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

Directory of Open Access Journals (Sweden)

Jasper J. van Thor

2015-01-01

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

Simultaneous X-ray diffraction from multiple single crystals of macromolecules

DEFF Research Database (Denmark)

Paithankar, Karthik S.; Sørensen, Henning Osholm; Wright, Jonathan P.

2011-01-01

The potential in macromolecular crystallography for using multiple crystals to collect X-ray diffraction data simultaneously from assemblies of up to seven crystals is explored. The basic features of the algorithms used to extract data and their practical implementation are described. The procedure...

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.

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.

A readout system for X-ray powder crystallography

CERN Document Server

Loukas, D; Pavlidis, A; Karvelas, E; Psycharis, K; Misiakos, V; Mousa, J; Dre, C

2000-01-01

A system for capturing and processing data, from radiation detectors, in the field of X-ray crystallography has been developed. The system includes a custom-made mixed analog-digital 16-channel VLSI circuit in 50 mu m pitch. Each channel comprises a charge amplifier, a shaper, a comparator and a 21-bit counter. The circuit can be scaled in a daisy chain configuration. Data acquisition is performed with a custom made PCI card while the control software is developed with Visual C++ under the MS Windows NT environment. Performance of a fully operational system, in terms of electronic noise, statistical variations and data capture speed is presented. The noise level permits counting of X-rays down to 8 keV while the counting capability is in excess of 200 kHz. The system is intended for X-ray crystallography with silicon detectors.

Polycapillary x-ray optics for macromolecular crystallography

International Nuclear Information System (INIS)

Owens, S.M.; Gibson, W.M.; Carter, D.C.; Sisk, R.C.; Ho, J.X.

1996-01-01

Polycapillary x-ray optics have found potential application in many different fields, including antiscatter and magnification in mammography, radiography, x-ray fluorescence, x-ray lithography, and x-ray diffraction techniques. In x-ray diffraction, an optic is used to collect divergent x-rays from a point source and redirect them into a quasi-parallel, or slightly focused beam. Monolithic polycapillary optics have been developed recently for macromolecular crystallography and have already shown considerable gains in diffracted beam intensity over pinhole collimation. Development is being pursued through a series of simulations and prototype optics. Many improvements have been made over the stage 1 prototype reported previously, which include better control over the manufacturing process, reducing the diameter of the output beam, and addition of a slight focusing at the output of the optic to further increase x-ray flux at the sample. The authors report the characteristics and performance of the stage 1 and stage 2 optics

Structure determination by X-ray crystallography

CERN Document Server

Ladd, M F C

1995-01-01

X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

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

International Nuclear Information System (INIS)

Huang, Chia-Ying; Olieric, Vincent; Ma, Pikyee; Panepucci, Ezequiel; Diederichs, Kay; Wang, Meitian; Caffrey, Martin

2015-01-01

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

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

Directory of Open Access Journals (Sweden)

Sam Horrell

2016-07-01

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

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

OpenAIRE

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

2013-01-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolec...

Solvent minimization induces preferential orientation and crystal clustering in serial micro-crystallography on micro-meshes, in situ plates and on a movable crystal conveyor belt.

Science.gov (United States)

Soares, Alexei S; Mullen, Jeffrey D; Parekh, Ruchi M; McCarthy, Grace S; Roessler, Christian G; Jackimowicz, Rick; Skinner, John M; Orville, Allen M; Allaire, Marc; Sweet, Robert M

2014-11-01

X-ray diffraction data were obtained at the National Synchrotron Light Source from insulin and lysozyme crystals that were densely deposited on three types of surfaces suitable for serial micro-crystallography: MiTeGen MicroMeshes™, Greiner Bio-One Ltd in situ micro-plates, and a moving kapton crystal conveyor belt that is used to deliver crystals directly into the X-ray beam. 6° wedges of data were taken from ∼100 crystals mounted on each material, and these individual data sets were merged to form nine complete data sets (six from insulin crystals and three from lysozyme crystals). Insulin crystals have a parallelepiped habit with an extended flat face that preferentially aligned with the mounting surfaces, impacting the data collection strategy and the design of the serial crystallography apparatus. Lysozyme crystals had a cuboidal habit and showed no preferential orientation. Preferential orientation occluded regions of reciprocal space when the X-ray beam was incident normal to the data-collection medium surface, requiring a second pass of data collection with the apparatus inclined away from the orthogonal. In addition, crystals measuring less than 20 µm were observed to clump together into clusters of crystals. Clustering required that the X-ray beam be adjusted to match the crystal size to prevent overlapping diffraction patterns. No additional problems were encountered with the serial crystallography strategy of combining small randomly oriented wedges of data from a large number of specimens. High-quality data able to support a realistic molecular replacement solution were readily obtained from both crystal types using all three serial crystallography strategies.

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

Science.gov (United States)

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

2014-07-17

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

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

Science.gov (United States)

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

2010-01-01

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

Solvent minimization induces preferential orientation and crystal clustering in serial micro-crystallography on micro-meshes, in situ plates and on a movable crystal conveyor belt

Energy Technology Data Exchange (ETDEWEB)

Soares, Alexei S., E-mail: soares@bnl.gov [Brookhaven National Laboratory, Upton, NY 11973 (United States); Mullen, Jeffrey D. [Brookhaven National Laboratory, Upton, NY 11973 (United States); University of Oregon, Eugene, OR 97403-1274 (United States); Parekh, Ruchi M. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Suffolk County Community College, Selden, NY 11784 (United States); McCarthy, Grace S.; Roessler, Christian G.; Jackimowicz, Rick; Skinner, John M. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Orville, Allen M. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Brookhaven National Laboratory, Upton, NY 11973 (United States); Allaire, Marc [Brookhaven National Laboratory, Upton, NY 11973 (United States); Sweet, Robert M. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Brookhaven National Laboratory, Upton, NY 11973 (United States)

2014-10-09

Strategies are described for optimizing the signal-to-noise of diffraction data, and for combining data from multiple crystals. One challenge that must be overcome is the non-random orientation of crystals with respect to one another and with respect to the surface that supports them. X-ray diffraction data were obtained at the National Synchrotron Light Source from insulin and lysozyme crystals that were densely deposited on three types of surfaces suitable for serial micro-crystallography: MiTeGen MicroMeshes™, Greiner Bio-One Ltd in situ micro-plates, and a moving kapton crystal conveyor belt that is used to deliver crystals directly into the X-ray beam. 6° wedges of data were taken from ∼100 crystals mounted on each material, and these individual data sets were merged to form nine complete data sets (six from insulin crystals and three from lysozyme crystals). Insulin crystals have a parallelepiped habit with an extended flat face that preferentially aligned with the mounting surfaces, impacting the data collection strategy and the design of the serial crystallography apparatus. Lysozyme crystals had a cuboidal habit and showed no preferential orientation. Preferential orientation occluded regions of reciprocal space when the X-ray beam was incident normal to the data-collection medium surface, requiring a second pass of data collection with the apparatus inclined away from the orthogonal. In addition, crystals measuring less than 20 µm were observed to clump together into clusters of crystals. Clustering required that the X-ray beam be adjusted to match the crystal size to prevent overlapping diffraction patterns. No additional problems were encountered with the serial crystallography strategy of combining small randomly oriented wedges of data from a large number of specimens. High-quality data able to support a realistic molecular replacement solution were readily obtained from both crystal types using all three serial crystallography strategies.

Solvent minimization induces preferential orientation and crystal clustering in serial micro-crystallography on micro-meshes, in situ plates and on a movable crystal conveyor belt

International Nuclear Information System (INIS)

Soares, Alexei S.; Mullen, Jeffrey D.; Parekh, Ruchi M.; McCarthy, Grace S.; Roessler, Christian G.; Jackimowicz, Rick; Skinner, John M.; Orville, Allen M.; Allaire, Marc; Sweet, Robert M.

2014-01-01

Strategies are described for optimizing the signal-to-noise of diffraction data, and for combining data from multiple crystals. One challenge that must be overcome is the non-random orientation of crystals with respect to one another and with respect to the surface that supports them. X-ray diffraction data were obtained at the National Synchrotron Light Source from insulin and lysozyme crystals that were densely deposited on three types of surfaces suitable for serial micro-crystallography: MiTeGen MicroMeshes™, Greiner Bio-One Ltd in situ micro-plates, and a moving kapton crystal conveyor belt that is used to deliver crystals directly into the X-ray beam. 6° wedges of data were taken from ∼100 crystals mounted on each material, and these individual data sets were merged to form nine complete data sets (six from insulin crystals and three from lysozyme crystals). Insulin crystals have a parallelepiped habit with an extended flat face that preferentially aligned with the mounting surfaces, impacting the data collection strategy and the design of the serial crystallography apparatus. Lysozyme crystals had a cuboidal habit and showed no preferential orientation. Preferential orientation occluded regions of reciprocal space when the X-ray beam was incident normal to the data-collection medium surface, requiring a second pass of data collection with the apparatus inclined away from the orthogonal. In addition, crystals measuring less than 20 µm were observed to clump together into clusters of crystals. Clustering required that the X-ray beam be adjusted to match the crystal size to prevent overlapping diffraction patterns. No additional problems were encountered with the serial crystallography strategy of combining small randomly oriented wedges of data from a large number of specimens. High-quality data able to support a realistic molecular replacement solution were readily obtained from both crystal types using all three serial crystallography strategies

The charm of protein crystals--Structural biology at a glance in the International Year of Crystallography

International Nuclear Information System (INIS)

Su Xiaodong; Cao Qin

2014-01-01

Crystallography is a typical intellectual endeavor that has spanned human history for centuries. Through the persistent efforts of generations of scientists, crystallography has been transformed from a mathematical hypothesis to actual physical reality, mainly thanks to X-ray diffraction technology. 2014 is celebrated as the International Year of Crystallography (IYCr-2014), to commemorate that about 100 years ago, when Max von Laue in Germany and the father-and-son Braggs (William Henry Bragg and William Lawrence Bragg) in England pioneered the use of X-rays to determine the atomic structure of crystals; for this pioneering work they were awarded Nobel prizes for physics in the years of 1914 and 1915. This article is dedicated to the IYCr to describe the use of protein crystals, an application that has developed into protein crystallography and subsequently structural biology. In our overview of the history and future prospects of this field, we discuss in detail one example of caspase-6, to demonstrate how protein crystallography can help us understand the structure-function relationship of important proteins. (authors)

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

Science.gov (United States)

Pinilla, Samuel; Poveda, Juan; Arguello, Henry

2018-03-01

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

Synthesis of new nano Schiff base complexes: X-ray crystallography ...

African Journals Online (AJOL)

This study presents synthesis and characterization of new nano uranyl Schiff base complexes. Electrochemistry of these complexes showed a quasireversible redox reaction without any successive reactions. Furthermore, X-ray crystallography exhibited that beside the coordination of tetradentate Schiff base, one solvent ...

The development of structural x-ray crystallography

Science.gov (United States)

Woolfson, M. M.

2018-03-01

From its birth in 1912, when only the simplest structures could be solved, x-ray structural crystallography is now able to solve macromolecular structures containing many thousands of independent non-hydrogen atoms. This progress has depended on, and been driven by, great technical advances in the development of powerful synchrotron x-ray sources, advanced automated equipment for the collection and storage of large data sets and powerful computers to deal with everything from data processing to running programmes employing complex algorithms for the automatic solution of structures. The sheer number of developments in the subject over the past century makes it impossible for this review to be exhaustive, but it will describe some major developments that will enable the reader to understand how the subject has grown from its humble beginnings to what it is today.

Novel organophosphorus compounds; synthesis, spectroscopy and X-ray crystallography

Czech Academy of Sciences Publication Activity Database

Shariatinia, Z.; Sohrabi, M.; Yousefi, M.; Kovaľ, Tomáš; Dušek, Michal

2012-01-01

Roč. 11, č. 2 (2012), s. 125-133 ISSN 1024-1221 Grant - others:AV ČR(CZ) AP0701 Program:Akademická prémie - Praemium Academiae Institutional research plan: CEZ:AV0Z10100521 Keywords : organophosphorus compounds * NMR * X-ray crystallography * hydrogen bond Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.686, year: 2012

CCD[charge-coupled device]-based synchrotron x-ray detector for protein crystallography: Performance projected from an experiment

International Nuclear Information System (INIS)

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

1986-01-01

The intense x radiation from a synchrotron source could, with a suitable detector, provide a complete set of diffraction images from a protein crystal before the crystal is damaged by radiation (2 to 3 min). An area detector consisting of a 40 mm dia. x-ray fluorescing phosphor, coupled with an image intensifier and lens to a CCD image sensor, was developed to determine the effectiveness of such a detector in protein crystallography. The detector was used in an experiment with a rotating anode x-ray generator. Diffraction patterns from a lysozyme crystal obtained with this detector are compared to those obtained with film. The two images appear to be virtually identical. The flux of 10 4 x-ray photons/s was observed on the detector at the rotating anode generator. At the 6-GeV synchrotron being designed at Argonne, the flux on an 80 x 80 mm 2 detector is expected to be >10 9 photons/s. The projected design of such a synchrotron detector shows that a diffraction-peak count >10 6 could be obtained in ∼0.5 s. With an additional ∼0.5 s readout time of a 512 x 512 pixel CCD, the data acquisition time per frame would be ∼1 s so that ninety 1 0 diffraction images could be obtained, with approximately 1% precision, in less than 3 min

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

Science.gov (United States)

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

2009-01-01

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

X-CHIP: an integrated platform for high-throughput protein crystallization and on-the-chip X-ray diffraction data collection

International Nuclear Information System (INIS)

Kisselman, Gera; Qiu, Wei; Romanov, Vladimir; Thompson, Christine M.; Lam, Robert; Battaile, Kevin P.; Pai, Emil F.; Chirgadze, Nickolay Y.

2011-01-01

The X-CHIP (X-ray Crystallography High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The X-CHIP (X-ray Crystallization High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The system has been designed for crystallization condition screening, visual crystal inspection, initial X-ray screening and data collection in a high-throughput fashion. X-ray diffraction data acquisition can be performed directly on-the-chip at room temperature using an in situ approach. The capabilities of the chip eliminate the necessity for manual crystal handling and cryoprotection of crystal samples, while allowing data collection from multiple crystals in the same drop. This technology would be especially beneficial for projects with large volumes of data, such as protein-complex studies and fragment-based screening. The platform employs hydrophilic and hydrophobic concentric ring surfaces on a miniature plate transparent to visible light and X-rays to create a well defined and stable microbatch crystallization environment. The results of crystallization and data-collection experiments demonstrate that high-quality well diffracting crystals can be grown and high-resolution diffraction data sets can be collected using this technology. Furthermore, the quality of a single-wavelength anomalous dispersion data set collected with the X-CHIP at room temperature was sufficient to generate interpretable electron-density maps. This technology is highly resource-efficient owing to the use of nanolitre-scale drop volumes. It does not require any modification for most in-house and synchrotron beamline systems and offers

X-CHIP: an integrated platform for high-throughput protein crystallization and on-the-chip X-ray diffraction data collection

Energy Technology Data Exchange (ETDEWEB)

Kisselman, Gera; Qiu, Wei; Romanov, Vladimir; Thompson, Christine M.; Lam, Robert [Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4 (Canada); Battaile, Kevin P. [Argonne National Laboratory, Argonne, Illinois 60439 (United States); Pai, Emil F.; Chirgadze, Nickolay Y., E-mail: nchirgad@uhnresearch.ca [Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4 (Canada); University of Toronto, Toronto, Ontario M5S 1A8 (Canada)

2011-06-01

The X-CHIP (X-ray Crystallography High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The X-CHIP (X-ray Crystallization High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The system has been designed for crystallization condition screening, visual crystal inspection, initial X-ray screening and data collection in a high-throughput fashion. X-ray diffraction data acquisition can be performed directly on-the-chip at room temperature using an in situ approach. The capabilities of the chip eliminate the necessity for manual crystal handling and cryoprotection of crystal samples, while allowing data collection from multiple crystals in the same drop. This technology would be especially beneficial for projects with large volumes of data, such as protein-complex studies and fragment-based screening. The platform employs hydrophilic and hydrophobic concentric ring surfaces on a miniature plate transparent to visible light and X-rays to create a well defined and stable microbatch crystallization environment. The results of crystallization and data-collection experiments demonstrate that high-quality well diffracting crystals can be grown and high-resolution diffraction data sets can be collected using this technology. Furthermore, the quality of a single-wavelength anomalous dispersion data set collected with the X-CHIP at room temperature was sufficient to generate interpretable electron-density maps. This technology is highly resource-efficient owing to the use of nanolitre-scale drop volumes. It does not require any modification for most in-house and synchrotron beamline systems and offers

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)

Synthesis, spectroscopy, X-ray crystallography, and DFT computations of nanosized phosphazenes

Czech Academy of Sciences Publication Activity Database

Shariatinia, Z.; Moghadam, E.J.; Maghsoudi, N.; Mousavi, H.S.M.; Dušek, Michal; Eigner, Václav

2015-01-01

Roč. 641, č. 5 (2015), s. 967-978 ISSN 0044-2313 Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : phosphazene * ultrasonic * nanoparticle * x-ray crystallography * DFT calculation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.261, year: 2015

The design of macromolecular crystallography diffraction experiments

International Nuclear Information System (INIS)

Evans, Gwyndaf; Axford, Danny; Owen, Robin L.

2011-01-01

Thoughts about the decisions made in designing macromolecular X-ray crystallography experiments at synchrotron beamlines are presented. The measurement of X-ray diffraction data from macromolecular crystals for the purpose of structure determination is the convergence of two processes: the preparation of diffraction-quality crystal samples on the one hand and the construction and optimization of an X-ray beamline and end station on the other. Like sample preparation, a macromolecular crystallography beamline is geared to obtaining the best possible diffraction measurements from crystals provided by the synchrotron user. This paper describes the thoughts behind an experiment that fully exploits both the sample and the beamline and how these map into everyday decisions that users can and should make when visiting a beamline with their most precious crystals

Protein crystal growth studies at the Center for Macromolecular Crystallography

International Nuclear Information System (INIS)

DeLucas, Lawrence J.; Long, Marianna M.; Moore, Karen M.; Harrington, Michael; McDonald, William T.; Smith, Craig D.; Bray, Terry; Lewis, Johanna; Crysel, William B.; Weise, Lance D.

2000-01-01

The Center for Macromolecular Crystallography (CMC) has been involved in fundamental studies of protein crystal growth (PCG) in microgravity and in our earth-based laboratories. A large group of co-investigators from academia and industry participated in these experiments by providing protein samples and by performing the x-ray crystallographic analysis. These studies have clearly demonstrated the usefulness of a microgravity environment for enhancing the quality and size of protein crystals. Review of the vapor diffusion (VDA) PCG results from nineteen space shuttle missions is given in this paper

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.

Structural Data on the Periplasmic Aldehyde Oxidoreductase PaoABC from Escherichia coli: SAXS and Preliminary X-ray Crystallography Analysis

Directory of Open Access Journals (Sweden)

Ana Rita Otrelo-Cardoso

2014-01-01

Full Text Available The periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli is a molybdenum enzyme involved in detoxification of aldehydes in the cell. It is an example of an αβγ heterotrimeric enzyme of the xanthine oxidase family of enzymes which does not dimerize via its molybdenum cofactor binding domain. In order to structurally characterize PaoABC, X-ray crystallography and small angle X-ray scattering (SAXS have been carried out. The protein crystallizes in the presence of 20% (w/v polyethylene glycol 3350 using the hanging-drop vapour diffusion method. Although crystals were initially twinned, several experiments were done to overcome twinning and lowering the crystallization temperature (293 K to 277 K was the solution to the problem. The non-twinned crystals used to solve the structure diffract X-rays to beyond 1.80 Å and belong to the C2 space group, with cell parameters a = 109.42 Å, b = 78.08 Å, c = 151.77 Å, β = 99.77°, and one molecule in the asymmetric unit. A molecular replacement solution was found for each subunit separately, using several proteins as search models. SAXS data of PaoABC were also collected showing that, in solution, the protein is also an αβγ heterotrimer.

Accounting for partiality in serial crystallography using ray-tracing principles

International Nuclear Information System (INIS)

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

2015-01-01

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

Accounting for partiality in serial crystallography using ray-tracing principles

Energy Technology Data Exchange (ETDEWEB)

Kroon-Batenburg, Loes M. J., E-mail: l.m.j.kroon-batenburg@uu.nl; Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Ravelli, Raimond B. G. [Maastricht University, PO Box 616, 6200 MD Maastricht (Netherlands); Gros, Piet [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands)

2015-08-25

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

A novel inert crystal delivery medium for serial femtosecond crystallography

Directory of Open Access Journals (Sweden)

Chelsie E. Conrad

2015-07-01

Full Text Available Serial femtosecond crystallography (SFX has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

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 data processing

OpenAIRE

Powell, Harold R.

2017-01-01

The method of molecular structure determination by X-ray crystallography is a little over a century old. The history is described briefly, along with developments in X-ray sources and detectors. The fundamental processes involved in measuring diffraction patterns on area detectors, i.e. autoindexing, refining crystal and detector parameters, integrating the reflections themselves and putting the resultant measurements on to a common scale are discussed, with particular reference to the most c...

Semi-empirical atom-atom interaction models and X-ray crystallography

International Nuclear Information System (INIS)

Braam, A.W.M.

1981-01-01

Several aspects of semi-empirical energy calculations in crystallography are considered. Solid modifications of ethane have been studied using energy calculations and a fast summation technique has been evaluated. The structure of tetramethylpyrazine has been determined at room temperature and at 100K and accurate structure factors have been derived from measured Bragg intensities. Finally electrostatic properties have been deduced from X-ray structure factors. (C.F.)

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method

International Nuclear Information System (INIS)

Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

2013-01-01

Using the high-pressure cryocooling method, the high-resolution X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. This is the first ultra-high-resolution structure obtained from a high-pressure cryocooled crystal. Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005 ▶) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method

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.

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

Science.gov (United States)

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

2018-05-01

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

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

Science.gov (United States)

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

2015-07-01

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

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

X-ray data processing.

Science.gov (United States)

Powell, Harold R

2017-10-31

The method of molecular structure determination by X-ray crystallography is a little over a century old. The history is described briefly, along with developments in X-ray sources and detectors. The fundamental processes involved in measuring diffraction patterns on area detectors, i.e. autoindexing, refining crystal and detector parameters, integrating the reflections themselves and putting the resultant measurements on to a common scale are discussed, with particular reference to the most commonly used software in the field. © 2017 The Author(s).

X-ray powder crystallography with vertex instrumentation

International Nuclear Information System (INIS)

Chatzisotiriou, V.; Christofis, I.; Dimitriou, N.; Karvelas, S.; Karydas, A.G.; Loukas, D.; Pavlidis, A.; Spirou, S.; Dre, C.; Haralabidis, N.; Misiakos, K.; Tsoi, E.; Perdikatsis, V.; Psycharis, V.; Terzis, A.; Turchetta, R.

1998-01-01

An X-ray Diffractometer for Powder Crystallography is described along with experimental results and future plans. This is an intermediate instrument toward a long linear array system. Three channels of a silicon microstrip detector, are the detecting elements in the present instrument. Each detector channel is followed by a VLSI readout chain, which consists of a charge preamplifier with pulse shaping circuitry, a discriminator, and a 16-bit counter. Control and data acquisition is performed with a custom made PC readout card. A motorized goniometer scans the angle range of interest. Calibration of the system is done with reference samples and data which are captured with a one-channel conventional NaI detector. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

One-dimensional curved wire chamber for powder x-ray crystallography

International Nuclear Information System (INIS)

Ortendahl, D.; Perez-Mendez, V.; Stoker, J.; Beyermann, W.

