at an energy remote from the Pb M absorption edges. As part of efforts towards understanding the crystallization of membrane proteins and membrane transport across the outer membrane of Gram-negative bacteria, the TonB-dependent haem outer membrane transporter ShuA of Shigella dysenteriae bound to heavy atoms was crystallized in several crystallization conditions using detergents. The insertion of a His 6 tag into an extracellular loop of ShuA, instead of downstream of the Escherichia coli peptide signal, allowed efficient targeting to the outer membrane and the rapid preparation of crystallizable protein. Crystals diffracting X-rays beyond 3.5 Å resolution were obtained by co-crystallizing ShuA with useful heavy atoms for phasing (Eu, Tb, Pb) by the MAD method at the synchrotron, and the SAD or SIRAS method at the Cu wavelength. The authors collected X-ray diffraction data at 2.3 Å resolution using one crystal of ShuA-Pb, and at 3.2 Å resolution at an energy remote from the Pb M absorption edges for phasing on PROXIMA-1 at SOLEIL

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

Science.gov (United States)

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

2013-07-01

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

Vibrational spectra, powder X-ray diffractions and physical properties of cyanide complexes with 1-ethylimidazole

Science.gov (United States)

Kürkçüoğlu, Güneş Süheyla; Kiraz, Fulya Çetinkaya; Sayın, Elvan

2015-10-01

The heteronuclear tetracyanonickelate(II) complexes of the type [M(etim)Ni(CN)4]n (hereafter, abbreviated as M-Ni-etim, M = Mn(II), Fe(II) or Co(II); etim = 1-ethylimidazole, C5H8N2) were prepared in powder form and characterized by FT-IR and Raman spectroscopy, powder X-ray diffraction (PXRD), thermal (TG; DTG and DTA), and elemental analysis techniques. The structures of these complexes were elucidated using vibrational spectra and powder X-ray diffraction patterns with the peak assignment to provide a better understanding of the structures. It is shown that the spectra are consistent with a proposed crystal structure for these compounds derived from powder X-ray diffraction measurements. Vibrational spectra of the complexes were presented and discussed with respect to the internal modes of both the etim and the cyanide ligands. The C, H and N analyses were carried out for all the complexes. Thermal behaviors of these complexes were followed using TG, DTG and DTA curves in the temperature range 30-700 °C in the static air atmosphere. The FT-IR, Raman spectra, thermal and powder X-ray analyses revealed no significant differences between the single crystal and powder forms. Additionally, electrical and magnetic properties of the complexes were investigated. The FT-IR and Raman spectroscopy, PXRD, thermal and elemental analyses results propose that these complexes are similar in structure to the Hofmann-type complexes.

X-ray topography and multiple diffraction

International Nuclear Information System (INIS)

Chang, S.-L.

1983-01-01

A short summary on X-ray topography, which is based on the dynamical theory of X-ray diffraction, is made. The applications and properties related to the use of the multiple diffraction technique are analized and discussed. (L.C.) [pt

Resolution of crystal structures by X-ray and neutrons powder diffraction using global optimisation methods; Resolution des structures cristallines par diffraction des rayons X et neutrons sur poudres en utilisant les methodes d'optimisation globale

Energy Technology Data Exchange (ETDEWEB)

Palin, L

2005-03-15

We have shown in this work that X-ray diffraction on powder is a powerful tool to analyze crystal structure. The purpose of this thesis is the resolution of crystal structures by X-ray and neutrons diffraction on powder using global optimisation methods. We have studied 3 different topics. The first one is the order-disorder phenomena observed in some globular organic molecular solids. The second is the opiate family of neuropeptides. These neurotransmitters regulate sensory functions including pain and control of respiration in the central nervous system. The aim of our study was to try to determine the crystal structure of Leu-enkephalin and some of its sub-fragments. The determination of the crystal structures has been done performing Monte Carlo simulations. The third one is the location of benzene in a sodium-X zeolite. The zeolite framework was already known and the benzene has been localized by simulated annealing and by the use of maximum entropy maps.

Evaluation of undoped ZnS single crystal materials for x-ray imaging applications

Science.gov (United States)

Saleh, Muad; Lynn, Kelvin G.; McCloy, John S.

2017-05-01

ZnS-based materials have a long history of use as x-ray luminescent materials. ZnS was one of the first discovered scintillators and is reported to have one of the highest scintillator efficiencies. The use of ZnS for high energy luminescence has been thus far limited to thin powder screens, such as ZnS:Ag which is used for detecting alpha radiation, due to opacity to its scintillation light, primarily due to scattering. ZnS in bulk form (chemical vapor deposited, powder processed, and single crystal) has high transmission and low scattering compared to powder screens. In this paper, the performance of single crystalline ZnS is evaluated for low energy x-ray (PLE) of several undoped ZnS single crystals is compared to their Radioluminescence (RL) spectra. It was found that the ZnS emission wavelength varies on the excitation source energy.

Revealing stacking sequences in inverse opals by microradian X-ray diffraction

NARCIS (Netherlands)

Sinitskii, A.; Abramova, V.; Grigorieva, N.; Grigoriev, S.; Snigirev, A.; Byelov, D.; Petukhov, A.V.

2010-01-01

We present the results of the structural analysis of inverse opal photonic crystals by microradian X-ray diffraction. Inverse opals based on different oxide materials (TiO2, SiO2 and Fe2O3) were fabricated by templating polystyrene colloidal crystal films grown by the vertical deposition technique.

Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8

International Nuclear Information System (INIS)

Scott, Stacy A.; Holloway, Gavan; Coulson, Barbara S.; Szyczew, Alex J.; Kiefel, Milton J.; Itzstein, Mark von; Blanchard, Helen

2005-01-01

The sialic acid-binding domain (VP8*) component of the porcine CRW-8 rotavirus spike protein has been overexpressed in E. coli, purified and co-crystallized with an N-acetylneuraminic acid derivative. X-ray diffraction data have been collected to 2.3 Å, which has enabled determination of the structure by molecular replacement. Rotavirus recognition and attachment to host cells involves interaction with the spike protein VP4 that projects outwards from the surface of the virus particle. An integral component of these spikes is the VP8* domain, which is implicated in the direct recognition and binding of sialic acid-containing cell-surface carbohydrates and facilitates subsequent invasion by the virus. The expression, purification, crystallization and preliminary X-ray diffraction analysis of VP8* from porcine CRW-8 rotavirus is reported. Diffraction data have been collected to 2.3 Å resolution, enabling the determination of the VP8* structure by molecular replacement

Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8

Energy Technology Data Exchange (ETDEWEB)

Scott, Stacy A. [Institute for Glycomics, Griffith University (Gold Coast Campus) PMB 50, Gold Coast Mail Centre, Queensland 9726 (Australia); Holloway, Gavan; Coulson, Barbara S. [Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010 (Australia); Szyczew, Alex J.; Kiefel, Milton J.; Itzstein, Mark von; Blanchard, Helen, E-mail: h.blanchard@griffith.edu.au [Institute for Glycomics, Griffith University (Gold Coast Campus) PMB 50, Gold Coast Mail Centre, Queensland 9726 (Australia)

2005-06-01

The sialic acid-binding domain (VP8*) component of the porcine CRW-8 rotavirus spike protein has been overexpressed in E. coli, purified and co-crystallized with an N-acetylneuraminic acid derivative. X-ray diffraction data have been collected to 2.3 Å, which has enabled determination of the structure by molecular replacement. Rotavirus recognition and attachment to host cells involves interaction with the spike protein VP4 that projects outwards from the surface of the virus particle. An integral component of these spikes is the VP8* domain, which is implicated in the direct recognition and binding of sialic acid-containing cell-surface carbohydrates and facilitates subsequent invasion by the virus. The expression, purification, crystallization and preliminary X-ray diffraction analysis of VP8* from porcine CRW-8 rotavirus is reported. Diffraction data have been collected to 2.3 Å resolution, enabling the determination of the VP8* structure by molecular replacement.