1978-01-01

A xenon filled single anode wire chamber with delay line readout has been constructed for use in powder x-ray crystallography using 8 to 20 keV x-rays. The entire chamber including the anode wire and the delay line which forms part of the cathode plane is a section of a circular arc whose center is the powder specimen. The anode wire--38 μm gold-plated tungsten--is suspended in a circular arc by the interaction of a current flowing through it and magnetic field provided by two permanent magnets, above and below the wire, extending along the active length of the chamber. When filled with xenon to 3 atmospheres the chamber has uniform sensitivity in excess of 80% at 8 keV and a spatial resolution better than 0.3 mm

Cloning, purification, crystallization and preliminary X-ray studies of flagellar hook scaffolding protein FlgD from Pseudomonas aeruginosa PAO1

International Nuclear Information System (INIS)

Luo, Miao; Niu, Siqiang; Yin, Yibing; Huang, Ailong; Wang, Deqiang

2009-01-01

In order to better elucidate the functions of FlgD in flagellar hook biosynthesis, the three-dimensional structure of FlgD is being determined by X-ray crystallography. Here, the expression, purification, crystallization and preliminary crystallographic analysis of FlgD from P. aeruginosa are reported. FlgD regulates the assembly of the hook cap structure to prevent leakage of hook monomers into the medium and hook monomer polymerization and also plays a role in determination of the correct hook length, with the help of the FliK protein. In order to better elucidate the functions of FlgD in flagellar hook biosynthesis, the three-dimensional structure of FlgD is being determined by X-ray crystallography. Here, the expression, purification, crystallization and preliminary crystallographic analysis of FlgD from P. aeruginosa are reported. The crystal belonged to space group I222 and diffracted to a resolution of 2.5 Å, with unit-cell parameters a = 116.47, b = 118.71, c = 118.85 Å. The crystals are most likely to contain three molecules in the asymmetric unit, with a V M value of 2.73 Å 3 Da −1

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method.

Science.gov (United States)

Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

2013-11-01

Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

FIST - a suite of X-ray powder crystallography programs for use with a HP-65 calculator

International Nuclear Information System (INIS)

Ferguson, I.F.; Turek, M.

1977-12-01

Programs for X-ray powder crystallography are defined for use with a Hewlett Packard HP-65 (programmable) pocket calculator. These include the prediction of all Bragg reflections for defined P-, F-, I-cubic, tetragonal, hexagonal and orthorhombic cells; the calculation of the position of a specific Bragg reflection from defined unit cells with all symmetries except triclinic; interconversion of theta, 2theta, sin 2 theta and d, as well as the calculation of the Nelson-Riley function; the computation of crystal densities; the interconversion of rhombohedral and hexagonal unit cells, lsub(c) determinations for graphite, the calculation of a and c for boron carbide; and Miller index transformations between various unit cells. (author)

History of protein crystallography in China.

Science.gov (United States)

Rao, Zihe

2007-06-29

China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein crystallography in China has reached a new climax with a number of outstanding accomplishments. Here, I review the history and progress of protein crystallography in China and detail some of the recent research highlights, including the crystal structures of two membrane proteins as well as the structural genomics initiative in China.

Imaging plate, a new type of x-ray area detector

International Nuclear Information System (INIS)

Kamiya, Nobuo; Amemiya, Yoshiyuki; Miyahara, Junji.

1986-01-01

In respective fields of X-ray crystallography, for the purpose of the efficient collection of reciprocal space information, two-dimensional X-ray detectors such as multiwire proportional chambers and X-ray television sets have been used together with conventional X-ray films. X-ray films are characterized by uniform sensitivity and high positional resolution over a wide area, but the sensitivity is low, and the range of action and the linearity of the sensitivity is problematic. They require the development process, accordingly lack promptitude. The MWPCs and X-ray television sets are superior in the sensitivity, its linearity, the range of action and promptitude, but interior in the uniformity and resolution to the films. Imaging plate is a new X-ray area detector developed by Fuji Photo Film Co., Ltd., for digital X-ray medical image diagnosis. This detector is superior in all the above mentioned performances, and it seems very useful also for X-ray crystallography. In this paper, the system composed of an imaging plate and its reader is described, and the basic performance as an X-ray area detector and the results of having recorded the diffraction images of protein crystals as the example of applying it to X-ray crystallography are reported. The imaging plate is that the crystalline fluorescent powder of BaFBr doped with Eu 2+ ions is applied on plastic films. (Kako, I.)

Recent advances in racemic protein crystallography.

Science.gov (United States)

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

2017-09-15

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

Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

CERN Document Server

Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

2002-01-01

A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

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

Science.gov (United States)

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

2015-09-01

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

Structural elucidation of dendritic host-guest complexes by X-ray crystallography and molecular dynamics simulations

NARCIS (Netherlands)

Chang, T.; Pieterse, K.; Broeren, M.A.C.; Kooijman, H.; Spek, A.L.; Hilbers, P.A.J.; Meijer, E.W.

2007-01-01

The multiple monovalent binding of adamantyl-urea poly(propyleneimine) dendrimers with carboxylic acid-urea guests was investigated using molecular dynamics simulations and X-ray crystallography to better understand the structure and behavior of the dynamic multivalent complex in solution. The

A history of experimental phasing in macromolecular crystallography

OpenAIRE

Isaacs, Neil

2016-01-01

It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some d...

Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography

Directory of Open Access Journals (Sweden)

Zhen Huang

2008-03-01

Full Text Available Selenium derivatization (via selenomethionine of proteins for crystal structure determination via MAD phasing has revolutionized protein X-ray crystallography. It is estimated that over two thirds of all new crystal structures of proteins have been determined via Se-Met derivatization. Similarly, selenium functionalities have also been successfully incorporated into nucleic acids to facilitate their structure studies and it has been proved that this Se-derivatization has advantages over halogen strategy, which was usually used as a traditional method in this field. This review reports the development of site-specific selenium derivatization of nucleic acids for phase determination since the year of 2001 (mainly focus on the 2’-position of the ribose. All the synthesis of 2’-SeMe modified phosphoramidite building blocks (U, C, T, A, G and the according oligonucleotides are included. In addition, several structures of selenium contained nucleic acid are also described in this paper.

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)

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

Science.gov (United States)

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

2010-10-01

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

X-ray dosimetry of TlGaSe2 single crystals

International Nuclear Information System (INIS)

Kerimova, E.M.; Mustafaeva, S.N.; Mamedbeili, S.D.; Jabarov, J.N.; Iskenderova, P.M.; Kazimov, S.B.

2002-01-01

TlGaSe 2 compound belongs to group of layered semiconductors of A 3 B 3 C 2 6 -type. Photoelectric and optical properties of TlGaSe 2 single crystals were investigated in detail. Influence of gamma-, electron and neutron radiation on photoelectric properties of TlGaSe 2 single crystals is investigated too. The present work deals with experimental results relative to X-ray dosimetric characteristics of TlGaSe 2 crystals at 300 K. X-ray conductivity and X-ray dosimetric characteristic measurements are carried out in low load resistance regime. The source of X-ray radiation is the installation of X-ray diffraction analysis (URS-55a) with the BCV-2(Cu). Intensity of X-ray radiation (E) is regulated by measurement with current variation in tube at each given value of X-ray radiation dose E (R/min) are measured by crystal dosimeter DRGZ-02. X-ray conductivity coefficients K σ characterising X-ray sensitivity of investigated crystals are determined as the relative change of conductivity under X-ray radiation a per dose. There have been determined values of characteristic coefficients of TlGaSe 2 single crystal X-ray conductivity at different values of accelerating voltage (V a ) on the tube and corresponding doses of X-ray radiation. Analysis of obtained data showed that X-ray conductivity coefficients K σ in studied crystals are regularly decreased (from 0.276 to 0.033) as with the rise of dose (E=0.75-78.0 R/min) as with the increase of values of V a on X-ray tube (V a =254-50 keV). One of the possible reasons of observed regularities is that X-ray conductivity in investigated crystals, especially at comparatively low V a is due predominantly to radiation of thin layer of crystal. In this case with the rise of radiation intensity there have been started to prevail the mechanism of surface quadratic recombination which leads to observed decrease of X-ray conductivity. With the rise of accelerating potential 'effective hardness' is increased, as a result of which there

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

X-ray streak crystal spectography

International Nuclear Information System (INIS)

Kauffman, R.L.; Brown, T.; Medecki, H.

1983-01-01

We have built an x-ray streaked crystal spectrograph for making time-resolved x-ray spectral measurements. This instrument can access Bragg angles from 11 0 to 38 0 and x-ray spectra from 200 eV to greater than 10 keV. We have demonstrated resolving powers, E/δE > 200 at 1 keV and time resolution less than 20 psec. A description of the instrument and an example of the data is given

Metalloprotein Crystallography: More than a Structure.

Science.gov (United States)

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

2016-04-19

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

Macromolecular crystallography using synchrotron radiation

International Nuclear Information System (INIS)

Bartunik, H.D.; Phillips, J.C.; Fourme, R.

1982-01-01

The use of synchrotron X-ray sources in macromolecular crystallography is described. The properties of synchrotron radiation relevant to macromolecular crystallography are examined. The applications discussed include anomalous dispersion techniques, the acquisition of normal and high resolution data, and kinetic studies of structural changes in macromolecules; protein data are presented illustrating these applications. The apparatus used is described including information on the electronic detectors, the monitoring of the incident beam and crystal cooling. (U.K.)

Development of Control Applications for High-Throughput Protein Crystallography Experiments

International Nuclear Information System (INIS)

Gaponov, Yurii A.; Matsugaki, Naohiro; Honda, Nobuo; Sasajima, Kumiko; Igarashi, Noriyuki; Hiraki, Masahiko; Yamada, Yusuke; Wakatsuki, Soichi

2007-01-01

An integrated client-server control system (PCCS) with a unified relational database (PCDB) has been developed for high-throughput protein crystallography experiments on synchrotron beamlines. The major steps in protein crystallographic experiments (purification, crystallization, crystal harvesting, data collection, and data processing) are integrated into the software. All information necessary for performing protein crystallography experiments is stored in the PCDB database (except raw X-ray diffraction data, which is stored in the Network File Server). To allow all members of a protein crystallography group to participate in experiments, the system was developed as a multi-user system with secure network access based on TCP/IP secure UNIX sockets. Secure remote access to the system is possible from any operating system with X-terminal and SSH/X11 (Secure Shell with graphical user interface) support. Currently, the system covers the high-throughput X-ray data collection stages and is being commissioned at BL5A and NW12A (PF, PF-AR, KEK, Tsukuba, Japan)

Contribution of X-ray crystallography in energy related problems

International Nuclear Information System (INIS)

Majid, C.A.; Hussain, M.A.

1995-01-01

Crystallography is concerned with the study of the structure of matter at the atomic level in condensed state. The great practical importance of scientific knowledge of the structure of solid is self evident when consideration is given to the definition of desired physical and chemical properties. The strength of steel girders, the corrosion of alloys, the plasticity of lime, the wearing properties of case hardness steel, the dielectric capacity of materials, the lubricating properties of long chain paraffin's or of graphite, the stretching of rubber and innumerable other practical phenomena of every day life depend upon ultimate structure of these materials. To understand function to control, manipulate and best utilize their properties, and to produce materials with properties meeting a desired set of specification it is essential to understand thoroughly both the characteristics and origin of each property. Origins of materials properties lie in a combination of natural laws with the detailed structure and composition of materials, i.e. the choice, location, bonding, etc. of every atom in the material object. Therefore, to understand their various properties, it is important to explore the structure property relationship in materials. X-ray crystallography is not only helping to develop new materials having desired properties, but also in improving existing materials. Radiation effects, electrolytes, superconductors and catalysts etc. are just a few examples of many areas where crystallography is helping. With the invent of new radiation sources like synchrotron and new detectors materials and techniques, this almost 80 years old discipline continues to capture the interest of solid state physicists and chemists alike. (author)

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.)

Quantum crystallography: A perspective.

Science.gov (United States)

Massa, Lou; Matta, Chérif F

2018-06-30

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

X-ray tests of microfocusing mono-capillary optic for protein crystallography

CERN Document Server

Bilderback, D H

2001-01-01

A single, borosilicate-glass capillary was drawn into a 30.5 cm long elliptical shape. The inside diameter was 0.40 mm at the large base end and 0.13 mm at the tip. With 12 keV X-rays from the CHESS D1 bending magnet, the single-bounce capillary produced a focus of better than 18 mu m in diameter (FHWM) at a 3 cm distance from the capillary tip. A flux gain of 110 in the focus position was observed along with a total flux in the spot of 4x10 sup 1 sup 0 X-rays/s (conditions: 5.3 GeV, 182 mA, 1.5% bandwidth multilayer, 12 keV X-rays). A measurement of the far field focus ring diameter yielded a divergence of 3.8 mrad, in good agreement with the 4 mrad design of the optic for protein crystallography. Using a small 25 mu m square beam, we measured the local reflectivity to be greater than 95% and the inner slope errors of the capillary to average about +-150 mu rad, both from raw and elliptically shaped tubing. Our conclusion is that more perfect starting tubing (i.e. one with lower slope errors) is needed to ma...

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.

SECCOX, a novel x-ray characterization bench for Bragg crystals and x-rays optics

International Nuclear Information System (INIS)

Caillaud, T.; Manson, M.; Desenne, D.; Goze, B.; Rivet, A.; Derouineau, Ph.

2007-01-01

Laser programs require the use of a large number of calibrated x-ray crystals implemented inside spectrometers and microscopes used in diagnostics. In this context, a new apparatus was designed in collaboration with CELIA laboratory, Saint-Gobain Crystals and Detectors and CEA to characterize x-ray Bragg crystals. Station d'Etude et de Caracterisation des Cristaux pour les Optiques X (SECCOX) is based on a micrometric x-ray source and an automated spectrometer equipped with a CCD camera. Properties such as homogeneity, resolution, radius of curvature and reflectivity are measured to guarantee diagnostic performance in laser-plasma physics experiments. We will present the experimental device, techniques and results of the calibration obtained. (authors)

Ultra-high resolution protein crystallography

International Nuclear Information System (INIS)

Takeda, Kazuki; Hirano, Yu; Miki, Kunio

2010-01-01

Many protein structures have been determined by X-ray crystallography and deposited with the Protein Data Bank. However, these structures at usual resolution (1.5< d<3.0 A) are insufficient in their precision and quantity for elucidating the molecular mechanism of protein functions directly from structural information. Several studies at ultra-high resolution (d<0.8 A) have been performed with synchrotron radiation in the last decade. The highest resolution of the protein crystals was achieved at 0.54 A resolution for a small protein, crambin. In such high resolution crystals, almost all of hydrogen atoms of proteins and some hydrogen atoms of bound water molecules are experimentally observed. In addition, outer-shell electrons of proteins can be analyzed by the multipole refinement procedure. However, the influence of X-rays should be precisely estimated in order to derive meaningful information from the crystallographic results. In this review, we summarize refinement procedures, current status and perspectives for ultra high resolution protein crystallography. (author)

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

Science.gov (United States)

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

2018-03-12

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

Crystallography: past and present

Science.gov (United States)

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

2007-12-01

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

Nanoflow electrospinning serial femtosecond crystallography

International Nuclear Information System (INIS)

Sierra, Raymond G.; Laksmono, Hartawan; Kern, Jan; Tran, Rosalie; Hattne, Johan; Alonso-Mori, Roberto; Lassalle-Kaiser, Benedikt; Glöckner, Carina; Hellmich, Julia; Schafer, Donald W.; Echols, Nathaniel; Gildea, Richard J.; Grosse-Kunstleve, Ralf W.; Sellberg, Jonas; McQueen, Trevor A.; Fry, Alan R.; Messerschmidt, Marc M.; Miahnahri, Alan; Seibert, M. Marvin; Hampton, Christina Y.; Starodub, Dmitri; Loh, N. Duane; Sokaras, Dimosthenis; Weng, Tsu-Chien; Zwart, Petrus H.; Glatzel, Pieter; Milathianaki, Despina; White, William E.; Adams, Paul D.; Williams, Garth J.; Boutet, Sébastien; Zouni, Athina; Messinger, Johannes; Sauter, Nicholas K.; Bergmann, Uwe; Yano, Junko; Yachandra, Vittal K.; Bogan, Michael J.

2012-01-01

A low flow rate liquid microjet method for delivery of hydrated protein crystals to X-ray lasers is presented. Linac Coherent Light Source data demonstrates serial femtosecond protein crystallography with micrograms, a reduction of sample consumption by orders of magnitude. An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14–3.1 µl min −1 to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min −1 and diffracted to beyond 4 Å resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption

Nanoflow electrospinning serial femtosecond crystallography

Energy Technology Data Exchange (ETDEWEB)

Sierra, Raymond G.; Laksmono, Hartawan [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Kern, Jan [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Tran, Rosalie; Hattne, Johan [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Alonso-Mori, Roberto [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Lassalle-Kaiser, Benedikt [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Glöckner, Carina; Hellmich, Julia [Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin (Germany); Schafer, Donald W. [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Echols, Nathaniel; Gildea, Richard J.; Grosse-Kunstleve, Ralf W. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Sellberg, Jonas [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Stockholm University, S-106 91 Stockholm (Sweden); McQueen, Trevor A. [Stanford University, Stanford, CA 94025 (United States); Fry, Alan R.; Messerschmidt, Marc M.; Miahnahri, Alan; Seibert, M. Marvin; Hampton, Christina Y.; Starodub, Dmitri; Loh, N. Duane; Sokaras, Dimosthenis; Weng, Tsu-Chien [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Zwart, Petrus H. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Glatzel, Pieter [European Synchrotron Radiation Facility, Grenoble (France); Milathianaki, Despina; White, William E. [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Williams, Garth J.; Boutet, Sébastien [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Zouni, Athina [Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin (Germany); Messinger, Johannes [Umeå Universitet, Umeå (Sweden); Sauter, Nicholas K. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bergmann, Uwe [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Yano, Junko; Yachandra, Vittal K. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bogan, Michael J., E-mail: mbogan@slac.stanford.edu [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States)

2012-11-01

A low flow rate liquid microjet method for delivery of hydrated protein crystals to X-ray lasers is presented. Linac Coherent Light Source data demonstrates serial femtosecond protein crystallography with micrograms, a reduction of sample consumption by orders of magnitude. An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14–3.1 µl min{sup −1} to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min{sup −1} and diffracted to beyond 4 Å resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.

Sources, instrumentation and detectors for protein crystallography

CERN Document Server

Nave, C

2001-01-01

Some of the requirements for protein crystallography experiments on a synchrotron are described. Although data from different types of crystal are often collected without changing the X-ray beam properties, there are benefits if the incident beam is matched to a particular crystal and its diffraction pattern. These benefits are described with some examples. Radiation damage and other effects impose limits on the dose and dose rate on a protein crystal if the maximum amount of data is to be obtained. These limitations have possible consequences for the X-ray source required. Presently available commercial detector systems provide excellent data for protein crystallography but do not quite reach the specifications of the 'ideal' detector. In order to collect the most accurate data (e.g. for very weak anomalous scattering applications) detectors that produce near photon counting statistics over a wide dynamic range are required. It is possible that developments in 'pixel' detectors will allow these demanding exp...

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.

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

Science.gov (United States)

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

2016-09-23

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

Synthesis, X-ray crystallography, spectroscopy, electrochemistry, thermal and kinetic study of uranyl Schiff base complexes

Czech Academy of Sciences Publication Activity Database

Asadi, Z.; Golzard, F.; Eigner, Václav; Dušek, Michal

2013-01-01

Roč. 66, č. 20 (2013), s. 3629-3646 ISSN 0095-8972 R&D Projects: GA ČR(CZ) GAP204/11/0809 Institutional support: RVO:68378271 Keywords : X-ray crystallography * uranyl Schiff base complex * kinetics of thermal decomposition * cyclic voltammetry * kinetics and mechanism Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.224, year: 2013

The bio-crystallography beamline (BL41XU) at SPring-8

CERN Document Server

Kawamoto, M; Kamiya, N

2001-01-01

The bio-crystallography beamline (BL41XU), one of two pilot beamlines at SPring-8, was constructed using a standard in-vacuum-type undulator and opened for general users from domestic and overseas countries. Many tests and improvements were carried out on beamline elements and equipment for macromolecular crystallography, especially on the so-called 'pin-post' water cooling crystal of rotated-inclined double crystal monochromator. The maximum brilliance at sample position reached to 4x10 sup 1 sup 5 photons/s/mm sup 2 /mrad sup 2 at an X-ray energy of 11 keV. Commercially available X-ray detectors of CCD and imaging plate were installed in the experimental station. A beamline control software system for beam tracking and an on-line reader for large-format imaging plate were newly developed.

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

Science.gov (United States)

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

2009-01-01

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

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

OpenAIRE

Soichiro Tsujino; Takashi Tomizaki

2016-01-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinn...

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

Science.gov (United States)

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

2018-03-01

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

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

Purification, crystallization and preliminary X-ray analysis of Escherichia coli UDP-N-acetylmuramoyl:L-alanine ligase (MurC).

Science.gov (United States)

Deva, Taru; Pryor, KellyAnn D; Leiting, Barbara; Baker, Edward N; Smith, Clyde A

2003-08-01

UDP-N-acetylmuramoyl:L-alanine ligase (MurC) is involved in the pathway leading from UDP-N-glucosamine to the UDP-N-acetylmuramoyl:pentapeptide unit, which is the building block for the peptidoglycan layer found in all bacterial cell walls. The pathways leading to the biosynthesis of the peptidoglycan layer are important targets for the development of novel antibiotics, since animal cells do not contain these pathways. MurC is the first of four similar ATP-dependent amide-bond ligases which share primary and tertiary structural similarities. The crystal structures of three of these have been determined by X-ray crystallography, giving insights into the binding of the carbohydrate substrate and the ATP. Diffraction-quality crystals of the enzyme MurC have been obtained in both native and selenomethionine forms and X-ray diffraction data have been collected at the Se edge at a synchrotron source. The crystals are orthorhombic, with unit-cell parameters a = 73.9, b = 93.6, c = 176.8 A, and diffraction has been observed to 2.6 A resolution.

Femtosecond X-ray diffraction from two-dimensional protein crystals

Directory of Open Access Journals (Sweden)

Matthias Frank

2014-03-01

Full Text Available X-ray diffraction patterns from two-dimensional (2-D protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

Imaging Macromolecules with X-ray laser pulses

CERN Multimedia

CERN. Geneva

2017-01-01

The short wavelength of X-rays allows us to resolve atoms, but in practise for biological materials the achievable resolution is limited by the destruction of the sample by the radiation that forms the image.  For over 100 years, the workaround to this problem of radiation damage has been to average signals from repeating copies of the object arranged in a large crystal.  It is now possible to overcome damage limits by using intense X-ray pulses that vaporise the sample, but which are short enough in duration to freeze any motion of the sample on the atomic scale.  With the advent of X-ray FELs we have been able to confirm this principle, and are now applying it to overcoming a major bottleneck for protein crystallography, which is the need for large well-diffracting crystals.  The intense pulses also open up opportunities to help solve the crystallographic phase problem.  In particular we have found that commonly-occurring disordered crystals that are usually not ...

X-FEL revolution - X-ray lasers to probe matter

International Nuclear Information System (INIS)

Collet, E.; Cammarata, M.; Harmand, M.; Couprie, M.E.

2015-01-01

X-ray free electron lasers (X-FEL) are now able to generate X-ray pulses of a few femto-seconds (1 fs = 10"-"1"5 s), which allows the real-time observation of the movements of atoms. The changes in the structure of a material can be seen whatever the material, this is illustrated with the PYP protein (that is the photo-receptor of a bacterium), the changes between an initial state and 100 ps after light excitation show the displacement of the atoms of the protein. The brightness of X-FEL can be so high that it allows the study of nano-metric structures but it enables X-FEL radiation to ionize matter and the crystal sample may be destroyed, this becomes the new limit of X-FEL applied to crystallography. Another application of X-FEL to structure studies is to allow the study of systems that are not crystal systems like macromolecules, proteins or even viruses. Hundreds of patterns of X-ray diffractions of an object are combined to form a 3-dimensional image of the object in the wave vector space and it is then possible but very complex to deduce the real 3-dimensional structure of the object. (A.C.)

X-ray photoelectron spectra and electronic structure of quasi-one-dimensional SbSeI crystals

Directory of Open Access Journals (Sweden)

J.Grigas

2007-01-01

Full Text Available The paper presents the X-ray photoelectron spectra (XPS of the valence band (VB and of the principal core levels from the (110 and (001 crystal surfaces for the quasi-one-dimensional high permittivity SbSeI single crystal isostructural to ferroelectric SbSI. The XPS were measured with monochromatized Al Ka radiation in the energy range of 0-1400 eV at room temperature. The VB is located from 1.6 to 20 eV below the Fermi level. Experimental energies of the VB and core levels are compared with the results of theoretical ab initio calculations of the molecular model of the SbSeI crystal. The electronic structure of the VB is revealed. Shifts in the core-level binding energies of surface atoms relative to bulk ones, which show a dependency on surface crystallography, have been observed. The chemical shifts of the core levels (CL in the SbSeI crystal for the Sb, I and Se states are obtained.

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

Science.gov (United States)

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

2017-10-01

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

X-ray diffraction studies of NbTe 2 single crystal

Indian Academy of Sciences (India)

The composition of the grown crystals was confirmed on the basis of energy dispersive analysis by X-ray (EDAX) and remaining structural characterization was also accomplished by X-ray diffraction (XRD) studies. Lattice parameters, volume and X-ray density have been carried out for the grown crystals. The particle size ...

X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

Energy Technology Data Exchange (ETDEWEB)

Yennawar, Hemant [Pennsylvania State University, 8 Althouse Laboratory, University Park, PA 16802 (United States); Møller, Magda [Cornell High Energy Synchrotron Source, Ithaca, NY 14853 (United States); University of Copenhagen, DK-2100 Copenhagen (Denmark); Gillilan, Richard [Cornell High Energy Synchrotron Source, Ithaca, NY 14853 (United States); Yennawar, Neela, E-mail: nhy1@psu.edu [Pennsylvania State University, 8 Althouse Laboratory, University Park, PA 16802 (United States)

2011-05-01

The X-ray crystal structure and a small-angle X-ray scattering solution structure of sheep liver sorbitol dehydrogenase have been determined. The details of the interactions that enable the tetramer scaffold to be the functional biological unit have been analyzed. The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystal symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X-ray scattering was also used to identify the quaternary structure of the tetramer of slSDH in solution.

FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images

DEFF Research Database (Denmark)

Beyerlein, Kenneth R.; White, Thomas A.; Yefanov, Oleksandr

2017-01-01

A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues-Frank space, in which all crystal systems can be represented without...

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.

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 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).

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

Science.gov (United States)

Pawar, Sunayna S; Koorbanally, Neil A

2014-06-01

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

X-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.

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

Energy Technology Data Exchange (ETDEWEB)

Kärtner, F.X., E-mail: franz.kaertner@cfel.de [Center for Free-Electron Laser Science, Hamburg (Germany); Institute for Experimental Physics, University of Hamburg, Hamburg (Germany); The Hamburg Center for Ultrafast Imaging, Hamburg (Germany); DESY, Hamburg (Germany); Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA (United States); Ahr, F. [Center for Free-Electron Laser Science, Hamburg (Germany); Institute for Experimental Physics, University of Hamburg, Hamburg (Germany); DESY, Hamburg (Germany); Max Planck Institute for the Structure and Dynamics of Matter, Hamburg (Germany); Calendron, A.-L. [Center for Free-Electron Laser Science, Hamburg (Germany); Institute for Experimental Physics, University of Hamburg, Hamburg (Germany); The Hamburg Center for Ultrafast Imaging, Hamburg (Germany); DESY, Hamburg (Germany); Çankaya, H. [Center for Free-Electron Laser Science, Hamburg (Germany); The Hamburg Center for Ultrafast Imaging, Hamburg (Germany); DESY, Hamburg (Germany); Carbajo, S. [Center for Free-Electron Laser Science, Hamburg (Germany); Institute for Experimental Physics, University of Hamburg, Hamburg (Germany); DESY, Hamburg (Germany); Chang, G.; Cirmi, G. [Center for Free-Electron Laser Science, Hamburg (Germany); The Hamburg Center for Ultrafast Imaging, Hamburg (Germany); DESY, Hamburg (Germany); Dörner, K. [Center for Free-Electron Laser Science, Hamburg (Germany); DESY, Hamburg (Germany); Dorda, U. [DESY, Hamburg (Germany); Fallahi, A. [Center for Free-Electron Laser Science, Hamburg (Germany); DESY, Hamburg (Germany); Hartin, A. [Center for Free-Electron Laser Science, Hamburg (Germany); Institute for Experimental Physics, University of Hamburg, Hamburg (Germany); DESY, Hamburg (Germany); Hemmer, M. [Center for Free-Electron Laser Science, Hamburg (Germany); DESY, Hamburg (Germany); and others

2016-09-01

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

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...

Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves.

Science.gov (United States)

Guo, Feng; Zhou, Weijie; Li, Peng; Mao, Zhangming; Yennawar, Neela H; French, Jarrod B; Huang, Tony Jun

2015-06-01

Advances in modern X-ray sources and detector technology have made it possible for crystallographers to collect usable data on crystals of only a few micrometers or less in size. Despite these developments, sample handling techniques have significantly lagged behind and often prevent the full realization of current beamline capabilities. In order to address this shortcoming, a surface acoustic wave-based method for manipulating and patterning crystals is developed. This method, which does not damage the fragile protein crystals, can precisely manipulate and pattern micrometer and submicrometer-sized crystals for data collection and screening. The technique is robust, inexpensive, and easy to implement. This method not only promises to significantly increase efficiency and throughput of both conventional and serial crystallography experiments, but will also make it possible to collect data on samples that were previously intractable. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

NATURAL CYCLOPENTANOID CYANOHYDRIN GLYCOSIDES .13. STRUCTURE DETERMINATION OF NATURAL EPOXYCYCLOPENTANES BY X-RAY CRYSTALLOGRAPHY AND NMR-SPECTROSCOPY

DEFF Research Database (Denmark)

Olafsdottir, E. S.; Sorensen, A. M.; Cornett, Claus

1991-01-01

nonannellated cyclopentane derivatives. The new glucosides were shown, by NMR spectroscopy (including NOE measurements), X-ray crystallography, and enzymatic hydrolysis to the corresponding cyanohydrins, to be (1R,2R,3R,4R)- and (1S,2S,3S,4S)-1-(beta-D-glucopyranosyloxy)-2,3-epoxy-4-hydroxycyclopenta ne-1...

Fab Chaperone-Assisted RNA Crystallography (Fab CARC).

Science.gov (United States)

Sherman, Eileen; Archer, Jennifer; Ye, Jing-Dong

2016-01-01

Recent discovery of structured RNAs such as ribozymes and riboswitches shows that there is still much to learn about the structure and function of RNAs. Knowledge learned can be employed in both biochemical research and clinical applications. X-ray crystallography gives unparalleled atomic-level structural detail from which functional inferences can be deduced. However, the difficulty in obtaining high-quality crystals and their phasing information make it a very challenging task. RNA crystallography is particularly arduous due to several factors such as RNA's paucity of surface chemical diversity, lability, repetitive anionic backbone, and flexibility, all of which are counterproductive to crystal packing. Here we describe Fab chaperone assisted RNA crystallography (CARC), a systematic technique to increase RNA crystallography success by facilitating crystal packing as well as expediting phase determination through molecular replacement of conserved Fab domains. Major steps described in this chapter include selection of a synthetic Fab library displayed on M13 phage against a structured RNA crystallization target, ELISA for initial choice of binding Fabs, Fab expression followed by protein A affinity then cation exchange chromatography purification, final choice of Fab by binding specificity and affinity as determined by a dot blot assay, and lastly gel filtration purification of a large quantity of chosen Fabs for crystallization.

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

Directory of Open Access Journals (Sweden)

C. Mueller

2015-09-01

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

A new fixed-target approach for serial crystallography at synchrotron light sources and X-ray free electron lasers

International Nuclear Information System (INIS)

Roedig, Philip

2017-07-01

In the framework of this thesis, a new method for high-speed fixed-target serial crystallography experiments and its applicability to biomacromolecular crystallography at both synchrotron light sources and X-ray free electron lasers (XFELs) is presented. The method is based on a sample holder, which can carry up to 20,000 microcrystals and which is made of single-crystalline silicon. Using synchrotron radiation, the structure of Operophtera brumata cytoplasmic polyhedrosis virus type 18 polyhedrin, lysozyme and cubic insulin was determined by collecting X-ray diffraction data from multiple microcrystals. Data collection was shown to be possible at both cryogenic and ambient conditions. For room-temperature measurements, both global and specific indications of radiation damage were investigated and characterized. Due to the sieve-like structure of the chip, the microcrystals tend to arrange themselves according to the micropore pattern, which allows for efficient sampling of the sample material. In combination with a high-speed scanning stage, the sample holder was furthermore shown to be highly suitable for serial femtosecond crystallography experiments. By fast raster scanning of the chip through the pulsed X-ray beam of an XFEL, structure determination of a virus, using the example of bovine enterovirus type 2, has been demonstrated at an XFEL for the first time. Hit rates of up to 100% were obtained by the presented method, which refers to a reduction in sample consumption by at least three orders of magnitude with respect to common liquid-jet injection methods used for sample delivery. In this way, the typical time needed for data collection in serial femtosecond crystallography is significantly decreased. The presented technique for sample loading of the chip is easy to learn and results in efficient removal of the surrounding mother liquor, thereby reducing the generated background signal. Since the chip is made of single-crystalline silicon, in principle no

A new fixed-target approach for serial crystallography at synchrotron light sources and X-ray free electron lasers

Energy Technology Data Exchange (ETDEWEB)

Roedig, Philip

2017-07-15

In the framework of this thesis, a new method for high-speed fixed-target serial crystallography experiments and its applicability to biomacromolecular crystallography at both synchrotron light sources and X-ray free electron lasers (XFELs) is presented. The method is based on a sample holder, which can carry up to 20,000 microcrystals and which is made of single-crystalline silicon. Using synchrotron radiation, the structure of Operophtera brumata cytoplasmic polyhedrosis virus type 18 polyhedrin, lysozyme and cubic insulin was determined by collecting X-ray diffraction data from multiple microcrystals. Data collection was shown to be possible at both cryogenic and ambient conditions. For room-temperature measurements, both global and specific indications of radiation damage were investigated and characterized. Due to the sieve-like structure of the chip, the microcrystals tend to arrange themselves according to the micropore pattern, which allows for efficient sampling of the sample material. In combination with a high-speed scanning stage, the sample holder was furthermore shown to be highly suitable for serial femtosecond crystallography experiments. By fast raster scanning of the chip through the pulsed X-ray beam of an XFEL, structure determination of a virus, using the example of bovine enterovirus type 2, has been demonstrated at an XFEL for the first time. Hit rates of up to 100% were obtained by the presented method, which refers to a reduction in sample consumption by at least three orders of magnitude with respect to common liquid-jet injection methods used for sample delivery. In this way, the typical time needed for data collection in serial femtosecond crystallography is significantly decreased. The presented technique for sample loading of the chip is easy to learn and results in efficient removal of the surrounding mother liquor, thereby reducing the generated background signal. Since the chip is made of single-crystalline silicon, in principle no

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

Science.gov (United States)

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

2017-01-17

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

Purification, crystallization and preliminary X-ray diffraction analysis of the glyoxalase II from Leishmania infantum

International Nuclear Information System (INIS)

Trincão, José; Sousa Silva, Marta; Barata, Lídia; Bonifácio, Cecília; Carvalho, Sandra; Tomás, Ana Maria; Ferreira, António E. N.; Cordeiro, Carlos; Ponces Freire, Ana; Romão, Maria João

2006-01-01

A glyoxalase II from L. infantum was cloned, purified and crystallized and its structure was solved by X-ray crystallography. In trypanosomatids, trypanothione replaces glutathione in all glutathione-dependent processes. Of the two enzymes involved in the glyoxalase pathway, glyoxalase I and glyoxalase II, the latter shows absolute specificity towards trypanothione thioester, making this enzyme an excellent model to understand the molecular basis of trypanothione binding. Cloned glyoxalase II from Leishmania infantum was overexpressed in Escherichia coli, purified and crystallized. Crystals belong to space group C222 1 (unit-cell parameters a = 65.6, b = 88.3, c = 85.2 Å) and diffract beyond 2.15 Å using synchrotron radiation. The structure was solved by molecular replacement using the human glyoxalase II structure as a search model. These results, together with future detailed kinetic characterization using lactoyltrypanothione, should shed light on the evolutionary selection of trypanothione instead of glutathione by trypano-somatids

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

Science.gov (United States)

Wesolowski, Steven S; Pivonka, Don E

2013-07-15

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

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

International Nuclear Information System (INIS)

Nakane, Takanori; Song, Changyong; Suzuki, Mamoru; Nango, Eriko; Kobayashi, Jun; Masuda, Tetsuya; Inoue, Shigeyuki; Mizohata, Eiichi; Nakatsu, Toru; Tanaka, Tomoyuki; Tanaka, Rie; Shimamura, Tatsuro; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Iwata, So; Sugahara, Michihiro

2015-01-01

Sulfur SAD phasing facilitates the structure determination of diverse native proteins using femtosecond X-rays from free-electron lasers via serial femtosecond crystallography. Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures

A history of experimental phasing in macromolecular crystallography.

Science.gov (United States)

Isaacs, Neil

2016-03-01

It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some decades before experimental phasing methods were developed. Many scientists contributed to this development and this paper presents the author's own perspective on this history. There will be other perspectives, so what follows is a history, rather than the history, of experimental phasing.

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.

Structural Characterization of Doped GaSb Single Crystals by X-ray Topography

Energy Technology Data Exchange (ETDEWEB)

Honnicke, M.G.; Mazzaro, I.; Manica, J.; Benine, E.; M da Costa, E.; Dedavid, B. A.; Cusatis, C.; Huang, X. R.

2009-09-13

We characterized GaSb single crystals containing different dopants (Al, Cd and Te), grown by the Czochralski method, by x-ray topography and high angular resolution x-ray diffraction. Lang topography revealed dislocations parallel and perpendicular to the crystal's surface. Double-crystal GaSb 333 x-ray topography shows dislocations and vertical stripes than can be associated with circular growth bands. We compared our high-angular resolution x-ray diffraction measurements (rocking curves) with the findings predicted by the dynamical theory of x-ray diffraction. These measurements show that our GaSb single crystals have a relative variation in the lattice parameter ({Delta}d/d) on the order of 10{sup -5}. This means that they can be used as electronic devices (detectors, for example) and as x-ray monochromators.

Colloquium: Femtosecond x-ray crystallography

International Nuclear Information System (INIS)

Rousse, Antoine; Rischel, Christian; Gauthier, Jean-Claude

2001-01-01

This article gives an overview of recent x-ray diffraction experiments with time resolutions down to 10 -13 s. The scientific motivation behind the development is outlined, using examples from solid state physics and biology. The ultrafast resolution may be provided either by fast detectors or short x-ray pulses, and the limitations of both techniques are discussed on the basis of state of the art experiments. In particular, it is shown that with present designs, high time resolution reduces the structural information attainable with high spatial resolution, thereby limiting feasible experiments on the ultrashort time-scale. The first experiment showing subpicosecond conformation changes was recently achieved with simple solids using an ultrafast laser-produced plasma x-ray source. The principles of this experiment are described in detail

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

Crystallography: past and present

International Nuclear Information System (INIS)

Hodeau, J.L.; Guinebretiere, R.

2007-01-01

In the 19th century, crystallography referred to the study of crystal shapes. A breakthrough appeared in 1912 with the use of X-rays by M. von Laue and W.H. and W.L. Bragg. This experimental development allowed the determination of the atomic content of each unit cell constituting the crystal and defined a crystal as ''any solid in which an atomic pattern is repeated periodically in three dimensions, that is, any solid that ''diffracts'' an incident X-ray beam''. Mathematical tools like the Patterson methods, the direct methods, were developed. Furthermore the development of new sources of neutrons, electrons and synchrotron X-rays allowed the studies of complex compounds like large macromolecules in biology. In our contribution we show by selected examples that these improvements were allowed (i) by the use of powerful sources, apparatus and detectors which allow micro-diffraction, in-situ diffraction, spectroscopy, resonant scattering, inelastic scattering, coherent scattering, (ii) by the development of methods like diffraction anomalous fine structure (DAFS), pair distribution function (PDF), simulated annealing, single object reconstruction, (iii) by combination of scattering and spectroscopy and by combination of scattering and microscopy. (orig.)

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.

Viscous hydrophilic injection matrices for serial crystallography

Directory of Open Access Journals (Sweden)

Gabriela Kovácsová

2017-07-01

Full Text Available Serial (femtosecond crystallography at synchrotron and X-ray free-electron laser (XFEL sources distributes the absorbed radiation dose over all crystals used for data collection and therefore allows measurement of radiation damage prone systems, including the use of microcrystals for room-temperature measurements. Serial crystallography relies on fast and efficient exchange of crystals upon X-ray exposure, which can be achieved using a variety of methods, including various injection techniques. The latter vary significantly in their flow rates – gas dynamic virtual nozzle based injectors provide very thin fast-flowing jets, whereas high-viscosity extrusion injectors produce much thicker streams with flow rates two to three orders of magnitude lower. High-viscosity extrusion results in much lower sample consumption, as its sample delivery speed is commensurate both with typical XFEL repetition rates and with data acquisition rates at synchrotron sources. An obvious viscous injection medium is lipidic cubic phase (LCP as it is used for in meso membrane protein crystallization. However, LCP has limited compatibility with many crystallization conditions. While a few other viscous media have been described in the literature, there is an ongoing need to identify additional injection media for crystal embedding. Critical attributes are reliable injection properties and a broad chemical compatibility to accommodate samples as heterogeneous and sensitive as protein crystals. Here, the use of two novel hydrogels as viscous injection matrices is described, namely sodium carboxymethyl cellulose and the thermo-reversible block polymer Pluronic F-127. Both are compatible with various crystallization conditions and yield acceptable X-ray background. The stability and velocity of the extruded stream were also analysed and the dependence of the stream velocity on the flow rate was measured. In contrast with previously characterized injection media, both new

Microscale X-ray Absorption Spectroscopy on the GSECARS Sector 13 at the APS

CERN Document Server

Stephen-Sutto

2000-01-01

GeoSoilEnviroCARS (GSECARS) is a national user facility for frontier research in the earth sciences using synchrotrons radiation at the Advanced Photon Source, Argonne National Laboratory. GSECARS provides earth scientists with access to the high-brilliance hard x-rays from this third-generation synchrotrons light source. The research conducted at this facility will advance our knowledge of the composition, structure and properties of earth materials, the processes they control and the processes that produce them. All principal synchrotron-based analytical techniques in demand by earth scientists are being brought to bear on earth science problems: (1) high-pressure/high-temperature crystallography and spectroscopy using the diamond anvil cell; (2) high-pressure/high-temperature crystallography using the large-volume press; (3) powder, single crystal and interface diffraction; (4) x-ray absorption fine structure (XAFS) spectroscopy; (5) x-ray fluorescence microprobe analysis and microspectroscopy; and (6) mic...

Identifying, studying and making good use of macromolecular crystals

Energy Technology Data Exchange (ETDEWEB)

Calero, Guillermo [University of Pittsburgh Medical School, Pittsburgh, PA 15261 (United States); Cohen, Aina E. [SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025 (United States); Luft, Joseph R. [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203 (United States); State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203 (United States); Newman, Janet [CSIRO Collaborative Crystallisation Centre, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Snell, Edward H., E-mail: esnell@hwi.buffalo.edu [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203 (United States); State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203 (United States); University of Pittsburgh Medical School, Pittsburgh, PA 15261 (United States)

2014-07-25

As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.

Identifying, studying and making good use of macromolecular crystals

International Nuclear Information System (INIS)

Calero, Guillermo; Cohen, Aina E.; Luft, Joseph R.; Newman, Janet; Snell, Edward H.

2014-01-01

As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed

X-ray crystallography, electrochemistry, spectral and thermal analysis of some tetradentate schiff base complexes and formation constant measurements

Czech Academy of Sciences Publication Activity Database

Asadi, Z.; Savarypour, N.; Dušek, Michal; Eigner, Václav

2017-01-01

Roč. 47, č. 11 (2017), s. 1501-1508 ISSN 2470-1556 R&D Projects: GA ČR(CZ) GA15-12653S Institutional support: RVO:68378271 Keywords : X-ray crystallography * transition metal Schiff base complexes * thermogravimetry * electrochemistry * formation constant measurements Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.)

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

Science.gov (United States)

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

2016-05-01

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

Crystallized solids characterization by X-ray diffraction

International Nuclear Information System (INIS)

Broll, N.

1996-01-01

This work deals with the crystallized solids characterization by X-ray diffraction. The powders diffraction principle is described. Then are given the different powders diffraction experimental methods. An X-ray diffraction device is essentially constituted of three parts: the X-rays source, the sample and the detector. The source is usually constituted by an X-rays tube whereas the sample can be fixed on a photographic chamber or put on a goniometer. The different photographic chambers which can be used (Debye-Scherrer, Seeman-Bohlin and Guinier) are described. The powders diffractometer the most used is a Bragg-Brentano focusing diffractometer because it allows to obtain very sharp spectral lines and an important diffracted intensity. The detectors which are the mainly used are the scintillation counters. The most important use in powders diffractometry is the identification of the different phases of a sample. The phases identification consists to compare the unknown sample spectrum at those of standard materials indexed until now. Two methods exist at present. They are explained and their limits in the phases search are given. Another use of the X-ray diffraction is the quantitative analysis. It consists to determine the concentrations of each crystal phases of a sample. The principles of these quantitative methods are given. The lattice parameters of a polycrystal material can be determined from its X-ray pattern too with a very high precision. The way to index powders patterns is given. The residual stresses of materials can also be estimated. The principle of this measured method is explained. It is at last possible to study from an X-ray pattern, the material grain orientations during the different steps of preparation and working. (O.M.). 13 refs., 19 figs., 1 tab

X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

DEFF Research Database (Denmark)

Yennawar, Hemant; Møller, Magda; Gillilan, Richard

2011-01-01

The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer...

Flexible X-ray detector based on sliced lead iodide crystal

Energy Technology Data Exchange (ETDEWEB)

Sun, Hui; Gao, Xiuying [College of Optoelectronic Technology, Chengdu University of Information Technology, Chengdu (China); Department of Materials Science, Sichuan University, Chengdu (China); Zhao, Beijun [Department of Materials Science, Sichuan University, Chengdu (China); Yang, Dingyu; Wangyang, Peihua; Zhu, Xinghua [College of Optoelectronic Technology, Chengdu University of Information Technology, Chengdu (China)

2017-02-15

A promising flexible X-ray detector based on inorganic semiconductor PbI{sub 2} crystal is reported. The sliced crystals mechanically cleaved from an as-grown PbI{sub 2} crystal act as the absorber directly converting the impinging X-ray photons to electron hole pairs. Due to the ductile feature of the PbI{sub 2} crystal, the detector can be operated under a highly curved state with the strain on the top surface up to 1.03% and still maintaining effective detection performance. The stable photocurrent and fast response were obtained with the detector repeated bending to a strain of 1.03% for 100 cycles. This work presents an approach for developing efficient and cost-effective PbI{sub 2}-based flexible X-ray detector. Photocurrent responses of the flexible PbI{sub 2} X-ray detector with the strain on the top surface up to 1.03% proposed in this work with the cross sectional structure and curved detector photograph as insets. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

NATO Advanced Study Institute on Chemical Crystallography with Pulsed Neutrons and Synchrotron X-Rays

CERN Document Server

Jeffrey, George

1988-01-01

X-ray and neutron crystallography have played an increasingly impor­ tant role in the chemical and biochemical sciences over the past fifty years. The principal obstacles in this methodology, the phase problem and com­ puting, have been overcome. The former by the methods developed in the 1960's and just recognised by the 1985 Chemistry Nobel Prize award to Karle and Hauptman, the latter by the dramatic advances that have taken place in computer technology in the past twenty years. Within the last decade, two new radiation sources have been added to the crystallographer's tools. One is synchrotron X-rays and the other is spallation neutrons. Both have much more powerful fluxes than the pre­ vious sources and they are pulsed rather than continuos. New techniques are necessary to fully exploit the intense continuos radiation spectrum and its pulsed property. Both radiations are only available from particular National Laboratories on a guest-user basis for scientists outside these Na­ tional Laboratories. Hi...