Polymorphous transformation in the crystal structure of [Mg(H.sub.2./sub.O).sub.6./sub. Br.sub.2./sub.][(C.sub.7./sub.H.sub.14./sub.N.sub.4./sub.).sub.2./sub.] . 4 (H.sub.2./sub.O) studied by powder and single crystal X-ray diffraction

Czech Academy of Sciences Publication Activity Database

Rivera, A.; Rohlíček, Jan; Sadat-Bernal, J.; Ríos-Motta, J.; Dušek, Michal

2014-01-01

Roč. 229, č. 4 (2014), s. 319-327 ISSN 0044-2968 Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : polymorphism * powder X-ray * single crystal diffraction * 1,3,6,8-tetraazatricyclo[4.3.1.13,ˑ 8]undecane * phase transformation * crystal structure analysis Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.310, year: 2014

RASOR: an advanced instrument for soft x-ray reflectivity and diffraction.

Science.gov (United States)

Beale, T A W; Hase, T P A; Iida, T; Endo, K; Steadman, P; Marshall, A R; Dhesi, S S; van der Laan, G; Hatton, P D

2010-07-01

We report the design and construction of a novel soft x-ray diffractometer installed at Diamond Light Source. The beamline endstation RASOR is constructed for general users and designed primarily for the study of single crystal diffraction and thin film reflectivity. The instrument is comprised of a limited three circle (theta, 2theta, and chi) diffractometer with an additional removable rotation (phi) stage. It is equipped with a liquid helium cryostat, and post-scatter polarization analysis. Motorized motions are provided for the precise positioning of the sample onto the diffractometer center of rotation, and for positioning the center of rotation onto the x-ray beam. The functions of the instrument have been tested at Diamond Light Source, and initial test measurements are provided, demonstrating the potential of the instrument.

Disorder and transport properties of In3SbTe2 - an X-ray, neutron and electron diffraction study

International Nuclear Information System (INIS)

Schroeder, Thorsten; Rosenthal, Tobias; Grott, Sebastian; Stiewe, Christian; Boor, Johannes de; Oeckler, Oliver

2013-01-01

Quenched metastable In 3 SbTe 2 was investigated by X-ray and neutron powder diffraction as well as by single-crystal X-ray diffraction. The average structure corresponds to the rocksalt type, the anion position being occupied by antimony and tellurium. Neutron data indicate no antisite disorder of indium and antimony. The compound is a high-temperature phase that can be quenched to yield a metastable compound at ambient temperature which, upon heating, decomposes at ca. 320 C into InSb and InTe. Diffuse scattering in reconstructed X-ray and selected area electron diffraction patterns indicates local distortions of the crystal structure due to static atom displacement along <100> from the average positions, caused by the different size of the anions, but no superstructure. The electrical conductivity of In 3 SbTe 2 is 3.2 x 10 4 S.cm -1 at 25 C, the temperature characteristics correspond to metallic behavior. Consequently, the thermal conductivity is also rather high. The decomposition into InSb and InTe reduces the electrical conductivity by a factor of 3 in heterogeneous microstructures. (Copyright copyright 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Formation and evaluation of convex-curved crystals of lithium fluoride for use in analyzing x-ray spectra

International Nuclear Information System (INIS)

Sellick, B.O.

1976-01-01

Lithium fluoride as received from the vendor in boule form is 38 x 38 x 13 mm thick. This block is cleaved to wafers of the desired thickness, x-ray-evaluated for ''d'' spacing and greatest intensity, bent to the required radius, and then acid-etched to remove foreign material. The diffraction and dispersion characteristics of a wafer are analyzed using well-collimated tungsten x rays that strike the crystal and are diffracted onto no-screen x-ray film. If the crystal is satisfactory, it is mounted in a spectrogoniometer and rotated through an x-ray beam while a detector is set at the optimized angle for the diffracted x rays. The average intensity across the length of the crystal is recorded by multichannel scaling. Any imperfections appear as peaks or dips compared to the average intensity. The crystal next goes to a 10-channel, filter-fluorescer x-ray unit that compares zero-order intensity to diffracted Kα and Kβ intensity. Counts for 100-s intervals are taken in groups of three and averaged. Correction factors for instrument geometry, air, pinhole diameter at zero order, Kα-Kβ, barometric pressure, temperature, etc., are added to the efficiency calculations to obtain the crystal efficiency (epsilon) vs keV data. The crystal is mounted in the spectrograph or spectrometer and calibrated to either the detector or film plane by using direct radiation with proper x-ray filters or absorbers. The crystal is then ready for use

Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330

International Nuclear Information System (INIS)

Aggarwal, Nidhi; Mandal, P. K.; Gautham, Namasivayam; Chadha, Anju

2013-01-01

The expression, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies on C. parapsilosis carbonyl reductase are reported. The NAD(P)H-dependent carbonyl reductase from Candida parapsilosis ATCC 7330 catalyses the asymmetric reduction of ethyl 4-phenyl-2-oxobutanoate to ethyl (R)-4-phenyl-2-hydroxybutanoate, a precursor of angiotensin-converting enzyme inhibitors such as Cilazapril and Benazepril. The carbonyl reductase was expressed in Escherichia coli and purified by GST-affinity and size-exclusion chromatography. Crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to 1.86 Å resolution. The asymmetric unit contained two molecules of carbonyl reductase, with a solvent content of 48%. The structure was solved by molecular replacement using cinnamyl alcohol dehydrogenase from Saccharomyces cerevisiae as a search model

Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis

International Nuclear Information System (INIS)

Suganuma, Masatoshi; Teh, Aik Hong; Makino, Masatomo; Shimizu, Nobutaka; Kaneko, Tomonori; Hirata, Kunio; Yamamoto, Masaki; Kumasaka, Takashi

2009-01-01

The bacterial PPM phosphatase RsbX from B. subtilis was expressed in E. coli, purified and crystallized. The crystal belonged to space group P1 and diffracted to 1.06 Å resolution. RsbX from Bacillus subtilis is a manganese-dependent PPM phosphatase and negatively regulates the signal transduction of the general stress response by the dephosphorylation of RsbS and RsbR, which are activators of the alternative RNA polymerase σ factor SigB. In order to elucidate the structural–functional relationship of its Ser/Thr protein-phosphorylation mechanism, an X-ray crystallographic diffraction study of RsbX was performed. Recombinant RsbX was expressed in Escherichia coli, purified and crystallized. Crystals were obtained using the sitting-drop vapour-diffusion method and X-ray diffraction data were collected to 1.06 Å resolution with an R merge of 8.1%. The crystals belonged to the triclinic space group P1, with unit-cell parameters a = 33.3, b = 41.7, c = 68.6 Å, α = 98.8, β = 90.0, γ = 108.4°

Diffraction enhanced x-ray imaging

International Nuclear Information System (INIS)

Thomlinson, W.; Zhong, Z.; Johnston, R.E.; Sayers, D.

1997-09-01

Diffraction enhanced imaging (DEI) is a new x-ray radiographic imaging modality using synchrotron x-rays which produces images of thick absorbing objects that are almost completely free of scatter. They show dramatically improved contrast over standard imaging applied to the same phantoms. The contrast is based not only on attenuation but also the refraction and diffraction properties of the sample. The diffraction component and the apparent absorption component (absorption plus extinction contrast) can each be determined independently. This imaging method may improve the image quality for medical applications such as mammography

Measurement of X-ray beam emittance using crystal optics at an X-ray undulator beamline

CERN Document Server

Kohmura, Y; Awaji, M; Tanaka, T; Hara, T; Goto, S; Ishikawa, T

2000-01-01

We present a method of using crystal optics to measure the emittance of the X-ray source. Two perfect crystals set in (++) configuration work as a high-resolution collimator. The phase-space diagram (i.e. beam cross-section and angular distribution) could be determined without any assumptions on the light source. When the measurement is done at short wavelength radiation from undulator, the electron beam emittance is larger than the diffraction limit of the X-rays. Therefore, the electron beam emittance could be estimated. The measurement was done with the hard X-rays of 18.5 and 55 keV from an undulator beamline, BL 47XU, of SPring-8. The horizontal emittance of the X-ray beam was estimated to be about 7.6 nmrad, close to the designed electron beam emittance of the storage ring (7 nmrad). Some portions of the instrumental functions, such as the scattering by filters and windows along the beamline and the slight bent of the crystal planes of the monochromator, could not be precisely evaluated, but an upper li...