Characteristic Ligand-Induced Crystal Forms of HIV-1 Protease Complexes: A Novel Discovery of X-Ray Crystallography

International Nuclear Information System (INIS)

Olajuyigbe, Folasade M.; Geremia, Silvano

2009-10-01

Mixtures of saquinavir (SQV) and ritonavir (RTV) were cocrystallized with HIV-1 protease (PR) in an attempt to compare their relative potencies using a crystallographic approach and factors responsible for the respective crystal forms obtained were examined. The mixture ratio of the SQV/RTV was in the range of 1:1 to 1:50 with increasing concentration of dimethyl sulphoxide (DMSO) used. Two crystal forms of PR complexes were obtained. At concentrations of 0.8 and 1.2 % DMSO using 1:1 and 1:15 ratios of SQV/RTV, the crystal form was monoclinic while increasing the concentration of DMSO to 3.2 and 5.0% using 1:15 and 1:50 ratios of SQV/RTV, the orthorhombic crystal form was obtained. The high resolution X-ray crystal structures of the PR/ inhibitor complexes reveal that crystal forms with respective space groups are dependent on the occupancy of either SQV or RTV in the active site of the PR. The occupancy of either of the PR inhibitors in the active site of PR has interestingly demonstrated unique cooperativity effects in crystallization of protein-ligand complexes. The crystal forms obtained were also related to the concentration of DMSO and ammonium sulphate in crystallization, and storage conditions of purified PR. Surprisingly, the relative occupancies of these inhibitors in the active site suggested a competition between the two inhibitors which were not inhibition constants related. Analysis of the structures in both crystal forms show no difference in DMSO content but at higher concentration of DMSO (3.2 - 5.0%) in the orthorhombic crystal forms, there were protein-sulphate interactions which were absent in the monoclinic forms with lower concentration (0.8 - 1.2%) of DMSO. This work has clearly demonstrated that there is cooperativity in crystallization and the conditions of crystallization influence specific intermolecular contacts in crystal packing (crystal form). (author)

The success story of crystallography.

Science.gov (United States)

Schwarzenbach, Dieter

2012-01-01

Diffractionists usually place the birth of crystallography in 1912 with the first X-ray diffraction experiment of Friedrich, Knipping and Laue. This discovery propelled the mathematical branch of mineralogy to global importance and enabled crystal structure determination. Knowledge of the geometrical structure of matter at atomic resolution had revolutionary consequences for all branches of the natural sciences: physics, chemistry, biology, earth sciences and material science. It is scarcely possible for a single person in a single article to trace and appropriately value all of these developments. This article presents the limited, subjective view of its author and a limited selection of references. The bulk of the article covers the history of X-ray structure determination from the NaCl structure to aperiodic structures and macromolecular structures. The theoretical foundations were available by 1920. The subsequent success of crystallography was then due to the development of diffraction equipment, the theory of the solution of the phase problem, symmetry theory and computers. The many structures becoming known called for the development of crystal chemistry and of data banks. Diffuse scattering from disordered structures without and with partial long-range order allows determination of short-range order. Neutron and electron scattering and diffraction are also mentioned.

Synthesis, x-ray crystallography and leishmanicidal activity of benzimidazolinyl piperidine derivative

International Nuclear Information System (INIS)

Saify, Z.S.; Begum, N.; Yousuf, S.; Ashraf, S.

2014-01-01

Protozoan parasites of the Leishmania genus are the main cause of vector-borne disease leishmaniasis throughout the world. It is caused by at least 17 different species of protozoan Leishmania and transmitted by the bite of infected sand flies. Leishmaniasis could be fatal. Present drugs have limitations to cure it due to the development of drug resistance. Hence, to design an effective leishmanicidal agent would be of great interest. Benzimidazolinyl piperidine has served as potential target due to a vast range of biological activities. In the present study a new 4-(2-keto-1-benzimidazolinyl)piperidine derivative, 1-(2-(4-fluorophenyl)-2-oxoethyl)-4-(2-oxo-2,3-dihydro-1H-benzo(d)imidazol) piperidinium bromide has been synthesized and characterized by X-ray crystallography, 1D and 2D NMR spectroscopy. Evaluation by in vitro leishmanicidal assay showed good activity. (author)

Crystal quality analysis and improvement using x-ray topography

International Nuclear Information System (INIS)

Maj, J.; Goetze, K.; Macrander, A.; Zhong, Y.; Huang, X.; Maj, L.

2008-01-01

The Topography X-ray Laboratory of the Advanced Photon Source (APS) at Argonne National Laboratory operates as a collaborative effort with APS users to produce high performance crystals for APS X-ray beamline experiments. For many years the topography laboratory has worked closely with an on-site optics shop to help ensure the production of crystals with the highest quality, most stress-free surface finish possible. It has been instrumental in evaluating and refining methods used to produce high quality crystals. Topographical analysis has shown to be an effective method to quantify and determine the distribution of stresses, to help identify methods that would mitigate the stresses and improve the Rocking curve, and to create CCD images of the crystal. This paper describes the topography process and offers methods for reducing crystal stresses in order to substantially improve the crystal optics.

Scattering of x-ray from crystal surfaces

International Nuclear Information System (INIS)

Andrews, S.R.; Cowley, R.A.

1985-01-01

X-ray measurements performed on a variety of materials demonstrate that it is possible to observe diffuse scattering that originates in the abrupt change of density at a crystal surface. Such a discontinuity gives rise, in general, to rods of scattering in reciprocal space which are most intense close to the Bragg peaks tau and are well defined for sufficiently smooth surfaces. For wave-vector transfer Q=tau+q the q-dependence of the intensity of scattering gives information on the topographic structure of the crystal surface. Experimental results on crystals of GaAs and KTaO 3 , with surfaces prepared in various ways, were obtained using conventional x-ray techniques with a rotating anode source and can be described by a continuum model of the surface. There are discrepancies between the predictions of the models and the experimental results and the suggest that further experiments are needed to achieve a more complete understanding. (author)

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)

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

Science.gov (United States)

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

2012-01-01

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

Neutron protein crystallography

Energy Technology Data Exchange (ETDEWEB)

Niimura, Nobuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

1998-10-01

X-ray diffraction of single crystal has enriched the knowledge of various biological molecules such as proteins, DNA, t-RNA, viruses, etc. It is difficult to make structural analysis of hydrogen atoms in a protein using X-ray crystallography, whereas neutron diffraction seems usable to directly determine the location of those hydrogen atoms. Here, neutron diffraction method was applied to structural analysis of hen egg-white lysozyme. Since the crystal size of a protein to analyze is generally small (5 mm{sup 3} at most), the neutron beam at the sample position in monochromator system was set to less than 5 x 5 mm{sup 2} and beam divergence to 0.4 degree or less. Neutron imaging plate with {sup 6}Li or Gd mixed with photostimulated luminescence material was used and about 2500 Bragg reflections were recorded in one crystal setting. A total of 38278 reflections for 2.0 A resolution were collected in less than 10 days. Thus, stereo views of Trp-111 omit map around the indol ring of Trp-111 was presented and the three-dimensional arrangement of 696H and 264D atoms in the lysozyme molecules was determined using the omit map. (M.N.)

X-ray scattering from surfaces of organic crystals

DEFF Research Database (Denmark)

Gidalevitz, D.; Feidenhans'l, R.; Smilgies, D.-M.

1997-01-01

X-ray scattering experiments have been performed on the surfaces of organic crystals. The (010) cleavage planes of beta-alanine and alpha-glycine were investigated, and both specular and off-specular crystal truncation rods were measured. This allowed a determination of the molecular layering...

The role of hydrogen bonds in the crystals of 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate and 4-hydroxybenzenesulfonate - X-ray and spectroscopic studies.

Science.gov (United States)

Bryndal, I; Marchewka, M; Wandas, M; Sąsiadek, W; Lorenc, J; Lis, T; Dymińska, L; Kucharska, E; Hanuza, J

2014-04-05

Two new organic-organic salts, 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate (AMNP-TFA), and 2-amino-4-methyl-5-nitropyridinium 4-hydroxybenzenesulfonate (AMNP-HBS), were obtained and characterized by means of FT-IR, FT-Raman and single crystal X-ray crystallography. In the former crystal, the cations, anions and water molecules are linked into layers by three types of hydrogen bonds, NPH⋯O, NAH⋯O and OH⋯O. These layers are connected by weaker CH⋯O hydrogen bonds. In the latter crystal, the cations and anions form one-dimensional structure through a number of hydrogen-bonding interactions involving the OH, NH(+) and NH2 groups as donors. In this case the NPH⋯O and NAH⋯O hydrogen bonds are formed. The combination of interactions between cations and anions results in the formation of columns. Additionally, there are π-π stacking interactions between the columns. The obtained X-ray structural data are related to the vibrational spectra of the studied crystals. Copyright © 2013 Elsevier B.V. All rights reserved.

Structural investigation of oxovanadium(IV) Schiff base complexes: X-ray crystallography, electrochemistry and kinetic of thermal decomposition.

Science.gov (United States)

Asadi, Mozaffar; Asadi, Zahra; Savaripoor, Nooshin; Dusek, Michal; Eigner, Vaclav; Shorkaei, Mohammad Ranjkesh; Sedaghat, Moslem

2015-02-05

A series of new VO(IV) complexes of tetradentate N2O2 Schiff base ligands (L(1)-L(4)), were synthesized and characterized by FT-IR, UV-vis and elemental analysis. The structure of the complex VOL(1)⋅DMF was also investigated by X-ray crystallography which revealed a vanadyl center with distorted octahedral coordination where the 2-aza and 2-oxo coordinating sites of the ligand were perpendicular to the "-yl" oxygen. The electrochemical properties of the vanadyl complexes were investigated by cyclic voltammetry. A good correlation was observed between the oxidation potentials and the electron withdrawing character of the substituents on the Schiff base ligands, showing the following trend: MeO5-H>5-Br>5-Cl. Furthermore, the kinetic parameters of thermal decomposition were calculated by using the Coats-Redfern equation. According to the Coats-Redfern plots the kinetics of thermal decomposition of studied complexes is of the first-order in all stages, the free energy of activation for each following stage is larger than the previous one and the complexes have good thermal stability. The preparation of VOL(1)⋅DMF yielded also another compound, one kind of vanadium oxide [VO]X, with different habitus of crystals, (platelet instead of prisma) and without L(1) ligand, consisting of a V10O28 cage, diaminium moiety and dimethylamonium as a counter ions. Because its crystal structure was also new, we reported it along with the targeted complex. Copyright © 2014 Elsevier B.V. All rights reserved.

CCD [charge-coupled device] sensors in synchrotron x-ray detectors

International Nuclear Information System (INIS)

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

1987-01-01

The intense photon flux from advanced synchrotron light sources, such as the 7-GeV synchrotron being designed at Argonne, require integrating-type detectors. Charge-coupled devices (CCDs) are well suited as synchrotron x-ray detectors. When irradiated indirectly via a phosphor followed by reducing optics, diffraction patterns of 100 cm 2 can be imaged on a 2 cm 2 CCD. With a conversion efficiency of ∼1 CCD electron/x-ray photon, a peak saturation capacity of >10 6 x rays can be obtained. A programmable CCD controller operating at a clock frequency of 20 MHz has been developed. The readout rate is 5 x 10 6 pixels/s and the shift rate in the parallel registers is 10 6 lines/s. The test detector was evaluated in two experiments. In protein crystallography diffraction patterns have been obtained from a lysozyme crystal using a conventional rotating anode x-ray generator. Based on these results we expect to obtain at a synchrotron diffraction images at the rate of ∼1 frame/s or a complete 3-dimensional data set from a single crystal in ∼2 min. 16 refs., 16 figs., 2 tabs

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.

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.

A short working distance multiple crystal x-ray spectrometer

Science.gov (United States)

Dickinson, B.; Seidler, G.T.; Webb, Z.W.; Bradley, J.A.; Nagle, K.P.; Heald, S.M.; Gordon, R.A.; Chou, I.-Ming

2008-01-01

For x-ray spot sizes of a few tens of microns or smaller, a millimeter-sized flat analyzer crystal placed ???1 cm from the sample will exhibit high energy resolution while subtending a collection solid angle comparable to that of a typical spherically bent crystal analyzer (SBCA) at much larger working distances. Based on this observation and a nonfocusing geometry for the analyzer optic, we have constructed and tested a short working distance (SWD) multicrystal x-ray spectrometer. This prototype instrument has a maximum effective collection solid angle of 0.14 sr, comparable to that of 17 SBCA at 1 m working distance. We find good agreement with prior work for measurements of the Mn K?? x-ray emission and resonant inelastic x-ray scattering for MnO, and also for measurements of the x-ray absorption near-edge structure for Dy metal using L??2 partial-fluorescence yield detection. We discuss future applications at third- and fourth-generation light sources. For concentrated samples, the extremely large collection angle of SWD spectrometers will permit collection of high-resolution x-ray emission spectra with a single pulse of the Linac Coherent Light Source. The range of applications of SWD spectrometers and traditional multi-SBCA instruments has some overlap, but also is significantly complementary. ?? 2008 American Institute of Physics.

Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography

Energy Technology Data Exchange (ETDEWEB)

Wall, Michael E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-10-16

X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins.

A multiple CCD X-ray detector and its first operation with synchrotron radiation X-ray beam

CERN Document Server

Suzuki, M; Kumasaka, T; Sato, K; Toyokawa, H; Aries, I F; Jerram, P A; Ueki, T

1999-01-01

A 4x4 array structure of 16 identical CCD X-ray detector modules, called the multiple CCD X-ray detector system (MCCDX), was submitted to its first synchrotron radiation experiment at the protein crystallography station of the RIKEN beamline (BL45XU) at the SPring-8 facility. An X-ray diffraction pattern of cholesterol powder was specifically taken in order to investigate the overall system performance.

Towards phasing using high X-ray intensity

Directory of Open Access Journals (Sweden)

Lorenzo Galli

2015-11-01

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

Towards phasing using high X-ray intensity

International Nuclear Information System (INIS)

Galli, Lorenzo; Son, Sang-Kil; Barends, Thomas R. M.; White, Thomas A.; Barty, Anton; Botha, Sabine; Boutet, Sebastien; Caleman, Carl; Doak, R. Bruce; Nanao, Max H.; Nass, Karol; Shoeman, Robert L.; Timneanu, Nicusor; Santra, Robin; Schlichting, Ilme; Chapman, Henry N.

2015-01-01

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

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

Serial Millisecond Crystallography of Membrane Proteins.

Science.gov (United States)

Jaeger, Kathrin; Dworkowski, Florian; Nogly, Przemyslaw; Milne, Christopher; Wang, Meitian; Standfuss, Joerg

2016-01-01

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a powerful method to determine high-resolution structures of pharmaceutically relevant membrane proteins. Recently, the technology has been adapted to carry out serial millisecond crystallography (SMX) at synchrotron sources, where beamtime is more abundant. In an injector-based approach, crystals grown in lipidic cubic phase (LCP) or embedded in viscous medium are delivered directly into the unattenuated beam of a microfocus beamline. Pilot experiments show the application of microjet-based SMX for solving the structure of a membrane protein and compatibility of the method with de novo phasing. Planned synchrotron upgrades, faster detectors and software developments will go hand-in-hand with developments at free-electron lasers to provide a powerful methodology for solving structures from microcrystals at room temperature, ligand screening or crystal optimization for time-resolved studies with minimal or no radiation damage.

X-ray Crystallography of Biological Macromolecules -RE ...

Indian Academy of Sciences (India)

trons of the atoms scatter X-rays and if identical molecules are arranged in a ... Institute of Science,. Bangalore. ... The first X-ray diffraction pictures were taken and the theory .... various processes involved in biological systems in detail. We.

Extending the methodology of X-ray crystallography to allow X-ray microscopy without X-ray optics

International Nuclear Information System (INIS)

Miao Jianwei; Kirz, Janos; Sayre, David; Charalambous, Pambos

2000-01-01

We demonstrate that the soft X-ray diffraction pattern from a micron-size noncrystalline specimen can be recorded and inverted to form a high-resolution image. The phase problem is overcome by oversampling the diffraction pattern. The image is obtained using an iterative algorithm. The technique provides a method for X-ray microscopy requiring no high-resolution X-ray optical elements or detectors. In the present work, a resolution of approximately 60 nm was obtained, but we believe that considerably higher resolution can be achieved

X-ray yields from high-energy heavy ions channeled through a crystal: their crystal thickness and projectile dependences

International Nuclear Information System (INIS)

Kondo, C.; Takabayashi, Y.; Muranaka, T.; Masugi, S.; Azuma, T.; Komaki, K.; Hatakeyama, A.; Yamazaki, Y.; Takada, E.; Murakami, T.

2005-01-01

X-rays emitted from Ar 17+ , Fe 24+ and Kr 35+ ions of about 400 MeV/u transmitting through a thin Si crystal of about 20 μm thickness have been measured in a planar channeling condition and compared with those in a random incident condition. We have found that the X-ray yield from Ar 17+ ions is larger for the channeling condition than for the random incidence, while those from Fe 24+ and Kr 35+ ions are rather smaller. Such tendencies are explained by considering the projectile dependences of excitation and ionization probabilities together with X-ray emission rates. A crude simulation has qualitatively reproduced these experimental results. When the crystal thickness is small, the X-ray yield is smaller in the channeling condition than in the random incident condition, because excitation is depressed. However, for thicker crystals, the X-ray yield is larger, since the survived population of projectile-bound electrons is larger due to small ionization probabilities under the channeling condition. This inversion occurs at a specific crystal thickness depending on projectile species. Whether the thickness of the used crystal is smaller or larger than the inversion thickness determines enhancement or depression of the X-ray yield in the channeling condition

Development of an X-ray fluorescence holographic measurement system for protein crystals

International Nuclear Information System (INIS)

Sato-Tomita, Ayana; Shibayama, Naoya; Okabe, Takahiro; Happo, Naohisa; Kimura, Koji; Matsushita, Tomohiro; Park, Sam-Yong; Sasaki, Yuji C.; Hayashi, Kouichi

2016-01-01

Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α_2β_2 tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm"3) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

X-Ray Crystallography: One Century of Nobel Prizes

Science.gov (United States)

Galli, Simona

2014-01-01

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

CCD-based X-ray detectors for X-ray diffraction studies

International Nuclear Information System (INIS)

Ito, K.; Amemiya, Y.

1999-01-01

CCD-based X-ray detectors are getting to be used for X-ray diffraction studies especially in the studies where real time (automated) measurements and time-resolved measurements are required. Principles and designs of two typical types of CCD-based detectors are described; one is ths system in which x-ray image intensifiers are coupled to maximize the detective quantum efficiency for time-resolved measurements, and the other is the system in which tapered optical fibers are coupled for the reduction of the image into the CCD, which is optimized for automated measurements for protein crystallography. These CCD-based X-ray detectors have an image distortion and non-uniformity of response to be corrected by software. Correction schemes which we have developed are also described. (author)

Development of an online UV–visible microspectrophotometer for a macromolecular crystallography beamline

Energy Technology Data Exchange (ETDEWEB)

Shimizu, Nobutaka, E-mail: nobutaka.shimizu@kek.jp [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Shimizu, Tetsuya [RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Baba, Seiki; Hasegawa, Kazuya [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Yamamoto, Masaki [RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Kumasaka, Takashi [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

2013-11-01

An online UV–visible microspectrophotometer has been developed for the macromolecular crystallography beamline at SPring-8. Details of this spectrophotometer are reported. Measurement of the UV–visible absorption spectrum is a convenient technique for detecting chemical changes of proteins, and it is therefore useful to combine spectroscopy and diffraction studies. An online microspectrophotometer for the UV–visible region was developed and installed on the macromolecular crystallography beamline, BL38B1, at SPring-8. This spectrophotometer is equipped with a difference dispersive double monochromator, a mercury–xenon lamp as the light source, and a photomultiplier as the detector. The optical path is mostly constructed using mirrors, in order to obtain high brightness in the UV region, and the confocal optics are assembled using a cross-slit diaphragm like an iris to eliminate stray light. This system can measure optical densities up to a maximum of 4.0. To study the effect of radiation damage, preliminary measurements of glucose isomerase and thaumatin crystals were conducted in the UV region. Spectral changes dependent on X-ray dose were observed at around 280 nm, suggesting that structural changes involving Trp or Tyr residues occurred in the protein crystal. In the case of the thaumatin crystal, a broad peak around 400 nm was also generated after X-ray irradiation, suggesting the cleavage of a disulfide bond. Dose-dependent spectral changes were also observed in cryo-solutions alone, and these changes differed with the composition of the cryo-solution. These responses in the UV region are informative regarding the state of the sample; consequently, this device might be useful for X-ray crystallography.

The Beginnings of X-ray Crystallography

Indian Academy of Sciences (India)

IAS Admin

significant change in his career came in 1904 when he gave a talk at Dunedin on ... In his personal reminiscences, W L Bragg talks about his school days in Australia. ... two Braggs on the occasion of the International Year of Crystallography .

Crystallization and preliminary X-ray analysis of the RAD protein from Antirrhinum majus

International Nuclear Information System (INIS)

Stevenson, Clare E. M.; Burton, Nicolas; Costa, Manuela; Nath, Utpal; Dixon, Ray A.; Coen, Enrico S.; Lawson, David M.

2005-01-01

An 8 kDa proteolytic fragment of the A. majus RADIALIS protein was crystallized and X-ray data were collected to 2 Å resolution. Crystals of the RADIALIS protein from Antirrhinum majus were grown by vapour diffusion after limited proteolysis. Mass spectrometry indicated that an 8 kDa fragment had been crystallized corresponding to the predicted MYB DNA-binding domain. X-ray data collected at room temperature were consistent with tetragonal symmetry, whereas data collected at 100 K using crystals cryoprotected by supplementing the mother liquor with ethylene glycol conformed to orthorhombic symmetry. It was subsequently shown that crystals soaked in cryoprotectants that were ‘osmolality-matched’ to the mother liquor retained tetragonal symmetry. Using these crystals, X-ray data were collected in-house to a maximum resolution of 2 Å

Development of an X-ray fluorescence holographic measurement system for protein crystals

Energy Technology Data Exchange (ETDEWEB)

Sato-Tomita, Ayana, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp; Shibayama, Naoya, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp; Okabe, Takahiro [Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke 329-0498 (Japan); Happo, Naohisa [Department of Computer and Network Engineering, Graduate School of Information Sciences, Hiroshima City University, Asa-Minami-Ku, Hiroshima 731-3194 (Japan); Kimura, Koji [Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan); Matsushita, Tomohiro [Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Sayo, Hyogo 679-5198 (Japan); Park, Sam-Yong [Drug Design Laboratory, Department of Medical Life Science, Yokohama City University, Suehiro, Tsurumi, Yokohama 230-0045 (Japan); Sasaki, Yuji C. [Department of Advanced Material Science, Graduate School of Frontier Science, The University of Tokyo, Kashiwanoha, Kashiwa 277-8561 (Japan); Hayashi, Kouichi, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp [Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan); Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan)

2016-06-15

Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α{sub 2}β{sub 2} tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm{sup 3}) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

X-ray spectroscopic study of high-temperature plasmas by curved crystal spectrometer

International Nuclear Information System (INIS)

Morita, Shigeru.