The CCP14 for single crystal and powder diffraction

International Nuclear Information System (INIS)

Cranswick, L.M.D.

1999-01-01

Full text: The Collaborative Computation Project Number 14 for Single Crystal and Powder Diffraction (CCP14) is continuing in its objective to provide freely available software and resources for the powder diffraction and crystallographic community. Using the Internet and World Wide Web, we are presently compiling software and web resources, creating tutorials and help files. It also endeavours to encourage and provide resources to assist program authors with developing their software. The CCP14 presently has its web-site at and a mirror at (at CSIRO, Melbourne, Australia). Auto web-mirroring is being implemented to allow users to obtain software and access to resources in a more time effective manner. For people in countries isolated from the Internet, the CCP14 on CD-ROM can be snail mailed on request. This is in the form of a Virtual World Wide Web/Virtual Internet; in the same vein as the existing Crystallographic Nexus CD-ROM. Copyright (1999) Australian X-ray Analytical Association Inc

Synthesis, characterization and single crystal X-ray analysis of chlorobis(N,N-dimethyldithiocarbamato-S,S′antimony(III

Directory of Open Access Journals (Sweden)

H.P.S. Chauhan

2015-07-01

Full Text Available The title compound chlorobis(N,N-dimethyldithiocarbamato-S,S′antimony(III has been prepared in distilled acetonitrile and characterized by physicochemical [melting point and molecular weight determination, elemental analysis (C, H, N, S & Sb], spectral [FT–IR, far IR, NMR (1H & 13C] studies. The crystal and molecular structure was further confirmed using single crystal X-ray diffraction analysis which features a five-coordinate geometry for antimony(III within a ClS4 donor set. The distortion in the co-planarity of ClSbS3 evidences the stereochemical influence exerts by the lone pair of electrons on antimony(III. Two centrosymmetrically related molecule held together via C–H···Cl secondary interaction result in molecular aggregation of the compound.

Extended X-ray absorption fine structure and X-ray diffraction studies on supported Ni catalysts

International Nuclear Information System (INIS)

Aldea, N.; Marginean, P.; Yaning, Xie; Tiandou, Hu; Tao, Liu; Wu, Zhongua; ZhenYa, Dai

1999-01-01

In the first part of this paper, we present a study based on EXAFS spectroscopy. This method can yield structural information about the local environment around a specific atomic constituent in the amorphous materials, the location and chemical state of any catalytic atom on any support or point defect structures, in alloys and composites. EXAFS is a specific technique of the scattering of X-ray on materials. The present study is aimed toward elucidation of the local structure of Ni atoms and their interaction with oxide support. The second goal of the paper consists in X-ray diffraction on the same samples. X-ray diffraction method that is capable to determine average particle size, microstrains, probability of faults as well as particle size distribution function of supported Ni catalysts is presented. The method is based on the Fourier analysis of a single X-Ray diffraction profile. The results obtained on supported nickel catalysts, which are used in H/D isotopic exchange reactions are reported. The global structure is obtained with a new fitting method based on the Generalised Fermi Function facilities for approximation and Fourier transform of the experimental X-Ray line profiles. Both types of measurements were performed on Beijing Synchrotron Radiation Facilities (BSRF). (authors)

X-ray beam monitor made by thin-film CVD single-crystal diamond.

Science.gov (United States)

Marinelli, Marco; Milani, E; Prestopino, G; Verona, C; Verona-Rinati, G; Angelone, M; Pillon, M; Kachkanov, V; Tartoni, N; Benetti, M; Cannatà, D; Di Pietrantonio, F

2012-11-01

A novel beam position monitor, operated at zero bias voltage, based on high-quality chemical-vapor-deposition single-crystal Schottky diamond for use under intense synchrotron X-ray beams was fabricated and tested. The total thickness of the diamond thin-film beam monitor is about 60 µm. The diamond beam monitor was inserted in the B16 beamline of the Diamond Light Source synchrotron in Harwell (UK). The device was characterized under monochromatic high-flux X-ray beams from 6 to 20 keV and a micro-focused 10 keV beam with a spot size of approximately 2 µm × 3 µm square. Time response, linearity and position sensitivity were investigated. Device response uniformity was measured by a raster scan of the diamond surface with the micro-focused beam. Transmissivity and spectral responsivity versus beam energy were also measured, showing excellent performance of the new thin-film single-crystal diamond beam monitor.

Diffracted X-ray tracking for monitoring intramolecular motion in individual protein molecules using broad band X-ray

Energy Technology Data Exchange (ETDEWEB)

Ichiyanagi, Kouhei; Sasaki, Yuji C. [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 609 Kiban Building 5-1-5 Kashiwanoha, Kahiwashi, Chiba 277-8561 (Japan); Japan Science and Technology Agency, CREST, CREST, Sasaki-Team, 609 Kiban Building, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan); Sekiguchi, Hiroshi; Hoshino, Masato; Kajiwara, Kentaro; Senba, Yasunori; Ohashi, Haruhiko; Ohta, Noboru [Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Hoshisashi, Kentaro; Jae-won, Chang; Tokue, Maki; Matsushita, Yufuku [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 609 Kiban Building 5-1-5 Kashiwanoha, Kahiwashi, Chiba 277-8561 (Japan); Nishijima, Masaki; Inoue, Yoshihisa [Department of Applied Chemistry and Office for University-Industry Collaboration, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Yagi, Naoto [Japan Science and Technology Agency, CREST, CREST, Sasaki-Team, 609 Kiban Building, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan); Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan)

2013-10-15

Diffracted X-ray tracking (DXT) enables the tilting and twisting motions of single protein molecules to be monitored with micro- to milliradian resolution using a highly brilliant X-ray source with a wide energy bandwidth. We have developed a technique to monitor single molecules using gold nanocrystals attached to individual protein molecules using the BL28B2 beamline at SPring-8. In this paper we present the installation of a single toroidal X-ray mirror at BL28B2 to focus X-rays in an energy range of 10–20 keV (△E/E = 82% for an X-ray with a wide energy bandwidth). With this beamline we tracked diffraction spots from gold nanocrystals over a wide angle range than that using quasi-monochromatic X-rays. Application of the wide angle DXT technique to biological systems enabled us to observe the on-site motions of single protein molecules that have been functionalized in vivo. We further extend the capability of DXT by observing the fractional tilting and twisting motions of inner proteins under various conditions. As a proof of this methodology and to determine instrumental performance the intramolecular motions of a human serum albumin complex with 2-anthracenecarboxylic acid was investigated using the BL28B2 beamline. The random tilting and twisting intramolecular motions are shown to be directly linked to the movement of individual protein molecules in the buffer solution.

Purification, crystallization, X-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease

International Nuclear Information System (INIS)

Meramveliotaki, Chrysi; Kotsifaki, Dina; Androulaki, Maria; Hountas, Athanasios; Eliopoulos, Elias; Kokkinidis, Michael

2007-01-01

PvuII is the first type II restriction endonuclease to be converted from its wild-type homodimeric form into an enzymatically active single-chain variant. The enzyme was crystallized and phasing was successfully performed by molecular replacement. The restriction endonuclease PvuII from Proteus vulgaris has been converted from its wild-type homodimeric form into the enzymatically active single-chain variant scPvuII by tandemly joining the two subunits through the peptide linker Gly-Ser-Gly-Gly. scPvuII, which is suitable for the development of programmed restriction endonucleases for highly specific DNA cleavage, was purified and crystallized. The crystals diffract to a resolution of 2.35 Å and belong to space group P4 2 , with unit-cell parameters a = b = 101.92, c = 100.28 Å and two molecules per asymmetric unit. Phasing was successfully performed by molecular replacement

Purification, crystallization and preliminary X-ray diffraction analysis of inner membrane complex (IMC) subcompartment protein 1 (ISP1) from Toxoplasma gondii

International Nuclear Information System (INIS)

Tonkin, Michelle L.; Brown, Shannon; Beck, Josh R.; Bradley, Peter J.; Boulanger, Martin J.

2012-01-01

To characterize the ISP family of proteins present in apicomplexan parasites, ISP1 from T. gondii was expressed, purified and crystallized. Two crystal forms (cubic and orthorhombic) were analyzed by X-ray diffraction and data were processed to 2.05 and 2.1 Å resolution, respectively. The protozoan parasites of the Apicomplexa phylum are devastating global pathogens. Their success is largely due to phylum-specific proteins found in specialized organelles and cellular structures. The inner membrane complex (IMC) is a unique apicomplexan structure that is essential for motility, invasion and replication. The IMC subcompartment proteins (ISP) have recently been identified in Toxoplasma gondii and shown to be critical for replication, although their specific mechanisms are unknown. Structural characterization of TgISP1 was pursued in order to identify the fold adopted by the ISPs and to generate detailed insight into how this family of proteins functions during replication. An N-terminally truncated form of TgISP1 was purified from Escherichia coli, crystallized and subjected to X-ray diffraction analysis. Two crystal forms of TgISP1 belonging to space groups P4 1 32 or P4 3 32 and P2 1 2 1 2 1 diffracted to 2.05 and 2.1 Å resolution, respectively

Crystallization and preliminary X-ray analysis of Escherichia coli RNase G

International Nuclear Information System (INIS)

Fang, Pengfei; Wang, Jing; Li, Xu; Guo, Min; Xing, Li; Cao, Xu; Zhu, Yi; Gao, Yan; Niu, Liwen; Teng, Maikun

2009-01-01

Full-length E. coli RNase G was overexpressed, purified and crystallized. Diffraction data were collected to a resolution of 3.4 Å. The homologous RNases RNase E and RNase G are widely distributed in bacteria and function in many important physiological processes, including mRNA degradation, rRNA maturation and so on. In this study, the crystallization and preliminary X-ray analysis of RNase G from Escherichia coli is described. Purified recombinant E. coli RNase G, which has 497 amino acids, was crystallized in the cubic space group F432, with unit-cell parameters a = b = c = 219.84 Å. X-ray diffraction data were collected to a resolution of 3.4 Å

The Scherrer equation and the dynamical theory of X-ray diffraction.

Science.gov (United States)

Muniz, Francisco Tiago Leitão; Miranda, Marcus Aurélio Ribeiro; Morilla Dos Santos, Cássio; Sasaki, José Marcos

2016-05-01

The Scherrer equation is a widely used tool to determine the crystallite size of polycrystalline samples. However, it is not clear if one can apply it to large crystallite sizes because its derivation is based on the kinematical theory of X-ray diffraction. For large and perfect crystals, it is more appropriate to use the dynamical theory of X-ray diffraction. Because of the appearance of polycrystalline materials with a high degree of crystalline perfection and large sizes, it is the authors' belief that it is important to establish the crystallite size limit for which the Scherrer equation can be applied. In this work, the diffraction peak profiles are calculated using the dynamical theory of X-ray diffraction for several Bragg reflections and crystallite sizes for Si, LaB6 and CeO2. The full width at half-maximum is then extracted and the crystallite size is computed using the Scherrer equation. It is shown that for crystals with linear absorption coefficients below 2117.3 cm(-1) the Scherrer equation is valid for crystallites with sizes up to 600 nm. It is also shown that as the size increases only the peaks at higher 2θ angles give good results, and if one uses peaks with 2θ > 60° the limit for use of the Scherrer equation would go up to 1 µm.

Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster

Science.gov (United States)

Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Popov, V. O.

2017-11-01

The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P3221. The structure was solved by the molecular replacement method. The structure refinement is currently underway.

High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging

Energy Technology Data Exchange (ETDEWEB)

Tokuhisa, Atsushi [RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Arai, Junya [The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Joti, Yasumasa [JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Ohno, Yoshiyuki; Kameyama, Toyohisa; Yamamoto, Keiji; Hatanaka, Masayuki; Gerofi, Balazs; Shimada, Akio; Kurokawa, Motoyoshi; Shoji, Fumiyoshi [RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047 (Japan); Okada, Kensuke [RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Sugimoto, Takashi [JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Yamaga, Mitsuhiro; Tanaka, Ryotaro [RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Yokokawa, Mitsuo; Hori, Atsushi [RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047 (Japan); Ishikawa, Yutaka, E-mail: ishikawa@is.s.u-tokyo.ac.jp [The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Hatsui, Takaki, E-mail: ishikawa@is.s.u-tokyo.ac.jp [RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Go, Nobuhiro [Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215 (Japan)

2013-11-01

A code with an algorithm for high-speed classification of X-ray diffraction patterns has been developed. Results obtained for a set of 1 × 10{sup 6} simulated diffraction patterns are also reported. Single-particle coherent X-ray diffraction imaging using an X-ray free-electron laser has the potential to reveal the three-dimensional structure of a biological supra-molecule at sub-nanometer resolution. In order to realise this method, it is necessary to analyze as many as 1 × 10{sup 6} noisy X-ray diffraction patterns, each for an unknown random target orientation. To cope with the severe quantum noise, patterns need to be classified according to their similarities and average similar patterns to improve the signal-to-noise ratio. A high-speed scalable scheme has been developed to carry out classification on the K computer, a 10PFLOPS supercomputer at RIKEN Advanced Institute for Computational Science. It is designed to work on the real-time basis with the experimental diffraction pattern collection at the X-ray free-electron laser facility SACLA so that the result of classification can be feedback for optimizing experimental parameters during the experiment. The present status of our effort developing the system and also a result of application to a set of simulated diffraction patterns is reported. About 1 × 10{sup 6} diffraction patterns were successfully classificatied by running 255 separate 1 h jobs in 385-node mode.

Time resolved X-ray micro-diffraction measurements of the dynamic local layer response to electric field in antiferroelectric liquid crystals

Energy Technology Data Exchange (ETDEWEB)

Takahashi, Yumiko; Iida, Atuso E-mail: atsuo.iida@kek.jp; Takanishi, Yoichi; Ogasawara, Toyokazu; Takezoe, Hideo

2001-07-21

The time-resolved synchrotron X-ray microbeam diffraction experiment has been carried out to reveal the local layer response to the electric field in the antiferroelectric liquid crystal. The X-ray microbeam of a few {mu}m spatial resolution was obtained with Kirkpatrick-Baez optics. The time-resolved small angle diffraction experiment was performed with a time resolution ranging from 10 {mu}s to a few ms. The reversible local layer change between the horizontal chevron and the quasi-bookshelf structure was confirmed by the triangular wave form. The transient layer response for the step form electric field was observed. The layer response closely related with an electric field induced antiferroelectric to ferroelectric phase transition.

Time resolved X-ray micro-diffraction measurements of the dynamic local layer response to electric field in antiferroelectric liquid crystals

International Nuclear Information System (INIS)

Takahashi, Yumiko; Iida, Atuso; Takanishi, Yoichi; Ogasawara, Toyokazu; Takezoe, Hideo

2001-01-01

The time-resolved synchrotron X-ray microbeam diffraction experiment has been carried out to reveal the local layer response to the electric field in the antiferroelectric liquid crystal. The X-ray microbeam of a few μm spatial resolution was obtained with Kirkpatrick-Baez optics. The time-resolved small angle diffraction experiment was performed with a time resolution ranging from 10 μs to a few ms. The reversible local layer change between the horizontal chevron and the quasi-bookshelf structure was confirmed by the triangular wave form. The transient layer response for the step form electric field was observed. The layer response closely related with an electric field induced antiferroelectric to ferroelectric phase transition

Crystallization and preliminary X-ray analysis of a novel Kunitz-type kallikrein inhibitor from Bauhinia bauhinioides

International Nuclear Information System (INIS)

Navarro, Marcos Vicente de A. S.; Vierira, Débora F.; Nagem, Ronaldo A. P.; Araújo, Ana Paula U. de; Oliva, Maria Luiza V.; Garratt, Richard C.