1983-07-01

Extensive studies have been carried out on the structure of X-ray spectra from the highly stripped ions of first transition elements and their behavior in high temperature plasma, using a high resolution crystal spectrometer. Calculation was made on the design and the use of a curved crystal spectrometer for plasma diagnostics. A Johann type crystal spectrometer for measuring X-ray lines was constructed on the basis of the calculation. The characteristics of curved crystals of LiF, Ge and quartz used for the measurement of Kα lines from first transition elements were investigated. Vacuum sparks have been formed for producing high temperature plasma which emits X-ray lines from highly stripped ions. Two different structures of vacuum spark plasma were shown, that is, thermalized point plasma and extended plasma associated with non-thermal electrons. The X-ray lines from the extended plasma, those associated with the K shell from the point plasma and the Kα lines of Ti through Zn from the point plasma have been observed. (Kako, I.)

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

Science.gov (United States)

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

2006-09-06

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

A CCD-based area detector for X-ray crystallography using synchrotron and laboratory sources

International Nuclear Information System (INIS)

Phillips, W.C.; Li Youli; Stanton, M.; Xie Yuanhui; O'Mara, D.; Kalata, K.

1993-01-01

The design and characteristics of a CCD-based area detector suitable for X-ray crystallographic studies using both synchrotron and laboratory sources are described. The active area is 75 mm in diameter, the FWHM of the point response function is 0.20 mm, and for Bragg peaks the dynamic range is 900 and the DQE ∼0.3. The 1320x1035-pixel Kodak CCD is read out into an 8 Mbyte memory system in 0.14 s and digitized to 12 bits. X-ray crystallographic data collected at the NSLS synchrotron from cubic insulin crystals are presented. (orig.)

Serial Femtosecond Crystallography

OpenAIRE

Chapman, Henry N.

2015-01-01

X-ray free-electron lasers produce brief flashes of X-rays that are of about a billion times higher peak brightness than achievable from storage ring sources. Such a tremendous jump in X-ray source capabilities, which came in 2009 when the Linac Coherent Light Source began operations, was unprecedented in the history of X-ray science. Protein structure determination through the method of macromolecular crystallography has consistently benefited from the many increases in source performance fr...

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

International Nuclear Information System (INIS)

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-01-01

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

Energy Technology Data Exchange (ETDEWEB)

McGreevy, Ryan; Singharoy, Abhishek [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Li, Qufei [The University of Chicago, Chicago, IL 60637 (United States); Zhang, Jingfen; Xu, Dong [University of Missouri, Columbia, MO 65211 (United States); Perozo, Eduardo [The University of Chicago, Chicago, IL 60637 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States)

2014-09-01

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Development of high-performance X-ray transparent crystallization plates for in situ protein crystal screening and analysis

Energy Technology Data Exchange (ETDEWEB)

Soliman, Ahmed S. M.; Warkentin, Matthew [Cornell University, Ithaca, New York (United States); Apker, Benjamin [MiTeGen LLC, Ithaca, New York (United States); Thorne, Robert E., E-mail: ret6@cornell.edu [Cornell University, Ithaca, New York (United States); MiTeGen LLC, Ithaca, New York (United States)

2011-07-01

An optically, UV and X-ray transparent crystallization plate suitable for in situ analysis has been developed. The plate uses contact line pinning rather than wells to confine the liquids. X-ray transparent crystallization plates based upon a novel drop-pinning technology provide a flexible, simple and inexpensive approach to protein crystallization and screening. The plates consist of open cells sealed top and bottom by thin optically, UV and X-ray transparent films. The plates do not need wells or depressions to contain liquids. Instead, protein drops and reservoir solution are held in place by rings with micrometre dimensions that are patterned onto the bottom film. These rings strongly pin the liquid contact lines, thereby improving drop shape and position uniformity, and thus crystallization reproducibility, and simplifying automated image analysis of drop contents. The same rings effectively pin solutions containing salts, proteins, cryoprotectants, oils, alcohols and detergents. Strong pinning by rings allows the plates to be rotated without liquid mixing to 90° for X-ray data collection or to be inverted for hanging-drop crystallization. The plates have the standard SBS format and are compatible with standard liquid-handling robots.

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)

Synthesis and X-ray Crystallography of [Mg(H2O)6][AnO2(C2H5COO)3]2 (An = U, Np, or Pu).

Science.gov (United States)

Serezhkin, Viktor N; Grigoriev, Mikhail S; Abdulmyanov, Aleksey R; Fedoseev, Aleksandr M; Savchenkov, Anton V; Serezhkina, Larisa B

2016-08-01

Synthesis and X-ray crystallography of single crystals of [Mg(H2O)6][AnO2(C2H5COO)3]2, where An = U (I), Np (II), or Pu (III), are reported. Compounds I-III are isostructural and crystallize in the trigonal crystal system. The structures of I-III are built of hydrated magnesium cations [Mg(H2O)6](2+) and mononuclear [AnO2(C2H5COO)3](-) complexes, which belong to the AB(01)3 crystallochemical group of uranyl complexes (A = AnO2(2+), B(01) = C2H5COO(-)). Peculiarities of intermolecular interactions in the structures of [Mg(H2O)6][UO2(L)3]2 complexes depending on the carboxylate ion L (acetate, propionate, or n-butyrate) are investigated using the method of molecular Voronoi-Dirichlet polyhedra. Actinide contraction in the series of U(VI)-Np(VI)-Pu(VI) in compounds I-III is reflected in a decrease in the mean An═O bond lengths and in the volume and sphericity degree of Voronoi-Dirichlet polyhedra of An atoms.

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.

Low-temperature crystallization of amorphous silicon and amorphous germanium by soft X-ray irradiation

Energy Technology Data Exchange (ETDEWEB)

Heya, Akira, E-mail: heya@eng.u-hyogo.ac.jp [Department of Materials Science and Chemistry, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671–2280 (Japan); Kanda, Kazuhiro [Laboratory of Advanced Science and Technology for Industry (LASTI), University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678–1205 (Japan); Toko, Kaoru; Sadoh, Taizoh [Department of Electronics, Kyushu University, 744 Nishi-ku, Motooka, Fukuoka 819–0395 (Japan); Amano, Sho [Laboratory of Advanced Science and Technology for Industry (LASTI), University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678–1205 (Japan); Matsuo, Naoto [Department of Materials Science and Chemistry, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671–2280 (Japan); Miyamoto, Shuji [Laboratory of Advanced Science and Technology for Industry (LASTI), University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678–1205 (Japan); Miyao, Masanobu [Department of Electronics, Kyushu University, 744 Nishi-ku, Motooka, Fukuoka 819–0395 (Japan); Mochizuki, Takayasu [Laboratory of Advanced Science and Technology for Industry (LASTI), University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678–1205 (Japan)

2013-05-01

The low-temperature-crystallization effects of soft X-ray irradiation on the structural properties of amorphous Si and amorphous Ge films were investigated. From the differences in crystallization between Si and Ge, it was found that the effects of soft X-ray irradiation on the crystallization strongly depended on the energy band gap and energy level. The crystallization temperatures of the amorphous Si and amorphous Ge films decreased from 953 K to 853 K and 773 K to 663 K, respectively. The decrease in crystallization temperature was also related to atoms transitioning into a quasi-nucleic phase in the films. The ratio of electron excitation and migration effects to thermal effects was controlled using the storage-ring current (photon flux density). Therefore, we believe that low-temperature crystallization can be realized by controlling atomic migration through electron excitation. - Highlights: • This work investigates the crystallization mechanism for soft X-ray irradiation. • The soft X-ray crystallization depended on the energy band gap and energy level. • The decrease in the crystallization temperature for Si and Ge films was 100 K. • This decrement was related to atoms transitioning into a quasi-nucleic phase.

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

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

Parallelization for X-ray crystal structural analysis program

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Hiroshi [Japan Atomic Energy Research Inst., Tokyo (Japan); Minami, Masayuki; Yamamoto, Akiji

1997-10-01

In this report we study vectorization and parallelization for X-ray crystal structural analysis program. The target machine is NEC SX-4 which is a distributed/shared memory type vector parallel supercomputer. X-ray crystal structural analysis is surveyed, and a new multi-dimensional discrete Fourier transform method is proposed. The new method is designed to have a very long vector length, so that it enables to obtain the 12.0 times higher performance result that the original code. Besides the above-mentioned vectorization, the parallelization by micro-task functions on SX-4 reaches 13.7 times acceleration in the part of multi-dimensional discrete Fourier transform with 14 CPUs, and 3.0 times acceleration in the whole program. Totally 35.9 times acceleration to the original 1CPU scalar version is achieved with vectorization and parallelization on SX-4. (author)

Synthesis, X-ray crystal structure, DNA binding and Nuclease activity ...

Indian Academy of Sciences (India)

s12039-016-1125-x. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity of lanthanide(III) complexes of 2-benzoylpyridine acetylhydrazone. KARREDDULA RAJA, AKKILI SUSEELAMMA and KATREDDI HUSSAIN REDDY. ∗.

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

Chromium(III) Complex Obtained from Dipicolinic Acid: Synthesis, Characterization, X-Ray Crystal Structure and Electrochemical Studies

Energy Technology Data Exchange (ETDEWEB)

Ghasemi, Khaled; Rezvani, Ali Reza; Ghasemi, Fatemeh [Univ. of Sistan and Baluchestan, Zahedan (Iran, Islamic Republic of); Razak, Ibrahim Abdul; Rosli, Mohd Mustaqim [Universiti Sains Malaysia, Penang (Malaysia)

2013-10-15

The synthesis, X-ray crystallography, spectroscopic (IR, UV-vis), and electrochemical properties of the title compound, [H{sub 3}O][Cr(dipic){sub 2}] [H{sub 3}O{sup +}.Cl{sup -}] (1), (H{sub 2}dipic = 2,6-pyridinedicarboxylic acid), are reported. This complex crystallizes in the monoclinic space group Cc with a = 14.9006(10) A, b = 12.2114(8) A, c = 8.6337(6) A, α = 90.00 .deg., β = 92.7460(10) .deg., γ = 90.00 .deg., and V = 1569.16(18) A3 with Z = 4. The hydrogen bonding and noncovalent interactions play roles in the stabilization of the structure. In order to gain a better understanding of the most important geometrical parameters in the structure of the complex, atoms in molecules (AIM) method at B3LYP/6-31G level of theory has been employed.

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

Racemic & quasi-racemic protein crystallography enabled by chemical protein synthesis.

Science.gov (United States)

Kent, Stephen Bh

2018-04-04

A racemic protein mixture can be used to form centrosymmetric crystals for structure determination by X-ray diffraction. Both the unnatural d-protein and the corresponding natural l-protein are made by total chemical synthesis based on native chemical ligation-chemoselective condensation of unprotected synthetic peptide segments. Racemic protein crystallography is important for structure determination of the many natural protein molecules that are refractory to crystallization. Racemic mixtures facilitate the crystallization of recalcitrant proteins, and give diffraction-quality crystals. Quasi-racemic crystallization, using a single d-protein molecule, can facilitate the determination of the structures of a series of l-protein analog molecules. Copyright © 2018 Elsevier Ltd. All rights reserved.

Phosphor Scanner For Imaging X-Ray Diffraction

Science.gov (United States)

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

1992-01-01

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

Radiation-shielded double crystal X-ray monochromator for JET

International Nuclear Information System (INIS)

Barnsley, R.; Morsi, H.W.; Rupprecht, G.; Kaellne, E.

1989-01-01

A double crystal X-ray monochromator for absolute wavelength and intensity measurements with very effective shielding of its detector against neutrons and hard X-rays was brought into operation at JET. Fast wavelength scans were taken of impurity line radiation in the wavelength region from about 0.1 nm to 2.3 nm, and monochromatic as well as spectral line scans, for different operational modes of JET. (author) 5 refs., 4 figs

Time dependence of X-ray polarizability of a crystal induced by an intense femtosecond X-ray pulse

Directory of Open Access Journals (Sweden)

A. Leonov

2014-11-01

Full Text Available The time evolution of the electron density and the resulting time dependence of Fourier components of the X-ray polarizability of a crystal irradiated by highly intense femtosecond pulses of an X-ray free-electron laser (XFEL is investigated theoretically on the basis of rate equations for bound electrons and the Boltzmann equation for the kinetics of the unbound electron gas. The photoionization, Auger process, electron-impact ionization, electron–electron scattering and three-body recombination have been implemented in the system of rate equations. An algorithm for the numerical solution of the rate equations was simplified by incorporating analytical expressions for the cross sections of all the electron configurations in ions within the framework of the effective charge model. Using this approach, the time dependence of the inner shell populations during the time of XFEL pulse propagation through the crystal was evaluated for photon energies between 4 and 12 keV and a pulse width of 40 fs considering a flux of 1012 photons pulse−1 (focusing on a spot size of ∼1 µm. This flux corresponds to a fluence ranging between 0.8 and 2.4 mJ µm−2. The time evolution of the X-ray polarizability caused by the change of the atomic scattering factor during the pulse propagation is numerically analyzed for the case of a silicon crystal. The time-integrated polarizability drops dramatically if the fluence of the X-ray pulse exceeds 1.6 mJ µm−2.

Anchoring protein crystals to mounting loops with hydrogel using inkjet technology.

Science.gov (United States)

Shinoda, Akira; Tanaka, Yoshikazu; Yao, Min; Tanaka, Isao

2014-11-01

X-ray crystallography is an important technique for structure-based drug discovery, mainly because it is the only technique that can reveal whether a ligand binds to the target protein as well as where and how it binds. However, ligand screening by X-ray crystallography involves a crystal-soaking experiment, which is usually performed manually. Thus, the throughput is not satisfactory for screening large numbers of candidate ligands. In this study, a technique to anchor protein crystals to mounting loops by using gel and inkjet technology has been developed; the method allows soaking of the mounted crystals in ligand-containing solution. This new technique may assist in the design of a fully automated drug-screening pipeline.

Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline.

Science.gov (United States)

Shimizu, Nobutaka; Shimizu, Tetsuya; Baba, Seiki; Hasegawa, Kazuya; Yamamoto, Masaki; Kumasaka, Takashi

2013-11-01

Measurement of the UV-visible absorption spectrum is a convenient technique for detecting chemical changes of proteins, and it is therefore useful to combine spectroscopy and diffraction studies. An online microspectrophotometer for the UV-visible region was developed and installed on the macromolecular crystallography beamline, BL38B1, at SPring-8. This spectrophotometer is equipped with a difference dispersive double monochromator, a mercury-xenon lamp as the light source, and a photomultiplier as the detector. The optical path is mostly constructed using mirrors, in order to obtain high brightness in the UV region, and the confocal optics are assembled using a cross-slit diaphragm like an iris to eliminate stray light. This system can measure optical densities up to a maximum of 4.0. To study the effect of radiation damage, preliminary measurements of glucose isomerase and thaumatin crystals were conducted in the UV region. Spectral changes dependent on X-ray dose were observed at around 280 nm, suggesting that structural changes involving Trp or Tyr residues occurred in the protein crystal. In the case of the thaumatin crystal, a broad peak around 400 nm was also generated after X-ray irradiation, suggesting the cleavage of a disulfide bond. Dose-dependent spectral changes were also observed in cryo-solutions alone, and these changes differed with the composition of the cryo-solution. These responses in the UV region are informative regarding the state of the sample; consequently, this device might be useful for X-ray crystallography.

Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

Directory of Open Access Journals (Sweden)

Przemyslaw Nogly

2015-03-01

Full Text Available Lipidic cubic phases (LCPs have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX at X-ray free-electron lasers (XFELs. Here, the adaptation of this technology to perform serial millisecond crystallography (SMX at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.

Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

International Nuclear Information System (INIS)

Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.; Sasajima, K.; Matsugaki, N.; Suzuki, M.; Kosuge, T.; Wakatsuki, S.

2004-01-01

An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view, create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments

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.

Asymmetrically cut crystal pair as x-ray magnifier for imaging at high intensity laser facilities

Energy Technology Data Exchange (ETDEWEB)

Szabo, C. I.; Feldman, U. [Artep Inc., 2922 Excelsior Spring Circle, Ellicott City, Maryland 21042 (United States); Seely, J. F. [Space Science Division, Naval Research Laboratory, Washington, DC 20375-5352 (United States); Curry, J. J.; Hudson, L. T.; Henins, A. [National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States)

2010-10-15

The potential of an x-ray magnifier prepared from a pair of asymmetrically cut crystals is studied to explore high energy x-ray imaging capabilities at high intensity laser facilities. OMEGA-EP and NIF when irradiating mid and high Z targets can be a source of high-energy x-rays whose production mechanisms and use as backlighters are a subject of active research. This paper studies the properties and potential of existing asymmetric cut crystal pairs from the National Institute of Standards and Technology (NIST) built in a new enclosure for imaging x-ray sources. The technique of the x-ray magnifier has been described previously. This new approach is aimed to find a design that could be used at laser facilities by magnifying the x-ray source into a screen far away from the target chamber center, with fixed magnification defined by the crystals' lattice spacing and the asymmetry angles. The magnified image is monochromatic and the imaging wavelength is set by crystal asymmetry and incidence angles. First laboratory results are presented and discussed.

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)

Operational experience of a large area x-ray camera for protein crystallography

International Nuclear Information System (INIS)

Joachimiak, A.; Jorden, A. R.; Loeffen, P. W.; Naday, I.; Sanishvili, R.; Westbrook, E. M.

1999-01-01

After 3 years experience of operating very large area (210mm x 210mm) CCD-based detectors at the Advanced Photon Source, operational experience is reported. Four such detectors have been built, two for Structural Biology Center (APS-1 and SBC-2), one for Basic Energy Sciences Synchrotrons Radiation Center (Gold-2) at Argonne National Laboratory's Advanced Photon Source and one for Osaka University by Oxford Instruments, for use at Spring 8 (PX-21O). The detector is specifically designed as a high resolution and fast readout camera for macromolecular crystallography. Design trade-offs for speed and size are reviewed in light of operational experience and future requirements are considered. Operational data and examples of crystallography data are presented, together with plans for more development

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....

Mechanical design of thin-film diamond crystal mounting apparatus for coherence preservation hard x-ray optics

International Nuclear Information System (INIS)

Shu, Deming; Shvyd’ko, Yuri V.; Stoupin, Stanislav; Kim, Kwang-Je

2016-01-01

A new thin-film diamond crystal mounting apparatus has been designed at the Advanced Photon Source (APS) for coherence preservation hard x-ray optics with optimized thermal contact and minimized crystal strain. This novel mechanical design can be applied to new development in the field of: x-ray optics cavities for hard x-ray free-electron laser oscillators (XFELOs), self-seeding monochromators for hard x-ray free-electron laser (XFEL) with high average thermal loading, high heat load diamond crystal monochromators and beam-sharing/beam-split-and-delay devices for XFEL facilities and future upgraded high-brightness coherent x-ray source in the MBA lattice configuration at the APS.

Mechanical design of thin-film diamond crystal mounting apparatus for coherence preservation hard x-ray optics

Energy Technology Data Exchange (ETDEWEB)

Shu, Deming, E-mail: shu@aps.anl.gov; Shvyd’ko, Yuri V.; Stoupin, Stanislav; Kim, Kwang-Je [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, U.S.A (United States)

2016-07-27

A new thin-film diamond crystal mounting apparatus has been designed at the Advanced Photon Source (APS) for coherence preservation hard x-ray optics with optimized thermal contact and minimized crystal strain. This novel mechanical design can be applied to new development in the field of: x-ray optics cavities for hard x-ray free-electron laser oscillators (XFELOs), self-seeding monochromators for hard x-ray free-electron laser (XFEL) with high average thermal loading, high heat load diamond crystal monochromators and beam-sharing/beam-split-and-delay devices for XFEL facilities and future upgraded high-brightness coherent x-ray source in the MBA lattice configuration at the APS.

Crystal structure and dynamics of K2-x(NH4)xSeO4 mixed crystals studied by x-ray and neutron scattering

International Nuclear Information System (INIS)

Smirnov, L.S.; Natkaniec, I.; Loose, A.

2006-01-01

The K 2-x (NH 4 ) x SeO 4 mixed crystals have been studied by powder X-ray and neutron diffraction and inelastic incoherent neutron scattering in a wide temperature range from 300 to 16 K. No phase transition is observed in (NH 4 ) 2 SeO 4 in the range from room temperature to 20 K. The reorientation potential barriers of ammonium ions in the K 2-x (NH 4 ) x SeO 4 mixed crystals increase with the increasing concentration of ammonium ions

Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography.

Science.gov (United States)

Pentelute, Brad L; Mandal, Kalyaneswar; Gates, Zachary P; Sawaya, Michael R; Yeates, Todd O; Kent, Stephen B H

2010-11-21

Here we report the total synthesis of kaliotoxin by 'one pot' native chemical ligation of three synthetic peptides. A racemic mixture of D- and L-kaliotoxin synthetic protein molecules gave crystals in the centrosymmetric space group P1 that diffracted to atomic-resolution (0.95 Å), enabling the X-ray structure of kaliotoxin to be determined by direct methods.

Room-temperature macromolecular serial crystallography using synchrotron radiation

Directory of Open Access Journals (Sweden)

Francesco Stellato

2014-07-01

Full Text Available A new approach for collecting data from many hundreds of thousands of microcrystals using X-ray pulses from a free-electron laser has recently been developed. Referred to as serial crystallography, diffraction patterns are recorded at a constant rate as a suspension of protein crystals flows across the path of an X-ray beam. Events that by chance contain single-crystal diffraction patterns are retained, then indexed and merged to form a three-dimensional set of reflection intensities for structure determination. This approach relies upon several innovations: an intense X-ray beam; a fast detector system; a means to rapidly flow a suspension of crystals across the X-ray beam; and the computational infrastructure to process the large volume of data. Originally conceived for radiation-damage-free measurements with ultrafast X-ray pulses, the same methods can be employed with synchrotron radiation. As in powder diffraction, the averaging of thousands of observations per Bragg peak may improve the ratio of signal to noise of low-dose exposures. Here, it is shown that this paradigm can be implemented for room-temperature data collection using synchrotron radiation and exposure times of less than 3 ms. Using lysozyme microcrystals as a model system, over 40 000 single-crystal diffraction patterns were obtained and merged to produce a structural model that could be refined to 2.1 Å resolution. The resulting electron density is in excellent agreement with that obtained using standard X-ray data collection techniques. With further improvements the method is well suited for even shorter exposures at future and upgraded synchrotron radiation facilities that may deliver beams with 1000 times higher brightness than they currently produce.

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.

Crystallization and preliminary X-ray analysis of argininosuccinate lyase from Streptococcus mutans

International Nuclear Information System (INIS)

Cao, Yan-Li; Li, Gui-Lan; Wang, Kai-Tuo; Zhang, Hong-Yin; Li, Lan-Fen

2011-01-01

Crystals of argininosuccinate lyase from S. mutans were obtained and X-ray data were collected to 2.5 Å resolution in space group R3. Argininosuccinate lyase (ASL) is an important enzyme in arginine synthesis and the urea cycle, which are highly conserved from bacteria to eukaryotes. The gene encoding Streptococcus mutans ASL (smASL) was amplified and cloned into expression vector pET28a. The recombinant smASL protein was expressed in a soluble form in Escherichia coli strain BL21 (DE3) and purified to homogeneity by two-step column chromatography. Crystals suitable for X-ray analysis were obtained and X-ray diffraction data were collected to a resolution of 2.5 Å. The crystals belonged to space group R3, with unit-cell parameters a = b = 254.5, c = 78.3 Å

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

What makes a crystal structure report valid?

NARCIS (Netherlands)

Spek, Anthony L.|info:eu-repo/dai/nl/156517566

2018-01-01

Single crystal X-ray crystallography has developed into a unique, highly automated and accessible tool to obtain detailed information on molecular structures. Proper archival makes that referees, readers and users of the results of reported crystal structures no longer need to depend solely on the

Structural enzymology using X-ray free electron lasers

Directory of Open Access Journals (Sweden)

Christopher Kupitz

2017-07-01

Full Text Available Mix-and-inject serial crystallography (MISC is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i room temperature structures at near atomic resolution, (ii time resolution ranging from microseconds to seconds, and (iii convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.

Synthesis and characterization of the 1.1 adducts of copper(1) halides with bidentatate N,N-bis(benzophenone)-1,2-diiminoethane Schiff bases: Crystal structures of [Cu(bz2en)2][CuX2](X=Br,l) complexes

NARCIS (Netherlands)

Kia, Reza; Mirkhani, Valiollah; Harkema, Sybolt; van Hummel, G.J.

2007-01-01

1:1 adducts of N,N′-bis(benzophenone)-1,2-diiminoethane (bz2en) with copper(I) chloride, bromide and iodide, [Cu(bz2en)2][CuX2] (X = Cl, Br, and I), have been synthesized and the structures of the solid bromide and iodide adducts were determined by X-ray crystallography from single-crystal data. The

Optics for protein microcrystallography using synchrotron and laboratory X-ray sources

International Nuclear Information System (INIS)

Varghese, J.N.; Van Donkelaar, A.; Balaic, D.X.; Barnea, Z.

2000-01-01

Full text: For protein crystallography, a highly-intense focused beam overcomes a serious constraint in current biological research: the inability of many protein molecules to form crystals larger than a few tens of microns in size. High structure-resolution X-ray diffraction analysis of microcrystals is currently only being studied at synchrotron X-ray sources. We shall examine how this is being carried out, and also report the development of a novel tapered glass monocapillary toroidal-mirror optic, which achieves a high-intensity, low-divergence focused beam from a rotating-anode Xray generator. We have used this optic, which demonstrates an ∼28x intensity gain at the beam focus to solve the structure of a plant exoglucanse/inhibtor complex microcrystal to 2.8 Angstroms, with volume equivalent to a 30-micron-edge cube

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

Graphene as a protein crystal mounting material to reduce background scatter.

Science.gov (United States)

Wierman, Jennifer L; Alden, Jonathan S; Kim, Chae Un; McEuen, Paul L; Gruner, Sol M

2013-10-01

The overall signal-to-noise ratio per unit dose for X-ray diffraction data from protein crystals can be improved by reducing the mass and density of all material surrounding the crystals. This article demonstrates a path towards the practical ultimate in background reduction by use of atomically thin graphene sheets as a crystal mounting platform for protein crystals. The results show the potential for graphene in protein crystallography and other cases where X-ray scatter from the mounting material must be reduced and specimen dehydration prevented, such as in coherent X-ray diffraction imaging of microscopic objects.

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

High-Resolution Detector For X-Ray Diffraction

Science.gov (United States)

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

1988-01-01

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

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°

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

Characterization of Metalloproteins and Biomaterials by X-ray Absorption Spectroscopy and X-ray Diffraction

DEFF Research Database (Denmark)

Frankær, Christian Grundahl

This thesis presents thework on combining complementary X-rays techniques for studying the structures of proteins and other biomaterials, and consists of three different projects: (i) Characterization of protein powders with X-ray powder diffraction (XRPD). (ii) The combination of X-ray...... crystallography and X-ray absorption spectroscopy (XAS) applied to studying different hexameric insulin conformations. (iii) The structures of polymorphs of strontium ranelate and the distribution of strontium in bone tissue. A procedure for fast identification and verification of protein powders using XRPD...... was correction for disordered bulk-solvent, but also correction for background and optimization of unit cell parameters have to be taken into account. A sample holder was designed for collecting powder diffraction data on a standard laboratory X-ray powder diffractometer. The background was reduced by use...

Ptychographic x-ray imaging of surfaces on crystal truncation rod

Energy Technology Data Exchange (ETDEWEB)

Zhu, Chenhui; Barbour, Andi; Liu, Yaohua; You, Hoydoo, E-mail: hyou@anl.gov [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Harder, Ross; Xu, Ruqing [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Diaz, Ana; Menzel, Andreas [Paul Scherrer Institut, Villigen PSI 5232 (Switzerland); Komanicky, Vladimir [Faculty of Sciences, Safarik University, Kosice 04154 (Slovakia); Huang, Xiaojing [National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973 (United States); Pierce, Michael S. [School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623 (United States)

2015-03-09

Ptychography is a high-resolution imaging technique, which does not require lenses for image magnification and which provides phase contrast with high sensitivity. Here, we propose to use x-ray ptychography for the imaging of surface structure in crystalline samples. We show that ptychography can be used to image atomic step structures using coherent diffraction patterns recorded along the crystal truncation rod of a crystal surface. In a proof-of-concept experiment on a Pt (111) sample, we present ptychographic reconstructions showing features consistent with surface steps. Due to the penetration power of x-rays, this method could find interesting applications for the study of surface structures under buried interfaces or in harsh environments.

Ptychographic x-ray imaging of surfaces on crystal truncation rod

International Nuclear Information System (INIS)

Zhu, Chenhui; Barbour, Andi; Liu, Yaohua; You, Hoydoo; Harder, Ross; Xu, Ruqing; Diaz, Ana; Menzel, Andreas; Komanicky, Vladimir; Huang, Xiaojing; Pierce, Michael S.

2015-01-01

Ptychography is a high-resolution imaging technique, which does not require lenses for image magnification and which provides phase contrast with high sensitivity. Here, we propose to use x-ray ptychography for the imaging of surface structure in crystalline samples. We show that ptychography can be used to image atomic step structures using coherent diffraction patterns recorded along the crystal truncation rod of a crystal surface. In a proof-of-concept experiment on a Pt (111) sample, we present ptychographic reconstructions showing features consistent with surface steps. Due to the penetration power of x-rays, this method could find interesting applications for the study of surface structures under buried interfaces or in harsh environments

1,4,8,11-Tetra[2-aryl-1-diazenyl]-1,4,8,11-tetraazacyclotetradecanes - synthesis, characterization, and x-ray crystallography of the first tetrakistriazenes to be reported

Energy Technology Data Exchange (ETDEWEB)

Clarke, J.D.; Vaughan, K. [Dept. of Chemistry, Saint Mary' s Univ., Halifax, Nova Scotia (Canada)], E-mail: keith.vaughan@smu.ca; Bertolasi, V. [Dipartimento di Chimica and Centro di Strutturistica Diffrattometrica, Universita' di Ferrara, Ferrara (Italy)

2006-10-15

The reactions of a series of arene diazonium salts with 1,4,8,11-tetraazacyclotetradecane (cyclam) afford the novel compounds, the 1,4,8,11-tetra[2-aryl-1-diazenyl]-1,4,8,11-tetraazacyclotetradecanes (1a-1f), which are the first examples of tetrakistriazenes to be reported. The tetrakistriazenes were characterized by IR spectroscopy, proton and carbon NMR, elemental analysis, high resolution electrospray mass spectrometry, and X-ray crystallography. The analogous reaction of a diazonium salt with 1,4,7-triazacyclononane or 1,5,9-triazacyclododecane yields the tristriazenes 2, 3a, and 3b. The structures of compounds 1c and 1e were solved by X-ray crystallography at low temperature (150 K). Both molecules display a conformation where the four phenyltriazenyl groups point alternately upwards and downwards with respect to the mean macrocyclic plane. (author)

1,4,8,11-Tetra[2-aryl-1-diazenyl]-1,4,8,11-tetraazacyclotetradecanes - synthesis, characterization, and x-ray crystallography of the first tetrakistriazenes to be reported

International Nuclear Information System (INIS)

Clarke, J.D.; Vaughan, K.; Bertolasi, V.

2006-01-01

The reactions of a series of arene diazonium salts with 1,4,8,11-tetraazacyclotetradecane (cyclam) afford the novel compounds, the 1,4,8,11-tetra[2-aryl-1-diazenyl]-1,4,8,11-tetraazacyclotetradecanes (1a-1f), which are the first examples of tetrakistriazenes to be reported. The tetrakistriazenes were characterized by IR spectroscopy, proton and carbon NMR, elemental analysis, high resolution electrospray mass spectrometry, and X-ray crystallography. The analogous reaction of a diazonium salt with 1,4,7-triazacyclononane or 1,5,9-triazacyclododecane yields the tristriazenes 2, 3a, and 3b. The structures of compounds 1c and 1e were solved by X-ray crystallography at low temperature (150 K). Both molecules display a conformation where the four phenyltriazenyl groups point alternately upwards and downwards with respect to the mean macrocyclic plane. (author)

History of protein crystallography in China

OpenAIRE

Rao, Zihe

2007-01-01

China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein cry...

Design parameters of transmission curved crystal spectrometer for hard X-ray diagnoses

International Nuclear Information System (INIS)

Qian Feng; Cao Leifeng; Zhou Weimin; Zhao Zongqing; Gu Yuqiu; Yan Yonghong; Wei Lai; Xiao Shali

2013-01-01

The high resolving measurement of hard X-ray spectra generated in laser-produced plasma is usually performed using a cylindrically curved crystal spectrometer. In this paper, theoretical analysis and numerical simulation are performed to investigate the dependence of the energy range and resolving power on various design parameters, including crystal bending radius, source to crystal standoff distance, source size, location of the detector, etc. The investigation provides a means to design and develop cylindrically transmission curved crystal spectrometer which is used in hard X-ray diagnostics. The results show that crystal bending radius has a great influence on energy range of spectra and resolving power, and the separation between the spectral lines increases with the distance behind the focal circle faster than the line width, resulting in increased resolving power with distance. (authors)

Bent crystal X-ray optics for the diagnosis and applications of laser-produced plasmas

International Nuclear Information System (INIS)

Loetzsch, Robert

2012-01-01

The present thesis discussed several aspects of X-ray optics based on bent crystals and a number of applications of these optics. First, a deeper insight into the reflection properties of elastically bent perfect crystal optics was gained by the consideration of all deformation effects. It was shown that the reflection properties depend on the lateral position on the crystal, an effect that was not addressed before, neither experimentally nor theoretically. To investigate this effect, an apparatus for the measurement of Bragg angles of bent crystals with high angular resolution was built. It was measured that the lattice plane distances of two-dimensionally bent crystals vary laterally by up to 10 -4 . This effect has to be considered in high resolution X-ray spectroscopy and imaging with these bent crystals. It can explain discrepancies in theoretical and experimental spectrometer resolution with spherically bent crystals. Besides these principal investigations, in this thesis a number of X-ray optics were presented that demonstrate the application potential of bent crystal optics. This includes two optics that are used in the field of applications of laser-produced plasmas as high repeating hard X-ray sources. It was shown that an X-ray spectrometer based on full cylinder rings of highly oriented pyrolytic graphite is capable to record the rather weak single shot pulses from a high repeating 1 er-plasma X-ray source. This is possible due to the high collection efficiency of the instrument of up to 5.10 -4 . Furthermore, X-ray optics based on toroidally bent crystals that make it possible to spectrally select a bandwidth of ∝1 eV and focus the ultrashort X-ray pulses from such a laser-plasma source, were designed, prepared and characterized. It was shown that these bent crystals provide the calculated integrated reflectivity, the predicted bandwidth and focus to spot sizes smaller than 60 μm. A novel application of toroidally bent crystals was pointed out: a

Room temperature X- and gamma-ray detectors using thallium bromide crystals

CERN Document Server

Hitomi, K; Shoji, T; Suehiro, T; Hiratate, Y

1999-01-01

Thallium bromide (TlBr) is a compound semiconductor with wide band gap (2.68 eV) and high X- and gamma-ray stopping power. The TlBr crystals were grown by the horizontal travelling molten zone (TMZ) method using purified material. Two types of room temperature X- and gamma-ray detectors were fabricated from the TlBr crystals: TlBr detectors with high detection efficiency for positron annihilation gamma-ray (511 keV) detection and TlBr detectors with high-energy resolution for low-energy X-ray detection. The detector of the former type demonstrated energy resolution of 56 keV FWHM (11%) for 511 keV gamma-rays. Energy resolution of 1.81 keV FWHM for 5.9 keV was obtained from the detector of the latter type. In order to analyze noise characteristics of the detector-preamplifier assembly, the equivalent noise charge (ENC) was measured as a function of the amplifier shaping time for the high-resolution detector. This analysis shows that parallel white noise and 1/f noise were dominant noise sources in the detector...

A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals

Energy Technology Data Exchange (ETDEWEB)

Broecker, Jana; Klingel, Viviane; Ou, Wei-Lin; Balo, Aidin R.; Kissick, David J.; Ogata, Craig M.; Kuo, Anling; Ernst, Oliver P.

2016-10-12

In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometerbased X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi. In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.

Investigation of a novel x-ray tube for the calibration of the x-ray crystal spectrometer in the KSTAR machine

International Nuclear Information System (INIS)

Bak, J.G.; Lee, S.G.

2007-01-01

A novel x-ray tube with a line filament has been developed for the in-situ calibration of the x-ray crystal spectrometer (XCS) in the KSTAR machine. The characteristics of the x-ray tube are investigated from the x-ray images obtained by using a pinhole and a CCD detector. It is found that the image has the width of about 0.1 mm, which is much improved as compared with the previous experimental results. In addition, there is a uniform region around the center of the image within its full length of 13.5 mm. This work may lead to the development of a novel x-ray tube with a line focus, which is required for the calibration of the XCS. Experimental results from the investigation of the x-ray tube are presented and the technical issues in a design of the in-situ calibration system using the x-ray tube for the KSTAR XCS are discussed. (author)

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.)

A diamond-anvil high-pressure cell for X-ray diffraction on a single crystal

International Nuclear Information System (INIS)

Malinowski, M.

1987-01-01

A new diamond-anvil high-pressure cell is described which can be used in single-crystal X-ray diffraction instruments to collect X-ray intensity data from single-crystal samples up to hydrostatic pressures of about 10 GPa. A unique design allows two types of diffraction geometry to be applied in single-crystal high-pressure diffraction experiments. More than 85% of the Ewald sphere is accessible, and a continuous range of 2θ values is available from 0 up to about 160 0 . Pressure may be calibrated by the ruby fluorescence technique or by the use of an internal X-ray-standard single crystal. The design of our diamond-anvil cell would allow, with little or no modification, operation at high and low temperatures, optical studies and powder diffractometer work. (orig.)

Cosmic ray effect on the X-ray Trigger Telescope of UFFO/Lomonosov using YSO scintillation crystal array in space

DEFF Research Database (Denmark)

Kim, M. B.; Jeong, S.; Jeong, H. M.

2017-01-01

UFFO Burst Alert and Trigger telescope (UBAT) is the X-ray trigger telescope of UFFO/Lomonosov to localize X-ray source with coded mask method and X-ray detector. Its X-ray detector is made up of 36 8×8 pixels Yttrium OxyorthoSilicate (Y2SiO5:Ce, YSO) scintillation crystal arrays and 36 64-channe...

Cylindrical Crystal Imaging Spectrometer (CCIS) for cosmic X-ray spectroscopy

Science.gov (United States)

Schnopper, H. W.; Taylor, P. O.

1981-01-01

A "stigmatic" focusing, Bragg crystal spectrometer was developed and used for high spectral resolution X-ray emission line diagnostics on hot laboratory plasmas. The concept be applied at the focal plane of an orbiting X-ray telescope where it offers several advantages over conventional spectrometers, i.e., mechanical simplicity, high resolving power and sensitivity, simultaneous measurement of an extended segment of spectrum, and good imaging properties. The instrument features a simple, unambiguous, non-scanning spectrum readout that is not adversely affected by either spacecraft pointing error or source extent. The performance of the instrument is estimated in the context of the Advanced X-Ray Astrophysical Facility mission.

Mapping the topographic epitope landscape on the urokinase plasminogen activator receptor (uPAR) by surface plasmon resonance and X-ray crystallography

DEFF Research Database (Denmark)

Zhao, Baoyu; Gandhi, Sonu; Yuan, Cai

2015-01-01

The urokinase-type plasminogen activator receptor (uPAR or CD87) is a glycolipid-anchored membrane protein often expressed in the microenvironment of invasive solid cancers and high levels are generally associated with poor patient prognosis (Kriegbaum et al., 2011 [1]). uPAR is organized as a dy...... of these mAbs by X-ray crystallography alone and in complex with uPAR [deposited in the PDB database as 4QTH and 4QTI, respectively]....

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.

X-ray Topographic Investigations of Domain Structure in Czochralski Grown PrxLa1-xAlO3 Crystals

International Nuclear Information System (INIS)

Wieteska, K.; Wierzchowski, W.; Malinowska, A.; Turczynski, S.; Pawlak, D.A.; Lukasiewicz, T.; Lefeld-Sosnowska, M.; Graeff, W.

2010-01-01

In the present paper X-ray diffraction topographic techniques were applied to a number of samples cut from Czochralski grown Pr x La 1-x AlO 3 crystals with different ratio of praseodymium and lanthanum. Conventional and synchrotron X-ray topographic investigations revealed differently developed domain structures dependent on the composition of mixed praseodymium lanthanum aluminium perovskites. Some large mosaic blocks were observed together with the domains. In the best crystals, X-ray topographs revealed striation fringes and individual dislocations inside large domains. Synchrotron topographs allowed us to indicate that the domains correspond to three different crystallographic planes, and to evaluate the lattice misorientation between domains in the range of 20-50 arc min (authors)

Analyzer-based x-ray phase-contrast microscopy combining channel-cut and asymmetrically cut crystals

International Nuclear Information System (INIS)

Hoennicke, M. G.; Cusatis, C.

2007-01-01

An analyzer-based x-ray phase-contrast microscopy (ABM) setup combining a standard analyzer-based x-ray phase-contrast imaging (ABI) setup [nondispersive 4-crystal setup (Bonse-Hart setup)] and diffraction by asymmetrically cut crystals is presented here. An attenuation-contrast microscopy setup with conventional x-ray source and asymmetrically cut crystals is first analyzed. Edge-enhanced effects attributed to phase jumps or refraction/total external reflection on the fiber borders were detected. However, the long exposure times and the possibility to achieve high contrast microscopies by using extremely low attenuation-contrast samples motivated us to assemble the ABM setup using a synchrotron source. This setup was found to be useful for low contrast attenuation samples due to the low exposure time, high contrast, and spatial resolution found. Moreover, thanks to the combination with the nondispersive ABI setup, the diffraction-enhanced x-ray imaging algorithm could be applied

Evaluation of bent-crystal x-ray backlighting and microscopy techniques for the Sandia Z machine.

Science.gov (United States)

Sinars, Daniel B; Bennett, Guy R; Wenger, David F; Cuneo, Michael E; Porter, John L

2003-07-01

X-ray backlighting and microscopy systems for the 1-10-keV range based on spherically or toroidally bent crystals are discussed. These systems are ideal for use on the Sandia Z machine, a megajoule-class x-ray facility. Near-normal-incidence crystal microscopy systems have been shown to be more efficient than pinhole cameras with the same spatial resolution and magnification [Appl. Opt. 37, 1784 (1998)]. We show that high-resolution (< or = 10 microm) x-ray backlighting systems using bent crystals can be more efficient than analogous point-projection imaging systems. Examples of bent-crystal-backlighting results that demonstrate 10-microm resolution over a 20-mm field of view are presented.

Evaluation of bent-crystal x-ray backlighting and microscopy techniques for the Sandia Z machine

International Nuclear Information System (INIS)

Sinars, Daniel B.; Wenger, David F.; Cuneo, Michael E.; Porter, John L.; Bennett, Guy R.

2003-01-01

X-ray backlighting and microscopy systems for the 1-10-keV range based on spherically or toroidally bent crystals are discussed. These systems are ideal for use on the Sandia Z machine, a megajoule-class x-ray facility. Near-normal-incidence crystal microscopy systems have been shown to be more efficient than pinhole cameras with the same spatial resolution and magnification [Appl. Opt. 37, 1784 (1998)]. We show that high-resolution (≤10 μm) x-ray backlighting systems using bent crystals can be more efficient than analogous point-projection imaging systems. Examples of bent-crystal-backlighting results that demonstrate 10-μm resolution over a 20-mm field of view are presented

Microdefects revealed by X-ray diffusion scattering in Czochralski-growth dislocation-free silicon single crystals

International Nuclear Information System (INIS)

Bublik, B.T.; Zotov, N.M.

1997-01-01

Microdefects in the regions of Si crystals having different thermal history defined by growth conditions was studied by the X-ray diffuse scattering method on a triple crystal X-ray diffractometer. It was shown that in such crystals the microdefects with positive strength are prevalent. However, between the above indicated regions the defects with the strength of opposite sign prevail

Doubly curved imaging Bragg crystal spectrometer for X-ray astronomy

DEFF Research Database (Denmark)

Byrnak, B. P.; Christensen, Finn Erland; Westergaard, Niels Jørgen Stenfeldt

1985-01-01

An X-ray spectrometer which is sensitive in the 0.5-7-keV energy range and is intended for use onboard astronomical satellites has been studied. The Bragg reflected rays from a doubly bent crystal positioned downstream of the focal plane of a grazing-incidence concentrator are focused along the a...

Multichannel X-ray detectors

Energy Technology Data Exchange (ETDEWEB)

Khabakhpashev, A

1980-10-01

A typical design is discussed of multiwire proportional counters and their characteristic feature is explained, ie., the possibility of showing one or two coordinates of the X-ray quantum absorption site. The advantages of such instruments are listed, such as increased sensitivity of determination, the possibility of recording radiations of a different intensity, the possibility of on-line data processing and of the digital display of results. The fields of application include X-ray structural analysis in solid state physics, crystallography, molecular biology, astronomy, materials testing, and medicine.

Azo coupling of 4-nitrophenyldiazonium chloride with aliphatic nucleophiles: an integrated organic synthesis and X-ray crystallography experiment; Acoplamento de cloreto de 4-nitrofenildiazonio com nucleofilos alifaticos: experimento integrado de sintese organica e cristalografia de raios X

Energy Technology Data Exchange (ETDEWEB)

Cunha, Silvio; Marques, Monique F.; Rocha, Valeria, E-mail: silviodc@ufba.br [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Instituto de Quimica; Lariucci, Carlito; Vencato, Ivo [Universidade Federal de Goiania (UFG), GO (Brazil). Instituto de Fisica

2013-11-01

This article describes an undergraduate experiment for the synthesis of p-nitrophenyldiazonium chloride and its coupling with acetylacetone and two enaminones, 4-phenylamino-pent-3-en-2-one and 4-amino-pent-3-en-2-one, in an adaptation of a previously reported synthetic protocol. The azo dyes 4-(E)-phenylamino-3-[(E)-2-(4-nitrophenylazo)]-3-penten-2-one and 4-(E)-amino-3-[(E)-2-(4-nitrophenylazo)]-3-penten-2-one were obtained, and the solid state structure of this latter azo compound was characterized by single crystal X-ray diffraction studies. This two-week integrated laboratory approach involves simple synthetic experiments and microwave chemistry in the organic laboratory plus crystallography analysis, suitable for novice students on undergraduate experimental chemistry courses. (author)

Magnetic x-ray microdiffraction

Energy Technology Data Exchange (ETDEWEB)

Evans, Paul G [Computer-Aided Engineering Center, University of Wisconsin, Madison, WI 53706 (United States); Isaacs, Eric D [Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439 (United States)

2006-08-07

Magnetic x-ray microdiffraction uses the structural specificity of x-ray diffraction to probe complex magnetic structures at the length scales relevant to physical phenomena including domain dynamics and phase transitions. Conventional magnetic crystallography techniques such as neutron or x-ray diffraction lack this spatial resolution. The combination of both reciprocal space and real space resolution with a rich magnetic cross section allows new microscopy techniques to be developed and applied to magnetism at the scale of single domains. Potential applications include a wide range of magnetic problems in nanomagnetism, the interaction of strain, polarization and magnetization in complex oxides and spatially resolved studies of magnetic phase transitions. We present the physical basis for x-ray microdiffraction and magnetic scattering processes, review microdiffraction domain imaging techniques in antiferromagnetic and ferromagnetic materials and discuss potential directions for studies. (topical review)

Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography

Directory of Open Access Journals (Sweden)

Marius Schmidt

2013-01-01

Full Text Available Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive substrate present in the crystal is activated. This has particular disadvantages that are circumvented when active substrate is directly provided by diffusion. However, then it is prohibitive to use macroscopic crystals because diffusion times become too long. With small micro- and nanocrystals diffusion times are adequately short for most enzymes and the reaction can be swiftly initiated. We demonstrate here that a time-resolved crystallographic experiment becomes feasible by mixing substrate with enzyme nanocrystals which are subsequently injected into the X-ray beam of a pulsed X-ray source.