2005-01-01

Crystallization and preliminary X-ray diffraction studies are reported for a novel Kunitz-type protease inhibitor from B. bauhinioides which contains no disulfide bridges. A Kunitz-type protease inhibitor (BbKI) found in Bauhinia bauhinioides seeds has been overexpressed in Escherichia coli and crystallized at 293 K using PEG 4000 as the precipitant. X-ray diffraction data have been collected to 1.87 Å resolution using an in-house X-ray generator. The crystals of the recombinant protein (rBbKI) belong to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 46.70, b = 64.14, c = 59.24 Å. Calculation of the Matthews coefficient suggests the presence of one monomer of rBbKI in the asymmetric unit, with a corresponding solvent content of 51% (V M = 2.5 Å 3 Da −1 ). Iodinated crystals were prepared and a derivative data set was also collected at 2.1 Å resolution. Crystals soaked for a few seconds in a cryogenic solution containing 0.5 M NaI were found to be reasonably isomorphous to the native crystals. Furthermore, the presence of iodide anions could be confirmed in the NaI-derivatized crystal. Data sets from native and derivative crystals are being evaluated for use in crystal structure determination by means of the SIRAS (single isomorphous replacement with anomalous scattering) method

Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals.

Science.gov (United States)

Awel, Salah; Kirian, Richard A; Wiedorn, Max O; Beyerlein, Kenneth R; Roth, Nils; Horke, Daniel A; Oberthür, Dominik; Knoska, Juraj; Mariani, Valerio; Morgan, Andrew; Adriano, Luigi; Tolstikova, Alexandra; Xavier, P Lourdu; Yefanov, Oleksandr; Aquila, Andrew; Barty, Anton; Roy-Chowdhury, Shatabdi; Hunter, Mark S; James, Daniel; Robinson, Joseph S; Weierstall, Uwe; Rode, Andrei V; Bajt, Saša; Küpper, Jochen; Chapman, Henry N

2018-02-01

High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.

Preparation of single-crystal copper ferrite nanorods and nanodisks

International Nuclear Information System (INIS)

Du Jimin; Liu Zhimin; Wu Weize; Li Zhonghao; Han Buxing; Huang Ying

2005-01-01

This article, for the first time, reports the preparation of single-crystal copper ferrite nanorods and nanodisks. Using amorphous copper ferrite nanoparticles synthesized by reverse micelle as reaction precursor, single-crystal copper ferrite nanorods were synthesized via hydrothermal method in the presence of surfactant polyethylene glycol (PEG), however, copper ferrite nanodisks were prepared through the same procedures except the surfactant PEG. The resulting nanomaterials have been characterized by powder X-ray diffraction (XRD), selected electron area diffraction (SEAD), and transmission electron microscopy (TEM). The bulk composition of the samples was determined by means of X-ray photoelectron spectroscopy (XPS)

Preliminary X-ray analysis of twinned crystals of sarcosine dimethylglycine methyltransferase from Halorhodospira halochoris

International Nuclear Information System (INIS)

Kallio, Juha Pekka; Jänis, Janne; Nyyssölä, Antti; Hakulinen, Nina; Rouvinen, Juha

2009-01-01

The crystallization and preliminary X-ray diffraction analysis of sarcosine dimethylglycine methyltransferase from H. halochoris is reported. Sarcosine dimethylglycine methyltransferase (EC 2.1.1.157) is an enzyme from the extremely halophilic anaerobic bacterium Halorhodospira halochoris. This enzyme catalyzes the twofold methylation of sarcosine to betaine, with S-adenosylmethionine (AdoMet) as the methyl-group donor. This study presents the crystallization and preliminary X-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in Escherichia coli. Mass spectroscopy was used to determine the purity and homogeneity of the enzyme material. Two different crystal forms, which initially appeared to be hexagonal and tetragonal, were obtained. However, on analyzing the diffraction data it was discovered that both crystal forms were pseudo-merohedrally twinned. The true crystal systems were monoclinic and orthorhombic. The monoclinic crystal diffracted to a maximum of 2.15 Å resolution and the orthorhombic crystal diffracted to 1.8 Å resolution

Crystallization and preliminary X-ray diffraction data of an LNA 7-mer duplex derived from a ricin aptamer

International Nuclear Information System (INIS)

Förster, Charlotte; Oberthuer, Dominik; Gao, Jiang; Eichert, André; Quast, Frederick G.; Betzel, Christian; Nitsche, Andreas; Erdmann, Volker A.; Fürste, Jens P.

2009-01-01

An all-LNA duplex was designed from the stem region of an RNA aptamer which has been generated against ricin. The LNA duplex was crystallized and preliminary X-ray diffraction analysis revealed diffraction to a resolution of up to 2.8 Å. Locked nucleic acids (LNAs) are modified nucleic acids which contain a modified sugar such as β-d-2′-O,4′-C methylene-bridged ribofuranose or other sugar derivatives in LNA analogues. The β-d-2′-O,4′-C methylene ribofuranose LNAs in particular possess high stability and melting temperatures, which makes them of interest for stabilizing the structure of different nucleic acids. Aptamers, which are DNAs or RNAs targeted against specific ligands, are candidates for substitution with LNAs in order to increase their stability. A 7-mer helix derived from the terminal part of an aptamer that was targeted against ricin was chosen. The ricin aptamer originally consisted of natural RNA building blocks and showed high affinity in ricin binding. For future stabilization of the aptamer, the terminal helix has been constructed as an ‘all-locked’ LNA and was successfully crystallized in order to investigate its structural properties. Optimization of crystal growth succeeded by the use of different metal salts as additives, such as CuCl 2 , MgCl 2 , MnCl 2 , CaCl 2 , CoCl 2 and ZnSO 4 . Preliminary X-ray diffraction data were collected and processed to 2.8 Å resolution. The LNA crystallized in space group P6 5 , with unit-cell parameters a = 50.11, b = 50.11, c = 40.72 Å. The crystals contained one LNA helix per asymmetric unit with a Matthews coefficient of 3.17 Å 3 Da −1 , which implies a solvent content of 70.15%

The Crystal Structure of the Malaria Pigment Hemozoin as Elucidated by X-ray Powder Diffraction

DEFF Research Database (Denmark)

Straasø, Tine

survival. Successful inhibition of hemozoin crystallization will lead to parasitic death and thus break the cycle. The aim of this thesis is to elucidate the structure of hemozoin by means of X-ray diffraction techniques. Knowledge of the structure will help facilitate intelligent drug design in the future....... As part of the project an all-in-vacuum powder diffractometer was developed, which provides data with a minimum background level and an improved signal-to-noise ratio. Moreover, the diffractometer is designed with the particular purpose of decreasing the number of parameters to be fitted. Installation...

Purification, crystallization and X-ray diffraction analysis of a novel ring-cleaving enzyme (BoxCC) from Burkholderia xenovorans LB400

International Nuclear Information System (INIS)

Bains, Jasleen; Boulanger, Martin J.

2008-01-01

Preliminary X-ray diffraction studies of a novel ring-cleaving enzyme from B. xenovorans LB400 encoded by the benzoate-oxidation (box) pathway. The assimilation of aromatic compounds by microbial species requires specialized enzymes to cleave the thermodynamically stable ring. In the recently discovered benzoate-oxidation (box) pathway in Burkholderia xenovorans LB400, this is accomplished by a novel dihydrodiol lyase (BoxC C ). Sequence analysis suggests that BoxC C is part of the crotonase superfamily but includes an additional uncharacterized region of approximately 115 residues that is predicted to mediate ring cleavage. Processing of X-ray diffraction data to 1.5 Å resolution revealed that BoxC C crystallized with two molecules in the asymmetric unit of the P2 1 2 1 2 1 space group, with a solvent content of 47% and a Matthews coefficient of 2.32 Å 3 Da −1 . Selenomethionine BoxC C has been purified and crystals are currently being refined for anomalous dispersion studies

Purification, crystallization and preliminary X-ray diffraction experiments on the breakage-reunion domain of the DNA gyrase from Mycobacterium tuberculosis

International Nuclear Information System (INIS)

Piton, Jérémie; Matrat, Stéphanie; Petrella, Stéphanie; Jarlier, Vincent; Aubry, Alexandra; Mayer, Claudine

2009-01-01

The breakage-reunion domain of M. tuberculosis DNA gyrase was crystallized using the hanging-drop vapour-diffusion method. One of the four crystal forms obtained belonged to space group C2 and diffraction data were collected to a resolution of 2.7 Å. Mycobacterium tuberculosis DNA gyrase, a nanomachine that is involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and hence is the sole target for fluoroquinolone action. The breakage-reunion domain of the A subunit plays an essential role in DNA binding during the catalytic cycle. Two constructs of 53 and 57 kDa (termed GA53BK and GA57BK) corresponding to this domain have been overproduced, purified and crystallized. Diffraction data were collected from four crystal forms. The resolution limits ranged from 4.6 to 2.7 Å depending on the crystal form. The best diffracting crystals belonged to space group C2, with a biological dimer in the asymmetric unit. This is the first report of the crystallization and preliminary X-ray diffraction analysis of the breakage-reunion domain of DNA gyrase from a species containing one unique type II topoisomerase

Electrochemical cell for in situ x-ray diffraction under ultrapure conditions

DEFF Research Database (Denmark)

Koop, T.; Schindler, W.; Kazimirov, A.