A phase-contrast X-ray imaging system--with a 60x30 mm field of view--based on a skew-symmetric two-crystal X-ray interferometer

Energy Technology Data Exchange (ETDEWEB)

Yoneyama, Akio E-mail: a-yoneya@rd.hitachi.co.jp; Takeda, Tohoru; Tsuchiya, Yoshinori; Wu Jin; Lwin, T.-T.; Koizumi, Aritaka; Hyodo, Kazuyuki; Itai, Yuji

2004-05-01

A phase-contrast X-ray imaging system - with a 60x30 mm field of view - for biomedical observations was developed. To extend the observation field of view, the system is fitted with a skew-symmetric two-crystal X-ray interferometer. To attain the required sub-nanoradian mechanical stability between the crystal blocks for precise operation, the interferometer was mounted on two extremely rigid positioning tables (one with a sleeve bearings) and was controlled by a feedback positioning system using phase-lock interferometry. The imaging system produced a 60x30 mm interference pattern with 60% visibility using 17.7 keV monochromatic synchrotron X-rays at the Photon Factory. It was then used to perform radiographic observation (i.e., phase mapping) of rat liver vessels. These results indicate that this imaging system can be used to perform observations of large and in vivo biological samples.

A phase-contrast X-ray imaging system--with a 60x30 mm field of view--based on a skew-symmetric two-crystal X-ray interferometer

International Nuclear Information System (INIS)

Yoneyama, Akio; Takeda, Tohoru; Tsuchiya, Yoshinori; Wu Jin; Lwin, T.-T.; Koizumi, Aritaka; Hyodo, Kazuyuki; Itai, Yuji

2004-01-01

A phase-contrast X-ray imaging system - with a 60x30 mm field of view - for biomedical observations was developed. To extend the observation field of view, the system is fitted with a skew-symmetric two-crystal X-ray interferometer. To attain the required sub-nanoradian mechanical stability between the crystal blocks for precise operation, the interferometer was mounted on two extremely rigid positioning tables (one with a sleeve bearings) and was controlled by a feedback positioning system using phase-lock interferometry. The imaging system produced a 60x30 mm interference pattern with 60% visibility using 17.7 keV monochromatic synchrotron X-rays at the Photon Factory. It was then used to perform radiographic observation (i.e., phase mapping) of rat liver vessels. These results indicate that this imaging system can be used to perform observations of large and in vivo biological samples

Crystal defect studies using x-ray diffuse scattering

Energy Technology Data Exchange (ETDEWEB)

Larson, B.C.

1980-01-01

Microscopic lattice defects such as point (single atom) defects, dislocation loops, and solute precipitates are characterized by local electronic density changes at the defect sites and by distortions of the lattice structure surrounding the defects. The effect of these interruptions of the crystal lattice on the scattering of x-rays is considered in this paper, and examples are presented of the use of the diffuse scattering to study the defects. X-ray studies of self-interstitials in electron irradiated aluminum and copper are discussed in terms of the identification of the interstitial configuration. Methods for detecting the onset of point defect aggregation into dislocation loops are considered and new techniques for the determination of separate size distributions for vacancy loops and interstitial loops are presented. Direct comparisons of dislocation loop measurements by x-rays with existing electron microscopy studies of dislocation loops indicate agreement for larger size loops, but x-ray measurements report higher concentrations in the smaller loop range. Methods for distinguishing between loops and three-dimensional precipitates are discussed and possibilities for detailed studies considered. A comparison of dislocation loop size distributions obtained from integral diffuse scattering measurements with those from TEM show a discrepancy in the smaller sizes similar to that described above.

Crystal defect studies using x-ray diffuse scattering

International Nuclear Information System (INIS)

Larson, B.C.

1980-01-01

Microscopic lattice defects such as point (single atom) defects, dislocation loops, and solute precipitates are characterized by local electronic density changes at the defect sites and by distortions of the lattice structure surrounding the defects. The effect of these interruptions of the crystal lattice on the scattering of x-rays is considered in this paper, and examples are presented of the use of the diffuse scattering to study the defects. X-ray studies of self-interstitials in electron irradiated aluminum and copper are discussed in terms of the identification of the interstitial configuration. Methods for detecting the onset of point defect aggregation into dislocation loops are considered and new techniques for the determination of separate size distributions for vacancy loops and interstitial loops are presented. Direct comparisons of dislocation loop measurements by x-rays with existing electron microscopy studies of dislocation loops indicate agreement for larger size loops, but x-ray measurements report higher concentrations in the smaller loop range. Methods for distinguishing between loops and three-dimensional precipitates are discussed and possibilities for detailed studies considered. A comparison of dislocation loop size distributions obtained from integral diffuse scattering measurements with those from TEM show a discrepancy in the smaller sizes similar to that described above

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

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.

Macromolecular crystallography beamline X25 at the NSLS

Energy Technology Data Exchange (ETDEWEB)

Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E., E-mail: berman@bnl.gov [Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000 (United States)

2014-04-08

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

Macromolecular crystallography beamline X25 at the NSLS

International Nuclear Information System (INIS)

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

2014-01-01

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

Improvement of graphite crystal analyzer for light elements on X-ray fluorescence holography measurement

Science.gov (United States)

Happo, Naohisa; Hada, Takuma; Kubota, Atsushi; Ebisu, Yoshihiro; Hosokawa, Shinya; Kimura, Koji; Tajiri, Hiroo; Matsushita, Tomohiro; Hayashi, Kouichi

2018-05-01

Using a graphite crystal analyzer, focused monochromatic fluorescent X-rays can be obtained on an X-ray fluorescence holography (XFH) measurement. To measure the holograms of elements lighter than Ti, we improved a cylindrical-type crystal analyzer and constructed a small C-shaped analyzer. Using the constructed C-shaped analyzer, a Ca Kα hologram of a fluorite single crystal was obtained, from which we reconstructed a clear atomic image. The XFH measurements for the K, Ca, and Sc elements become possible using the presently constructed analyzer.

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)

X-ray and neutron single-crystal diffraction on [Rbx(NH4)1-x]3H(SO4)2. I. Refinement of crystal structure of phase II with x=0.11 at 300 K

International Nuclear Information System (INIS)

Loose, A.; Wozniak, K.; Dominiak, P.; Smirnov, L.S.; Natkaniec, I.; Frontas'eva, M.V.; Pomyakushina, E.V.; Baranov, A.I.; Dolbinina, V.V

2006-01-01

The study of [Rb x (NH 4 ) 1-x ] 3 H(SO 4 ) 2 mixed crystals by X-ray single-crystal diffraction is known up to now only for x=0.57 at the temperatures 293 and 180 K. The crystal structures at these temperatures as was determined [1] belong to monoclinic phase II (C2/c sp. gr., Z=4). In accordance with this work, ammonium ions should be considered as deformed tetrahedra. Monoclinic phase II on the x-T phase diagram of [Rb x (NH 4 ) 1-x ] 3 H(SO 4 ) 2 mixed crystals, which has earlier been determined by the dielectric spectroscopy, is stabilized below room temperature if Rb concentration exceeds 9%. The presented results of X-ray and neutron single-crystal diffraction of the [Rb 0.11 (NH 4 ) 0.89 ] 3 H(SO 4 ) 2 mixed crystal at T= 300 K show that ammonium ions could be considered as regular tetrahedra

In vacuo X-ray data collection from graphene-wrapped protein crystals

Energy Technology Data Exchange (ETDEWEB)

Warren, Anna J. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Crawshaw, Adam D. [Newcastle University, Newcastle upon Tyne NE2 4HH (United Kingdom); Trincao, Jose; Aller, Pierre; Alcock, Simon; Nistea, Ioana [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Salgado, Paula S. [Newcastle University, Newcastle upon Tyne NE2 4HH (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

2015-09-26

A method is reported for collecting room-temperature data from protein crystals under vacuum by protecting them with a thin graphene layer. The measurement of diffraction data from macromolecular crystal samples held in vacuo holds the promise of a very low X-ray background and zero absorption of incident and scattered beams, leading to better data and the potential for accessing very long X-ray wavelengths (>3 Å) for native sulfur phasing. Maintaining the hydration of protein crystals under vacuum is achieved by the use of liquid jets, as with serial data collection at free-electron lasers, or is side-stepped by cryocooling the samples, as implemented at new synchrotron beamlines. Graphene has been shown to protect crystals from dehydration by creating an extremely thin layer that is impermeable to any exchanges with the environment. Furthermore, owing to its hydrophobicity, most of the aqueous solution surrounding the crystal is excluded during sample preparation, thus eliminating most of the background caused by liquid. Here, it is shown that high-quality data can be recorded at room temperature from graphene-wrapped protein crystals in a rough vacuum. Furthermore, it was observed that graphene protects crystals exposed to different relative humidities and a chemically harsh environment.

In vacuo X-ray data collection from graphene-wrapped protein crystals

International Nuclear Information System (INIS)

Warren, Anna J.; Crawshaw, Adam D.; Trincao, Jose; Aller, Pierre; Alcock, Simon; Nistea, Ioana; Salgado, Paula S.; Evans, Gwyndaf

2015-01-01

A method is reported for collecting room-temperature data from protein crystals under vacuum by protecting them with a thin graphene layer. The measurement of diffraction data from macromolecular crystal samples held in vacuo holds the promise of a very low X-ray background and zero absorption of incident and scattered beams, leading to better data and the potential for accessing very long X-ray wavelengths (>3 Å) for native sulfur phasing. Maintaining the hydration of protein crystals under vacuum is achieved by the use of liquid jets, as with serial data collection at free-electron lasers, or is side-stepped by cryocooling the samples, as implemented at new synchrotron beamlines. Graphene has been shown to protect crystals from dehydration by creating an extremely thin layer that is impermeable to any exchanges with the environment. Furthermore, owing to its hydrophobicity, most of the aqueous solution surrounding the crystal is excluded during sample preparation, thus eliminating most of the background caused by liquid. Here, it is shown that high-quality data can be recorded at room temperature from graphene-wrapped protein crystals in a rough vacuum. Furthermore, it was observed that graphene protects crystals exposed to different relative humidities and a chemically harsh environment

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

International Nuclear Information System (INIS)

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

2004-01-01

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

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

Science.gov (United States)

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

2004-11-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2004-08-01

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

[Research on increasing X-ray protection capability based on photonic crystal technology].

Science.gov (United States)

Li, Ping; Zhao, Peng; Zhang, Rui

2014-06-01

Light cannot be propagated within the range of photonic crystal band gaps. Based on this unique property, we proposed a method to improve anti-radiation capability through one-dimensional photonic crystal coating. Using transmission matrix method, we determined the appropriate dielectric materials, thickness and periodic numbers of photonic crystals through Matlab programming simulation. Then, compound one-dimensional photonic crystal coating was designed which was of high anti-radiation rate within the range of X-ray. As is shown through simulation experiments, the reflection rate against X-ray was higher than 90 percent, and the desired anti-radiation effect was achieved. Thus, this method is able to help solve the technical problems facing the inorganic lead glass such as thickness, weightiness, costliness, high lead equivalent, low transparency and high cost. This method has won China's national invention patent approval, and the patent number is 201220228549.2.

Covering complete proteomes with X-ray structures: a current snapshot

Energy Technology Data Exchange (ETDEWEB)

Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher [University of Alberta, Edmonton, Alberta T6G 2V4 (Canada); Joachimiak, Andrzej, E-mail: andrzejj@anl.gov [Argonne National Laboratory, Argonne, IL 60439 (United States); Kurgan, Lukasz, E-mail: andrzejj@anl.gov [University of Alberta, Edmonton, Alberta T6G 2V4 (Canada)

2014-11-01

The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

Covering complete proteomes with X-ray structures: a current snapshot

International Nuclear Information System (INIS)

Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

2014-01-01

The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined

Crystallography beyond periodic Crystal perfection

International Nuclear Information System (INIS)

Estevez-Rams, E.

2008-01-01

Full text: The discovery of the quasi-crystals [D. Schechtman et. Al., Phys.] Rev. Lett. [53, 1951-1953 (1984)] made very narrow definition of the crystalline state based on the periodicity of a local arrangement of atoms. Since the definition of this State has been a matter of much controversy [G.R. Desiraju, Nature 423, 485 (2003); S. van Smaalen, IUCR Aperiodic Commission Reports. August 7, 2002; International Union of Crystallography. Report of the Executive Committee for 1991; ACTA Cryst. A48, 922-946 (1992)]. We will make a presentation of the current time of the crystallography in this regard from the conceptual point of view. We show the use of the formalism of algorithmic complexity or Kolmogorov [M. Li and P. Vitanyi, An Introduction to Kolmogorov Complexity and Its Applications (Springer Verlag, Heidelberg, 1993), W.H. Zurek, Phys.] Rev. 40, 4731 (1989); Nature 341, 119-124 (1989)] provides a different perspective on the nature of the Crystallographic order. Infinite crystals can be considered solid with zero algorithmic complexities by atom. Show statistical analysis of inorganic compounds [J.L.C. Daams et al., Atlas of Crystal Structure Types for Intermetallic Phases (ASM International, Ohio, 1991), Fachinformationszentrum/NIST Inorganic Crystal Structure Database, Karlsruhe (2003) icsd.fkf.mpg.de] demonstrating that the minimization of complexity is a trend in the crystalline arrangement. We will then compare the degree of disorder of some typical solids according to their algorithmic complexity. Finally, space diffraction will be studied from this same perspective and will be discussed that zero algorithmic complexities by point in space of diffraction does not necessarily imply the same thing for the Atomic arrangement. The discrete portion of the diffraction pattern is a fingerprint of the underlying order but not the actual existence of long-range order. Experimental results will be showcased [E. Estévez-Rams et al., Physical Review B, 63 (2001

Wave-dispersive x-ray spectrometer for simultaneous acquisition of several characteristic lines based on strongly and accurately shaped Ge crystal

International Nuclear Information System (INIS)

Hayashi, Kouichi; Nakajima, Kazuo; Fujiwara, Kozo; Nishikata, Susumu

2008-01-01

Si and Ge are widely used as analyzing crystals for x-rays. Drastic and accurate shaping of Si or Ge gives significant advance in the x-ray field, although covalently bonded Si or Ge crystals have long been believed to be not deformable to various shapes. Recently, we developed a deformation technique for obtaining strongly and accurately shaped Si or Ge wafers of high crystal quality, and the use of the deformed wafer made it possible to produce fine-focused x-rays. In the present study, we prepared a cylindrical Ge wafer with a radius of curvature of 50 mm, and acquired fluorescent x-rays simultaneously from four elements by combining the cylindrical Ge wafer with a position-sensitive detector. The energy resolution of the x-ray fluorescence spectrum was as good as that obtained using a flat single crystal, and its gain was over 100. The demonstration of the simultaneous acquisition of high-resolution x-ray fluorescence spectra indicated various possibilities of x-ray spectrometry, such as one-shot x-ray spectroscopy and highly efficient wave-dispersive x-ray spectrometers

X-ray crystal imagers for inertial confinement fusion experiments (invited)

International Nuclear Information System (INIS)

Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Pawley, C.; Brown, C.M.; Seely, J.

1999-01-01

We report on our continued development of high resolution monochromatic x-ray imaging system based on spherically curved crystals. This system can be extensively used in the relevant experiments of the inertial confinement fusion (ICF) program. The system is currently used, but not limited to diagnostics of the targets ablatively accelerated by the Nike KrF laser. A spherically curved quartz crystal (2d=6.68703 Angstrom, R=200mm) has been used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. Another quartz crystal (2d=8.5099 Angstrom, R=200mm) with the H-like Mg resonance line (1473 eV) has been used for backlit imaging with higher contrast. The spatial resolution of the x-ray optical system is 1.7 μm in selected places and 2 - 3 μm over a larger area. A second crystal with a separate backlighter was added to the imaging system. This makes it possible to make use of all four strips of the framing camera. Time resolved, 20x magnified, backlit monochromatic images of CH planar targets driven by the Nike facility have been obtained with spatial resolution of 2.5 μm in selected places and 5 μm over the focal spot of the Nike laser. We are exploring the enhancement of this technique to the higher and lower backlighter energies. copyright 1999 American Institute of Physics

Applied Crystallography - Proceedings of the XVth Conference

Science.gov (United States)

Morawiec, H.; Ströż, D.

1993-06-01

The Table of Contents for the full book PDF is as follows: * Foreword * The International Centre for Diffraction Data and Its Future Developments * The Rietveld Method - A Historical Perspective * Real Structure in Quantitative Powder Diffraction Phase Analysis * Neutron Focusing Optics in Applied Crystallography * The Crystal Structures of Oxygen Deficient Rare Earth Oxides * Short-Range Order in Layer-Structured Ba1-xSrxBi2Nb2O9 Ferroelectrics * Radial Distribution Function as a Tool of Structural Studies on Noncrystalline Materials * Determination of Radial Distribution Function (RDF) of Electrodeposited Cu-Cd Alloys After Annealing * Spheres Packing as a Factor Describing the Local Environment and Structure Stability * X-Ray Stress Measurement of Samples Combined with Diffraction Line Analysis * Phase Stability and Martensitic Transformation in Cu-Zn and Cu-Zn-Al Single Crystals * Order, Defects, Precipitates and the Martensitic Transformation in β Cu-Zn-Al * Effect of γ Precipitates on the Martensitic Transformation in Cu-Zn-Al Alloys * Phase Transitions and Shape Memory Effect in a Thermomechanically Treated NiTi Alloy * Structure of Martensite and Bainite in CuAlMn Alloys * Glass-Ceramics * Mechanism of Texture Formation at the Rolling of Low Stacking Fault Energy Metals and Alloys * Shear Texture of Zinc and the Conditions of Its Occuring * The Development of Texture of ZnAlMg Sheets Depending on Deformation Geometry * Texture Stability of the D.S. NiAlMoCrTi Alloy After Heat Treatment * X-Ray Diffraction Method for Controlling of Texture Evolution in Layers * Texture and Lattice Imperfections Study of Some Low Alloyed Copper Alloys * Selected Examples of the Calculation of the Orientation Distribution Function for Low Crystal and Sample Symmetries * Automatical X-Ray Quantitative Phase Analysis * Application of a PC Computer for Crystallographic Calculations * Electron Diffraction Analysis using a Personal Computer * CA.R.INE Crystallography Version 2

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

Science.gov (United States)

Soirat, Arnaud J. A.

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

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 crystallographic analysis of dioscorin from Dioscorea japonica

International Nuclear Information System (INIS)

Xue, You-Lin; Miyakawa, Takuya; Sawano, Yoriko; Tanokura, Masaru

2012-01-01

Dioscorin from D. japonica was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. The dioscorin crystal diffracted X-rays to 2.11 Å resolution. Dioscorin, the major tuber storage protein in yam, has been reported to possess carbonic anhydrase, trypsin inhibitor, angiotensin-converting enzyme (ACE) inhibitor, free-radical scavenger, dehydroascorbate reductase and monodehydroascorbate reductase activities. Recent research has also found that dioscorin can enhance immune modulation via the toll-like receptor 4 (TLR-4) signal transduction pathway in RAW 264.7 cells, murine bone-marrow cells and human monocytes ex vivo. Resolving the structure of dioscorin would help in better understanding its activities and would provide clues to understanding the mechanism of its multiple functions. The full-length protein (residues 1–246) with an additional His 6 tag at the N-terminus was expressed in Escherichia coli Rosetta (DE3) cells. After His-tag cleavage and purification, the protein was crystallized by the sitting-drop vapour-diffusion method at 278 K. An X-ray diffraction data set was collected to a resolution of 2.11 Å using a synchrotron X-ray source. The crystal belonged to space group C222 1 , with unit-cell parameters a = 83.5, b = 156.8, c = 83.6 Å, and was estimated to contain two protein molecules per asymmetric unit

Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II

Energy Technology Data Exchange (ETDEWEB)

Budayova-Spano, Monika [European Molecular Biology Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble (France); Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble (France); Fisher, S. Zoë [Department of Biochemistry and Molecular Biology, PO Box 100245, University of Florida, Gainesville, FL 32610 (United States); Dauvergne, Marie-Thérèse [European Molecular Biology Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble (France); Agbandje-McKenna, Mavis [Department of Biochemistry and Molecular Biology, PO Box 100245, University of Florida, Gainesville, FL 32610 (United States); Silverman, David N. [Department of Pharmacology and Therapeutics, PO Box 100267, University of Florida, Gainesville, FL 32610 (United States); Myles, Dean A. A. [European Molecular Biology Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble (France); Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831 (United States); McKenna, Robert, E-mail: rmckenna@ufl.edu [Department of Biochemistry and Molecular Biology, PO Box 100245, University of Florida, Gainesville, FL 32610 (United States); European Molecular Biology Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble (France)

2006-01-01

This article reports the production, crystallization and X-ray structure determination of perdeuterated human carbonic anhydrase (HCA II). The refined structure is shown to be highly isomorphous with hydrogenated HCA II, especially with regard to the active site architecture and solvent network. Human carbonic anhydrase II (HCA II) is a zinc metalloenzyme that catalyzes the reversible hydration and dehydration of carbon dioxide and bicarbonate, respectively. The rate-limiting step in catalysis is the intramolecular transfer of a proton between the zinc-bound solvent (H{sub 2}O/OH{sup −}) and the proton-shuttling residue His64. This distance (∼7.5 Å) is spanned by a well defined active-site solvent network stabilized by amino-acid side chains (Tyr7, Asn62, Asn67, Thr199 and Thr200). Despite the availability of high-resolution (∼1.0 Å) X-ray crystal structures of HCA II, there is currently no definitive information available on the positions and orientations of the H atoms of the solvent network or active-site amino acids and their ionization states. In preparation for neutron diffraction studies to elucidate this hydrogen-bonding network, perdeuterated HCA II has been expressed, purified, crystallized and its X-ray structure determined to 1.5 Å resolution. The refined structure is highly isomorphous with hydrogenated HCA II, especially with regard to the active-site architecture and solvent network. This work demonstrates the suitability of these crystals for neutron macromolecular crystallography.

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.

Crystallization and preliminary X-ray analysis of cecropin B from Bombyx mori

International Nuclear Information System (INIS)

Liu, Zhongyuan; Zhou, Qiangjun; Mao, Xinfang; Zheng, Xiangdong; Guo, Jiubiao; Zhang, Fuchun; Wen, Tingyi; Pang, Hai

2010-01-01

Cecropin B derived from the hemolymph of Bombyx mori has been crystallized by the hanging-drop vapour-diffusion method. The crystal diffracted to 1.43 Å resolution using X-ray radiation. Cecropin B is a 37-residue cationic antimicrobial peptide derived from the haemolymph of Bombyx mori. The precise mechanism by which cecropins exert their antimicrobial and cytolytic activities is not well understood. Crystals of cecropin B were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant at 289 K. The crystal diffracted to 1.43 Å resolution using X-ray radiation and belonged to the orthorhombic space group P1, with unit-cell parameters a = 15.08, b = 22.75, c = 30.20 Å, α = 96.9, β = 103.1, γ = 96.5°. The asymmetric unit contained only one molecule of cecropin B, with a calculated Matthews coefficient of 2.48 Å 3 Da −1 and a solvent content of 50.4%

Racemic DNA crystallography.