1998-01-01

within a few seconds. The oxygen level in the electrolyte is reduced by continuous N(2) flow to less than 0.2% compared to that of a fresh electrolyte. This can be done while rotating the cell by 360 degrees about the surface normal. The electrode potential is accurately measured at the position......An electrochemical cell has been developed for in situ x-ray diffraction from a working electrode under clean conditions equivalent to ultrahigh vacuum conditions of 5 x 10(-10) mbar. The substrate crystals can be prepared ex situ and transferred into the cell under protection of ultrapure water...... of the crystal using a Luggin capillary and a standard reference electrode. We demonstrate the performance of our cell by in situ synchrotron x-ray diffraction measurements on ultrathin Co layers electrodeposited on Cu(001) in an aqueous H(2)SO(4)/CoSO(4) solution. (C) 1998 American Institute of Physics....

Evaluation of In-Vacuum Imaging Plate Detector for X-Ray Diffraction Microscopy

International Nuclear Information System (INIS)

Nishino, Yoshinori; Takahashi, Yukio; Yamamoto, Masaki; Ishikawa, Tetsuya

2007-01-01

We performed evaluation tests of a newly developed in-vacuum imaging plate (IP) detector for x-ray diffraction microscopy. IP detectors have advantages over direct x-ray detection charge-coupled device (CCD) detectors, which have been commonly used in x-ray diffraction microscopy experiments, in the capabilities for a high photon count and for a wide area. The detector system contains two IPs to make measurement efficient by recording data with the one while reading or erasing the other. We compared speckled diffraction patterns of single particles taken with the IP and a direct x-ray detection CCD. The IP was inferior to the CCD in spatial resolution and in signal-to-noise ratio at a low photon count

Synthesis, structural, X-ray photoelectron spectroscopy (XPS) studies and IR induced anisotropy of Tl{sub 4}HgI{sub 6} single crystals

Energy Technology Data Exchange (ETDEWEB)

Parasyuk, O.V. [Department of Inorganic and Physical Chemistry, Lesya Ukrainka Eastern European National University, Voli Ave. 13, Lutsk, 43025 (Ukraine); Khyzhun, O.Y. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky St., 03142, Kyiv (Ukraine); Piasecki, M. [Institute of Physics, J. Dlugosz University Częstochowa, Armii Krajowej 13/15, Częstochowa (Poland); Kityk, I.V., E-mail: iwank74@gmail.com [Electrical Engineering Department, Czestochowa University Technology, Armii Krajowej 17, PL-42-217, Czestochowa (Poland); Lakshminarayana, G. [Wireless and Photonic Networks Research Centre, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor (Malaysia); Luzhnyi, I. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky St., 03142, Kyiv (Ukraine); Fochuk, P.M. [Yuriy Fed’kovych Chernivtsi National University, 2 Kotziubynskoho Str., 58012, Chernivtsi (Ukraine); Fedorchuk, A.O. [Department of Inorganic and Organic Chemistry, Lviv National University of Veterinary Medicine and Biotechnologies, Pekarska Street 50, 79010, Lviv (Ukraine); Levkovets, S.I.; Yurchenko, O.M.; Piskach, L.V. [Department of Inorganic and Physical Chemistry, Lesya Ukrainka Eastern European National University, Voli Ave. 13, Lutsk, 43025 (Ukraine)

2017-02-01

In the present work, we report on the synthesis and structural properties including X-ray protoelectron spectroscopy (XPS) analysis of Tl{sub 4}HgI{sub 6} crystals that were grown by Bridgman-Stockbarger method up to 80 mm in length and 18 mm in diameter. The existence of the ternary compound Tl{sub 4}HgI{sub 6} that melts incongruently at 641 K was confirmed. Phase equilibria and structural properties for the TlI–HgI{sub 2} system were investigated by differential thermal analysis (DTA) and X-ray diffraction (XRD) methods. X-ray photoelectron spectra were measured for both pristine and Ar{sup +} ion-bombarded Tl{sub 4}HgI{sub 6} single crystal surfaces. The data reveal that the Tl{sub 4}HgI{sub 6} single crystal is sensitive with respect to Ar{sup +} ion-bombardment as 3.0 keV Ar{sup +} irradiation over 5 min at an ion current density 14 μA/cm{sup 2} induces changes to the elemental stoichiometry of the Tl{sub 4}HgI{sub 6} surface, leading to a decrease of the mercury content in the topmost surface layers. X-ray photoelectron spectroscopy (XPS) measurements indicate very low hygroscopic nature of the Tl{sub 4}HgI{sub 6} single crystal surface. The IR coherent bicolor laser treatment at wavelengths 10.6/5.3 μm has shown an occurrence of anisotropy at wavelengths 1540 nm of Er:glass laser. This may open the applications of Tl{sub 4}HgI{sub 6} as a material for IR laser triggering. - Highlights: • Phase diagram of the HgI{sub 2}–TlI system was built. • Tl{sub 4}HgI{sub 6} single crystals were grown by Bridgman Stockbarger method. • XRD, XPS analysis was done. • Ir induced anisotropy was established. • The compounds may be proposed as Ir laser operated polarizers.

Crystallization and preliminary X-ray diffraction analysis of a cold-adapted catalase from Vibrio salmonicida

International Nuclear Information System (INIS)

Riise, Ellen Kristin; Lorentzen, Marit Sjo; Helland, Ronny; Willassen, Nils Peder

2005-01-01

Monoclinic (P2 1 ) crystals of a His-tagged form of V. salmonicida catalase without cofactor diffract X-rays to 1.96 Å. Catalase (EC 1.11.1.6) catalyses the breakdown of hydrogen peroxide to water and molecular oxygen. Recombinant Vibrio salmonicida catalase (VSC) possesses typical cold-adapted features, with higher catalytic efficiency, lower thermal stability and a lower temperature optimum than its mesophilic counterpart from Proteus mirabilis. Crystals of VSC were produced by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. The crystals belong to the monoclinic space group P2 1 , with unit-cell parameters a = 98.15, b = 217.76, c = 99.28 Å, β = 110.48°. Data were collected to 1.96 Å and a molecular-replacement solution was found with eight molecules in the asymmetric unit

Crystallization and preliminary X-ray diffraction analysis of a cold-adapted catalase from Vibrio salmonicida

Energy Technology Data Exchange (ETDEWEB)

Riise, Ellen Kristin [The Norwegian Structural Biology Centre, Faculty of Science, University of Tromsø, N-9037 Tromsø (Norway); Lorentzen, Marit Sjo [Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø (Norway); Helland, Ronny [The Norwegian Structural Biology Centre, Faculty of Science, University of Tromsø, N-9037 Tromsø (Norway); Willassen, Nils Peder, E-mail: nilspw@fagmed.uit.no [The Norwegian Structural Biology Centre, Faculty of Science, University of Tromsø, N-9037 Tromsø (Norway); Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø (Norway)

2006-01-01

Monoclinic (P2{sub 1}) crystals of a His-tagged form of V. salmonicida catalase without cofactor diffract X-rays to 1.96 Å. Catalase (EC 1.11.1.6) catalyses the breakdown of hydrogen peroxide to water and molecular oxygen. Recombinant Vibrio salmonicida catalase (VSC) possesses typical cold-adapted features, with higher catalytic efficiency, lower thermal stability and a lower temperature optimum than its mesophilic counterpart from Proteus mirabilis. Crystals of VSC were produced by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. The crystals belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 98.15, b = 217.76, c = 99.28 Å, β = 110.48°. Data were collected to 1.96 Å and a molecular-replacement solution was found with eight molecules in the asymmetric unit.

Cs2AgBiBr6 single-crystal X-ray detectors with a low detection limit

Science.gov (United States)

Pan, Weicheng; Wu, Haodi; Luo, Jiajun; Deng, Zhenzhou; Ge, Cong; Chen, Chao; Jiang, Xiaowei; Yin, Wan-Jian; Niu, Guangda; Zhu, Lujun; Yin, Lixiao; Zhou, Ying; Xie, Qingguo; Ke, Xiaoxing; Sui, Manling; Tang, Jiang

2017-11-01

Sensitive X-ray detection is crucial for medical diagnosis, industrial inspection and scientific research. The recently described hybrid lead halide perovskites have demonstrated low-cost fabrication and outstanding performance for direct X-ray detection, but they all contain toxic Pb in a soluble form. Here, we report sensitive X-ray detectors using solution-processed double perovskite Cs2AgBiBr6 single crystals. Through thermal annealing and surface treatment, we largely eliminate Ag+/Bi3+ disordering and improve the crystal resistivity, resulting in a detector with a minimum detectable dose rate as low as 59.7 nGyair s-1, comparable to the latest record of 0.036 μGyair s-1 using CH3NH3PbBr3 single crystals. Suppressed ion migration in Cs2AgBiBr6 permits relatively large external bias, guaranteeing efficient charge collection without a substantial increase in noise current and thus enabling the low detection limit.

Structural investigation of GaInP nanowires using X-ray diffraction

DEFF Research Database (Denmark)

Kriegner, D.; Persson, Johan Mikael; Etzelstorfer, T.

2013-01-01

In this work the structure of ternary GaxIn1−xP nanowires is investigated with respect to the chemical composition and homogeneity. The nanowires were grown by metal–organic vapor-phase epitaxy. For the investigation of ensemble fluctuations on several lateral length scales, X-ray diffraction...... gradients along the sample by recording diffraction patterns at different positions. In addition, compositional variations were found also within single nanowires in X-ray energy dispersive spectroscopy measurements....

Crystallization and preliminary X-ray diffraction analysis of the carbohydrate-recognizing domain (VP8*) of bovine rotavirus strain NCDV

International Nuclear Information System (INIS)

Yu, Xing; Guillon, Annabel; Szyczew, Alex J.; Kiefel, Milton J.; Coulson, Barbara S.; Itzstein, Mark von; Blanchard, Helen

2008-01-01

NCDV VP8* 64–224 was expressed in E. coli, purified and crystallized in the presence of a sialic acid derivative. X-ray diffraction data were obtained to a resolution of 2.0 Å and the crystallographic structure was determined by molecular replacement. The infectivity of rotavirus is dramatically enhanced by proteolytic cleavage of its outer layer VP4 spike protein into two functional domains, VP8* and VP5*. The carbohydrate-recognizing domain VP8* is proposed to bind sialic acid-containing host cell-surface glycans and this is followed by a series of subsequent virus–cell interactions. Live attenuated human and bovine rotavirus vaccine candidates for the prevention of gastroenteritis have been derived from bovine rotavirus strain NCDV. The NCDV VP8* 64–224 was overexpressed, purified to homogeneity and crystallized in the presence of an N-acetylneuraminic acid derivative. X-ray diffraction data were collected to a resolution of 2.0 Å and the crystallographic structure of NCDV VP8* 64–224 was determined by molecular replacement

Cloning, purification, crystallization and preliminary X-ray diffraction studies of Escherichia coli PapD-like protein (EcpD)

International Nuclear Information System (INIS)

Pandey, Nishant Kumar; Pal, Ravi Kant; Kashyap, Maruthi; Bhavesh, Neel Sarovar

2012-01-01

The Escherichia coli PapD-like protein (EcpD), from uropathogenic Escherichia coli (UPEC), which is a periplasmic chaperon of Yad fimbriae was cloned, overexpressed, purified and crystallized. The crystals obtained diffracted X-rays to 1.67 Å resolution and belonged to space group C222 1 . Many Gram-negative bacteria are characterized by hair-like proteinaceous appendages on their surface known as fimbriae. In uropathogenic strains of Escherichia coli, fimbriae mediate attachment by binding to receptors on the host cell, often contributing to virulence and disease. E. coli PapD-like protein (EcpD) is a periplasmic chaperone that plays an important role in the proper folding and guiding of Yad fimbrial proteins to the outer membrane usher protein in a process known as pilus biogenesis. EcpD is essential for pilus biogenesis in uropathogenic E. coli and plays an important role in virulence. In the present study, EcpD was cloned, overexpressed, purified and crystallized by the hanging-drop vapour-diffusion method. The crystals diffracted to 1.67 Å resolution and belonged to the orthorhombic space group C222 1 , with unit-cell parameters a = 100.3, b = 127.6, c = 45.9 Å. There was a single molecule in the asymmetric unit and the corresponding Matthews coefficient was calculated to be 3.02 Å 3 Da −1 , with 59% solvent content. Initial phases were determined by molecular replacement

Expression, purification, crystallization and preliminary X-ray diffraction analysis of the aspartate transcarbamoylase domain of human CAD

International Nuclear Information System (INIS)

Ruiz-Ramos, Alba; Lallous, Nada; Grande-García, Araceli; Ramón-Maiques, Santiago

2013-01-01

The recombinant aspartate transcarbamoylase domain of human CAD was expressed in E. coli, purified and crystallized in the presence and absence of the inhibitor PALA. X-ray diffraction data sets were collected for both crystal forms at 2.1 Å resolution. Aspartate transcarbamoylase (ATCase) catalyzes the synthesis of N-carbamoyl-l-aspartate from carbamoyl phosphate and aspartate in the second step of the de novo biosynthesis of pyrimidines. In prokaryotes, the first three activities of the pathway, namely carbamoyl phosphate synthetase (CPSase), ATCase and dihydroorotase (DHOase), are encoded as distinct proteins that function independently or in noncovalent association. In animals, CPSase, ATCase and DHOase are part of a 243 kDa multifunctional polypeptide named CAD. Up-regulation of CAD is essential for normal and tumour cell proliferation. Although the structures of numerous prokaryotic ATCases have been determined, there is no structural information about any eukaryotic ATCase. In fact, the only detailed structural information about CAD is that it self-assembles into hexamers and trimers through interactions of the ATCase domains. Here, the expression, purification and crystallization of the ATCase domain of human CAD is reported. The recombinant protein, which was expressed in bacteria and purified with good yield, formed homotrimers in solution. Crystallization experiments both in the absence and in the presence of the inhibitor PALA yielded small crystals that diffracted X-rays to 2.1 Å resolution using synchrotron radiation. The crystals appeared to belong to the hexagonal space group P6 3 22, and Matthews coefficient calculation indicated the presence of one ATCase subunit per asymmetric unit, with a solvent content of 48%. However, analysis of the intensity statistics suggests a special case of the P2 1 lattice with pseudo-symmetry and possibly twinning

Measurement of X-ray beam emittance using crystal optics at an X-ray undulator beamline

International Nuclear Information System (INIS)

Kohmura, Yoshiki; Suzuki, Yoshio; Awaji, Mitsuhiro; Tanaka, Takashi; Hara, Toru; Goto, Shunji; Ishikawa, Tetsuya

2000-01-01

We present a method of using crystal optics to measure the emittance of the X-ray source. Two perfect crystals set in (++) configuration work as a high-resolution collimator. The phase-space diagram (i.e. beam cross-section and angular distribution) could be determined without any assumptions on the light source. When the measurement is done at short wavelength radiation from undulator, the electron beam emittance is larger than the diffraction limit of the X-rays. Therefore, the electron beam emittance could be estimated. The measurement was done with the hard X-rays of 18.5 and 55 keV from an undulator beamline, BL 47XU, of SPring-8. The horizontal emittance of the X-ray beam was estimated to be about 7.6 nmrad, close to the designed electron beam emittance of the storage ring (7 nmrad). Some portions of the instrumental functions, such as the scattering by filters and windows along the beamline and the slight bent of the crystal planes of the monochromator, could not be precisely evaluated, but an upper limit for the vertical emittance of the electron beam could be obtained as 0.14 nmrad

Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C

International Nuclear Information System (INIS)

Orville, A.M.; Buono, R.; Cowan, M.; Heroux, A.; Shea-McCarthy, G.; Schneider, D.K.; Skinner, J.M.; Skinner, M.J.; Stoner-Ma, D.; Sweet, R.M.

2011-01-01

The research philosophy and new capabilities installed at NSLS beamline X26-C to support electronic absorption and Raman spectroscopies coupled with X-ray diffraction are reviewed. This beamline is dedicated full time to multidisciplinary studies with goals that include revealing the relationship between the electronic and atomic structures in macromolecules. The beamline instrumentation has been fully integrated such that optical absorption spectra and X-ray diffraction images are interlaced. Therefore, optical changes induced by X-ray exposure can be correlated with X-ray diffraction data collection. The installation of Raman spectroscopy into the beamline is also briefly reviewed. Data are now routinely generated almost simultaneously from three complementary types of experiments from the same sample. The beamline is available now to the NSLS general user population.

X-ray diffraction and measurement of residual stresses

International Nuclear Information System (INIS)

Maeder, G.; Lebrun, J.L.; Corcaud, L.

1977-01-01

X-ray diffraction technique is a non destructive method for measuring the residual stresses in mechanical parts. This method, called sin 2 PSI method is investigated. It is applied to the measurement of elastic constants in different directions of crystals of Zr alloy (Zircaloy 4) and Ti alloy (TA6V). Stresses in TA6V sheets welded by TIG and electron beam processes are also studied [fr

Crystal structure investigations on cation-substituted alums by X-ray and neutron diffraction

International Nuclear Information System (INIS)

Abdeen, A.M.

1980-04-01

The crystal structures of the three alums: NH 4 Al(SO 4 ) 2 .12H 2 O, (NH 3 CH 3 )Al(SO 4 ) 2 .12H 2 O and (NH 3 OH)Al(SO 4 ) 2 .12H 2 O have been determined from three-dimensional neutron diffraction data enhanced by X-ray diffraction when necessary. These compounds crystallize cubic in space group Pa3. The structures of the three alums exhibit partial occupancies of crystallographic sites for the NH 4 , (NH 3 CH 3 ) and (NH 3 OH) group atoms. This can be explained by a quantized rotation of the three groups around an axis perpendicular to the [111] direction. Some of the (SO 4 ) 2- groups in the NH 4 -alum are disordered with about 17% of the sulfate tetrahedra being in a reversed orientation around the sulfur atom. The disorder in (NH 3 CH 3 ) and (NH 3 OH)-alums is only 4,3% and 3.0% respectively. The atoms in the alum structures are held together by a system of hydrogen bonds between the water molecules and between the water molecules and the sulfate oxygen atoms. In these three structures there is a strong indication that shorter hydrogen bonds tend to be nearly linear. (orig.)

X-ray Absorption and Diffraction Studies of the Mixed-phase State of (CrxV1-x)2O3

Energy Technology Data Exchange (ETDEWEB)

D Pease; A Frenkel; V Krayzman; T Huang; P Shanthakumar; J Budnick; P Metcalf; F Chudnovsky; E Stern

2011-12-31

X-ray diffraction and vanadium x-ray absorption near-edge structure (XANES) data have been obtained for (V{sub 1-x}Cr{sub x}){sub 2}O{sub 3} samples containing several concentrations of Cr, crossing the metal-insulator transition boundary. For single-phase single-crystal samples our theoretical results are generally in good qualitative agreement with our experimental single-crystal XANES, for both crystal orientations relative to the incident-beam electric vector. However, an anomalous peak occurs for both orientations in the K pre-edge of the single-crystal sample containing 1.2% Cr, a paramagnetic insulator sample that is in the concentration regime corresponding to the room-temperature two-phase (coexistence) region of the phase diagram. Upon increasing the temperature of the 0.4% Cr powdered material to 400 K so that one enters the two-phase region of the phase diagram, a similar peak appears and then diminishes at 600 K. These results, as well as experiments done by others involving room-temperature and low-temperature XANES of a 1.1% Cr sample, suggest that this feature in the V pre-edge structure is associated with the appearance under some circumstances of a small amount of highly distorted VO{sub 6} octahedra in the interface region between coexisting metal and insulating phases. Finally, we find that, for the two-phase regime, the concentration ratio of the metal-to-insulating phase varies between different regions from a sample batch of uniform composition made by the skull melting method.

A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals

International Nuclear Information System (INIS)

Nederlof, Igor; Genderen, Eric van; Li, Yao-Wang; Abrahams, Jan Pieter

2013-01-01

An ultrasensitive Medipix2 detector allowed the collection of rotation electron-diffraction data from single three-dimensional protein nanocrystals for the first time. The data could be analysed using the standard X-ray crystallography programs MOSFLM and SCALA. When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irrespective of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e − Å −2 ), a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resolution, indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that volumes of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-analysis software (MOSFLM and SCALA) from X-ray protein crystallography can be used in principle for analysing electron-diffraction data from three-dimensional nanocrystals of proteins

I19, the small-molecule single-crystal diffraction beamline at Diamond Light Source.

Science.gov (United States)

Nowell, Harriott; Barnett, Sarah A; Christensen, Kirsten E; Teat, Simon J; Allan, David R

2012-05-01

The dedicated small-molecule single-crystal X-ray diffraction beamline (I19) at Diamond Light Source has been operational and supporting users for over three years. I19 is a high-flux tunable-wavelength beamline and its key details are described in this article. Much of the work performed on the beamline involves structure determination from small and weakly diffracting crystals. Other experiments that have been supported to date include structural studies at high pressure, studies of metastable species, variable-temperature crystallography, studies involving gas exchange in porous materials and structural characterizations that require analysis of the diffuse scattering between Bragg reflections. A range of sample environments to facilitate crystallographic studies under non-ambient conditions are available as well as a number of options for automation. An indication of the scope of the science carried out on the beamline is provided by the range of highlights selected for this paper.

X-ray diffraction investigation of spin reorientation in SmFe2

International Nuclear Information System (INIS)

Gaviko, V.S.; Korolyov, A.V.; Mushnikov, N.V.

1996-01-01

Spontaneous magnetoelastic crystal lattice distortions in the spin reorientation region of high magnetostrictive SmFe 2 have been investigated by X-ray diffraction in the temperature range 80-300 K. Comparison of experimental shapes of X-ray diffraction lines with calculated shapes shows that, in the region of the spin reorientation transition, a mixture of left angle 110 right angle and left angle 111 right angle phases rather than the angular left angle uuw right angle -type phase is realized. The temperature dependence of the relative volume content of left angle 110 right angle and left angle 111 right angle phases is determined using least-squares fitting. (orig.)

Instrument and method for X-ray diffraction, fluorescence, and crystal texture analysis without sample preparation

Science.gov (United States)

Gendreau, Keith (Inventor); Martins, Jose Vanderlei (Inventor); Arzoumanian, Zaven (Inventor)

2010-01-01

An X-ray diffraction and X-ray fluorescence instrument for analyzing samples having no sample preparation includes a X-ray source configured to output a collimated X-ray beam comprising a continuum spectrum of X-rays to a predetermined coordinate and a photon-counting X-ray imaging spectrometer disposed to receive X-rays output from an unprepared sample disposed at the predetermined coordinate upon exposure of the unprepared sample to the collimated X-ray beam. The X-ray source and the photon-counting X-ray imaging spectrometer are arranged in a reflection geometry relative to the predetermined coordinate.