Science.gov (United States)

Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

2014-12-22

Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal glass used for X ray and gamma radiation shielding - Part two

International Nuclear Information System (INIS)

Antonio Filho, Joao

2007-01-01

Crystal glass has been widely used as shielding material in gamma radiation sources as well as x-ray generating equipment to replace the plumbiferous glass, in order to minimize exposure to individuals. However, properties of the radiation attenuation of crystal glass commercially available in Brazil, for the different types of energy are not known. For this reason, this work was carried out aiming to determine the radiation attenuation, transmission curves and Half Value Layer. In this work, ten plates of crystal glass, with dimensions of 20 cm x 20 cm and range of thicknesses from 0.5 to 2.0 cm, were used. The plates were X-ray irradiated with potential constants of 60, 80, 110, 150 kV and gamma radiation of 60 Co. Analysis in the properties of the 60 Co radiation attenuation of barite plaster and barite concrete commercially available in Brazil were also carried out. The curves of attenuation and of transmission were obtained for crystal glass, barite plaster and barite concrete (mGy/mA.min) at 1 meter as a function of thickness. The thickness equivalent of a half value layer and deci value layer of crystal glass for all types of radiation and energies studied was also determined. (author)

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

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.

A new paradigm for macromolecular crystallography beamlines derived from high-pressure methodology and results

Energy Technology Data Exchange (ETDEWEB)

Fourme, Roger, E-mail: roger.fourme@synchrotron-soleil.fr [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Girard, Eric [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France); Dhaussy, Anne-Claire [CRISMAT, ENSICAEN, 6 Boulevard du Maréchal Juin, 14000 Caen (France); Medjoubi, Kadda [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Prangé, Thierry [LCRB (UMR 8015 CNRS), Université Paris Descartes, Faculté de Pharmacie, 4 avenue de l’Observatoire, 75270 Paris (France); Ascone, Isabella [ENSCP (UMR CNRS 7223), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Mezouar, Mohamed [ESRF, BP 220, 38043 Grenoble (France); Kahn, Richard [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)

2011-01-01

Macromolecular crystallography at high pressure (HPMX) is a mature technique. Shorter X-ray wavelengths increase data collection efficiency on cryocooled crystals. Extending applications and exploiting spin-off of HPMX will require dedicated synchrotron radiation beamlines based on a new paradigm. Biological structures can now be investigated at high resolution by high-pressure X-ray macromolecular crystallography (HPMX). The number of HPMX studies is growing, with applications to polynucleotides, monomeric and multimeric proteins, complex assemblies and even a virus capsid. Investigations of the effects of pressure perturbation have encompassed elastic compression of the native state, study of proteins from extremophiles and trapping of higher-energy conformers that are often of biological interest; measurements of the compressibility of crystals and macromolecules were also performed. HPMX results were an incentive to investigate short and ultra-short wavelengths for standard biocrystallography. On cryocooled lysozyme crystals it was found that the data collection efficiency using 33 keV photons is increased with respect to 18 keV photons. This conclusion was extended from 33 keV down to 6.5 keV by exploiting previously published data. To be fully exploited, the potential of higher-energy photons requires detectors with a good efficiency. Accordingly, a new paradigm for MX beamlines was suggested, using conventional short and ultra-short wavelengths, aiming at the collection of very high accuracy data on crystals under standard conditions or under high pressure. The main elements of such beamlines are outlined.

Microcontroller-based servo for two-crystal X-ray monochromators.

Science.gov (United States)

Siddons, D P

1998-05-01

Microcontrollers have become increasingly easy to incorporate into instruments as the architectures and support tools have developed. The PIC series is particularly easy to use, and this paper describes a controller used to stabilize the output of a two-crystal X-ray monochromator at a given offset from its peak intensity position, as such monochromators are generally used.

Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography

Energy Technology Data Exchange (ETDEWEB)

Feld, Geoffrey K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); National Institute of Environmental Health Science, Research Triangle Park, NC (United States); Heymann, Michael [Brandeis Univ., Waltham, MA (United States); Univ. of Hamburg and DESY, Hamburg (Germany); Benner, W. Henry [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pardini, Tommaso [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Tsai, Ching -Ju [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Boutet, Sebastien [SLAC National Accelerator Lab., Menlo Park, CA (United States); Coleman, Matthew A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hunter, Mark S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States); Li, Xiaodan [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Messerschmidt, Marc [SLAC National Accelerator Lab., Menlo Park, CA (United States); BioXFEL Science and Technology Center, Buffalo, NY (United States); Opathalage, Achini [Brandeis Univ., Waltham, MA (United States); Pedrini, Bill [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Williams, Garth J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Krantz, Bryan A. [Univ. of California, Berkeley, CA (United States); Fraden, Seth [Brandeis Univ., Waltham, MA (United States); Hau-Riege, Stefan [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Evans, James E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Segelke, Brent W. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Frank, Matthias [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-06-27

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introduction via a translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Z plastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. In conclusion, the benefits and limitations of these low-Z fixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

Design of a High-Throughput Biological Crystallography Beamline for Superconducting Wiggler

International Nuclear Information System (INIS)

Tseng, P.C.; Chang, C.H.; Fung, H.S.; Ma, C.I.; Huang, L.J.; Jean, Y.C.; Song, Y.F.; Huang, Y.S.; Tsang, K.L.; Chen, C.T.

2004-01-01

We are constructing a high-throughput biological crystallography beamline BL13B, which utilizes the radiation generated from a 3.2 Tesla, 32-pole superconducting multipole wiggler, for multi-wavelength anomalous diffraction (MAD), single-wavelength anomalous diffraction (SAD), and other related experiments. This beamline is a standard double crystal monochromator (DCM) x-ray beamline equipped with a collimating mirror (CM) and a focusing mirror (FM). Both the CM and FM are one meter long and made of Si substrate, and the CM is side-cooled by water. Based on detailed thermal analysis, liquid nitrogen (LN2) cooling for both crystals of the DCM has been adopted to optimize the energy resolution and photon beam throughput. This beamline will deliver, through a 100 μm diameter pinhole, photon flux of greater than 1011 photons/sec in the energy range from 6.5 keV to 19 keV, which is comparable to existing protein crystallography beamlines from bending magnet source at high energy storage rings

Purification, crystallization and preliminary X-ray characterization of a haemagglutinin from the seeds of Jatropha curcas

International Nuclear Information System (INIS)

Nair, Divya N.; Suresh, C. G.; Singh, Desh Deepak

2011-01-01

A novel haemagglutinin from Jatropha curcas seeds is purified and crystallized. X-ray diffraction data collected from the rod-shaped crystals were processed in the orthorhombic space group P2 1 2 1 2 1 and the crystals diffracted to 2.8 Å resolution at 103 K. The plant Jatropha curcas (Euphorbiaceae) is an important source of biofuel from the inedible oil present in its toxic seeds. The toxicity arises from the presence of curcin, a ribosome-inactivating protein showing haemagglutination activity. In this communication, the purification, crystallization and preliminary X-ray characterization are reported of a small protein isolated from J. curcas seeds with a molecular mass of ∼10 kDa that agglutinates rabbit erythrocytes. The protein was crystallized using the hanging-drop vapour-diffusion method and also by the microbatch method in 72-well HLA plates, using PEG 8000 as the precipitant in both conditions. X-ray diffraction data collected from the rod-shaped crystals were processed in the orthorhombic space group P2 1 2 1 2 1 . The crystals diffracted to 2.8 Å resolution at 103 K

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.

X-Ray Topography of the Subsurface Crystal Layers in the Skew Asymmetric Reflection Geometry

Directory of Open Access Journals (Sweden)

Swiątek Z.

2016-12-01

Full Text Available The technique of X ray topography with the asymmetric reflection geometry of X-ray diffraction presented in this paper as useful tool for structural characterization of materials, particularly, epitaxial thin films and semiconductor multi-layered crystal systems used for the optoelectronic devices. New possibilities of this technique for a layer-by-layer visualization of structural changes in the subsurface crystal layers are demonstrated for semiconductors after various types of surface treatment, such as chemical etching, laser irradiation and ion implantation.

Purification, crystallization and preliminary X-ray structure analysis of the laccase from Ganoderma lucidum

International Nuclear Information System (INIS)

Lyashenko, Andrey V.; Belova, Oksana; Gabdulkhakov, Azat G.; Lashkov, Alexander A.; Lisov, Alexandr V.; Leontievsky, Alexey A.; Mikhailov, Al’bert M.

2011-01-01

The purification, crystallization and preliminary X-ray structure analysis of the laccase from G. lucidum are reported. The ligninolytic enzymes of the basidiomycetes play a key role in the global carbon cycle. A characteristic property of these enzymes is their broad substrate specificity, which has led to their use in various biotechnologies, thus stimulating research into the three-dimensional structures of ligninolytic enzymes. This paper presents the purification, crystallization and preliminary X-ray analysis of the laccase from the ligninolytic basidiomycete Ganoderma lucidum

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.

Instrumentations in x-ray plasma polarization spectroscopy. Crystal spectrometer, polarimeter and detectors for astronomical observations

Energy Technology Data Exchange (ETDEWEB)

Baronova, Elena O.; Stepanenko, Mikhail M. [RRC Kurchatov Institute, Nuclear Fusion Institute, Moscow (Russian Federation); Jakubowski, Lech [Soltan Institute for Nuclear Studies, Swierk-Otwock (Poland); Tsunemi, Hiroshi [Osaka Univ., Graduate School of Science, Osaka (Japan)

2002-08-01

This report discusses the various problems which are encountered when a crystal spectrometer is used for the purpose of observing polarized x-ray lines. A polarimeter is proposed based on the novel idea of using two series of equivalent atomic planes in a single crystal. The present status of the astronomical x-ray detection techniques are described with emphasis on two dimensional detectors which are polarization sensitive. (author)

Molecular form factors in X-ray crystallography

NARCIS (Netherlands)

Groenewegen, P.P.M.; Feil, D.

1969-01-01

The calculation of molecular form factors from ab initio molecular electronic wavefunctions is discussed, and a scheme for application to X-ray diffraction structure analysis is given. The method is used to calculate the form factor of the NH+4 molecular ion from three accurate molecular

The application of X-ray, γ-ray and neutron diffraction to the characterization of single crystal perfection

International Nuclear Information System (INIS)

Freund, A.; Schneider, J.R.

1976-01-01

The work is divided into the following three chapters: 1) diffraction by perfect and imperfect crystals, 2) experimental apparatus (describing gamma ray, X-ray and neutron diffractometers), 3) application of diffraction methods to the development of neutron monochromators. (WBU) [de

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

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)

Outrunning free radicals in room-temperature macromolecular crystallography

International Nuclear Information System (INIS)

Owen, Robin L.; Axford, Danny; Nettleship, Joanne E.; Owens, Raymond J.; Robinson, James I.; Morgan, Ann W.; Doré, Andrew S.; Lebon, Guillaume; Tate, Christopher G.; Fry, Elizabeth E.; Ren, Jingshan; Stuart, David I.; Evans, Gwyndaf

2012-01-01

A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A 2A adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macromolecular crystallography

Outrunning free radicals in room-temperature macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Owen, Robin L., E-mail: robin.owen@diamond.ac.uk; Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Nettleship, Joanne E.; Owens, Raymond J. [Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Robinson, James I.; Morgan, Ann W. [University of Leeds, Leeds LS9 7FT (United Kingdom); Doré, Andrew S. [Heptares Therapeutics Ltd, BioPark, Welwyn Garden City AL7 3AX (United Kingdom); Lebon, Guillaume; Tate, Christopher G. [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom); Fry, Elizabeth E.; Ren, Jingshan [The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Evans, Gwyndaf [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

2012-06-15

A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A{sub 2A} adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macromolecular crystallography.

X-ray absorption spectroscopy investigation of structurally modified lithium niobate crystals

International Nuclear Information System (INIS)

Vitova, Tonya

2008-02-01

The type and concentration of impurity centers in different valence states are crucial for tuning the photorefractive properties of doped Lithium Niobate (LN) crystals. X-ray Absorption Spectroscopy (XAS) is an appropriate tool for studying the local structure of impurity centers. XAS combined with absorption in UV/VIS/IR and High Resolution X-ray Emission Spectroscopy (HRXES) provide information about the valence state of the dopant ions in as-grown, reduced or oxidized doped LN crystals. Cu (Cu 1+ and Cu 2+ ) and Fe (Fe 2+ and Fe 3+ ) atoms are found in two different valence states, whereas there are indications for a third Mn valency, in addition to Mn 2+ and Mn 3+ in manganese-doped LN crystals. One of the charge compensation mechanisms during reduction of copper- doped LN crystals is outgassing of oxygen atoms. Cu ions in the reduced crystals have at least two different site symmetries: twofold (Cu 1+ ) and sixfold (Cu 2+ ) coordinated by O atoms. Fe and Mn atoms are coordinated by six O atoms. Cu and Fe ions are found to occupy only Li sites, whereas Mn ions are also incorporated into Li and Nb sites. The refractive index change in LN crystals irradiated with 3 He 2+ ions is caused by structurally disordered centers, where Nb atoms are displaced from normal crystallographic sites and Li or/and O vacancies are present. (orig.)

Catalytic Mechanism of Nitrile Hydratase Proposed by Time-resolved X-ray Crystallography Using a Novel Substrate, tert-Butylisonitrile*S⃞

Science.gov (United States)

Hashimoto, Koichi; Suzuki, Hiroyuki; Taniguchi, Kayoko; Noguchi, Takumi; Yohda, Masafumi; Odaka, Masafumi

2008-01-01

Nitrile hydratases (NHases) have an unusual iron or cobalt catalytic center with two oxidized cysteine ligands, cysteine-sulfinic acid and cysteine-sulfenic acid, catalyzing the hydration of nitriles to amides. Recently, we found that the NHase of Rhodococcus erythropolis N771 exhibited an additional catalytic activity, converting tert-butylisonitrile (tBuNC) to tert-butylamine. Taking advantage of the slow reactivity of tBuNC and the photoreactivity of nitrosylated NHase, we present the first structural evidence for the catalytic mechanism of NHase with time-resolved x-ray crystallography. By monitoring the reaction with attenuated total reflectance-Fourier transform infrared spectroscopy, the product from the isonitrile carbon was identified as a CO molecule. Crystals of nitrosylated inactive NHase were soaked with tBuNC. The catalytic reaction was initiated by photo-induced denitrosylation and stopped by flash cooling. tBuNC was first trapped at the hydrophobic pocket above the iron center and then coordinated to the iron ion at 120 min. At 440 min, the electron density of tBuNC was significantly altered, and a new electron density was observed near the isonitrile carbon as well as the sulfenate oxygen of αCys114. These results demonstrate that the substrate was coordinated to the iron and then attacked by a solvent molecule activated by αCys114-SOH. PMID:18948265

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.)

Ultrasmall-angle X-ray scattering analysis of photonic crystal structure

International Nuclear Information System (INIS)

Abramova, V. V.; Sinitskii, A. S.; Grigor'eva, N. A.; Grigor'ev, S. V.; Belov, D. V.; Petukhov, A. V.; Mistonov, A. A.; Vasil'eva, A. V.; Tret'yakov, Yu. D.

2009-01-01

The results of an ultrasmall-angle X-ray scattering study of iron(III) oxide inverse opal thin films are presented. The photonic crystals examined are shown to have fcc structure with amount of stacking faults varying among the samples. The method used in this study makes it possible to easily distinguish between samples with predominantly twinned fcc structure and nearly perfect fcc stacking. The difference observed between samples fabricated under identical conditions is attributed to random layer stacking in the self-assembled colloidal crystals used as templates for fabricating the inverse opals. The present method provides a versatile tool for analyzing photonic crystal structure in studies of inverse opals made of various materials, colloidal crystals, and three-dimensional photonic crystals of other types.

The X-ray crystal bichromator – possible modifications and applications

Energy Technology Data Exchange (ETDEWEB)

Hrdý, Jaromír, E-mail: hrdy@fzu.cz

2017-05-11

The X-ray crystal bichromator is a device which delivers two arbitrarily chosen wavelengths in one beam. The principle and alignment was described in our previous work (Hrdý et al., 2016). With some modifications this device may be used for time-resolved experiments and dual energy imaging.

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

Science.gov (United States)

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

2012-10-08

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

Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls

Directory of Open Access Journals (Sweden)

Aaron J. Oakley

2012-10-01

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

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.

The use of Co2+ for crystallization and structure determination, using a conventional monochromatic X-ray source, of flax rust avirulence protein

International Nuclear Information System (INIS)

Gunčar, Gregor; Wang, Ching-I A.; Forwood, Jade K.; Teh, Trazel; Catanzariti, Ann-Maree; Ellis, Jeffrey G.; Dodds, Peter N.; Kobe, Boštjan

2007-01-01

It is demonstrated that anomalous diffraction based on the signal from a cobalt ion measured on a conventional monochromatic X-ray source can be used to determine the structure of a protein with a novel fold (M. lini avirulence protein AvrL567-A). The approach could be applicable to many metal-binding proteins, particularly when synchrotron radiation is not readily available. Metal-binding sites are ubiquitous in proteins and can be readily utilized for phasing. It is shown that a protein crystal structure can be solved using single-wavelength anomalous diffraction based on the anomalous signal of a cobalt ion measured on a conventional monochromatic X-ray source. The unique absorption edge of cobalt (1.61 Å) is compatible with the Cu Kα wavelength (1.54 Å) commonly available in macromolecular crystallography laboratories. This approach was applied to the determination of the structure of Melampsora lini avirulence protein AvrL567-A, a protein with a novel fold from the fungal pathogen flax rust that induces plant disease resistance in flax plants. This approach using cobalt ions may be applicable to all cobalt-binding proteins and may be advantageous when synchrotron radiation is not readily available

Collecting data in the home laboratory: evolution of X-ray sources, detectors and working practices

Energy Technology Data Exchange (ETDEWEB)

Skarzynski, Tadeusz, E-mail: tadeusz.skarzynski@agilent.com [Agilent Technologies, 10 Mead Road, Yarnton, Oxfordshire (United Kingdom)

2013-07-01

Recent developments in X-ray crystallographic hardware related to structural biology research are presented and discussed. While the majority of macromolecular X-ray data are currently collected using highly efficient beamlines at an ever-increasing number of synchrotrons, there is still a need for high-performance reliable systems for in-house experiments. In addition to crystal screening and optimization of data-collection parameters before a synchrotron trip, the home system allows the collection of data as soon as the crystals are produced to obtain the solution of novel structures, especially by the molecular-replacement method, and is invaluable in achieving the quick turnover that is often required for ligand-binding studies in the pharmaceutical industry. There has been a continuous evolution of X-ray sources, detectors and software developed for in-house use in recent years and a diverse range of tools for structural biology laboratories are available. An overview of the main directions of these developments and examples of specific solutions available to the macromolecular crystallography community are presented in this paper, showing that data collection ‘at home’ is still an attractive proposition complementing the use of synchrotron beamlines.

Phosphoramidates: synthesis, spectroscopy, and X-ray crystallography

Czech Academy of Sciences Publication Activity Database

Shariatinia, Z.; Sohrabi, M.; Yousefi, M.; Kovaľ, Tomáš; Dušek, Michal

2012-01-01

Roč. 23, č. 5 (2012), s. 478-485 ISSN 1042-7163 Grant - others:AV ČR(CZ) AP0701 Program:Akademická prémie - Praemium Academiae Institutional research plan: CEZ:AV0Z10100521 Keywords : phosphoramidates * X-ray diffraction * spectroscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.577, year: 2012

High resolution monochromatic X-ray imaging system based on spherically bent crystals

International Nuclear Information System (INIS)

Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C. M.; Seely, J.; Feldman, U.; Holland, G.

1997-01-01

We have developed a new X-ray imaging system based on spherically curved crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser. The imaging system is used for plasma diagnostics of the main target and for characterization of potential backlighters. A spherically curved quartz crystal (2d=6.687 A, R=200 mm) is used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the X-ray optical system is 3-4 μm. Time resolved backlit monochromatic images of CH planar targets driven by the Nike facility have been obtained with 6-7 μm spatial resolution

Feasibility study into the use of silicon photo-diodes for the alignment of collimated X-rays on the SRS

CERN Document Server

Buffey, S G

1999-01-01

Dynamic alignment of beam on the crystal during data collection was studied. Development of silicon photo-diode detectors for the vacuum ultraviolet and soft X-ray spectral regions has led to the use of such devices as beam alignment tools for Protein Crystallography beamlines on the Synchrotron Radiation Source at Daresbury. Quadrant photo-diodes are used to provide signals proportional to the number of photons hitting each photo-diode, these are amplified, digitised and then summed to give the x-y position of the beam centre. (author)

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources.

Science.gov (United States)

Tang, M X; Zhang, Y Y; E, J C; Luo, S N

2018-05-01

Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic-plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of the diffraction patterns is discussed.

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources

Energy Technology Data Exchange (ETDEWEB)

Tang, M. X.; Zhang, Y. Y.; E, J. C.; Luo, S. N.

2018-04-24

Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic–plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of the diffraction patterns is discussed.

Langmuir-Blodgett nanotemplates for protein crystallography.

Science.gov (United States)

Pechkova, Eugenia; Nicolini, Claudio

2017-12-01

The new generation of synchrotrons and microfocused beamlines has enabled great progress in X-ray protein crystallography, resulting in new 3D atomic structures for proteins of high interest to the pharmaceutical industry and life sciences. It is, however, often still challenging to produce protein crystals of sufficient size and quality (order, intensity of diffraction, radiation stability). In this protocol, we provide instructions for performing the Langmuir-Blodgett (LB) nanotemplate method, a crystallization approach that can be used for any protein (including membrane proteins). We describe how to produce highly ordered 2D LB protein monolayers at the air-water interface and deposit them on glass slides. LB-film formation can be observed by surface-pressure measurements and Brewster angle microscopy (BAM), although its quality can be characterized by atomic force microscopy (AFM) and nanogravimetry. Such films are then used as a 2D template for triggering 3D protein crystal formation by hanging-drop vapor diffusion. The procedure for forming the 2D template takes a few minutes. Structural information about the protein reorganization in the LB film during the crystallization process on the nano level can be obtained using an in situ submicron GISAXS (grazing-incidence small-angle X-ray scattering) method. MicroGISAXS spectra, measured directly at the interface of the LB films and protein solution in real time, as described in this protocol, can be interpreted in terms of the buildup of layers, islands, or holes. In our experience, the obtained LB crystals take 1-10 d to prepare and they are more ordered and radiation stable as compared with those produced using other crystallization methods.

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

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°

Phase modulation due to crystal diffraction by ptychographic imaging

Science.gov (United States)

Civita, M.; Diaz, A.; Bean, R. J.; Shabalin, A. G.; Gorobtsov, O. Yu.; Vartanyants, I. A.; Robinson, I. K.

2018-03-01

Solving the phase problem in x-ray crystallography has occupied a considerable scientific effort in the 20th century and led to great advances in structural science. Here we use x-ray ptychography to demonstrate an interference method which measures the phase of the beam transmitted through a crystal, relative to the incoming beam, when diffraction takes place. The observed phase change of the direct beam through a small gold crystal is found to agree with both a quasikinematical model and full dynamical theories of diffraction. Our discovery of a diffraction contrast mechanism will enhance the interpretation of data obtained from crystalline samples using the ptychography method, which provides some of the most accurate x-ray phase-contrast images.

Injection Methods and Instrumentation for Serial X-ray Free Electron Laser Experiments

Science.gov (United States)

James, Daniel

Scientists have used X-rays to study biological molecules for nearly a century. Now with the X-ray free electron laser (XFEL), new methods have been developed to advance structural biology. These new methods include serial femtosecond crystallography, single particle imaging, solution scattering, and time resolved techniques. The XFEL is characterized by high intensity pulses, which are only about 50 femtoseconds in duration. The intensity allows for scattering from microscopic particles, while the short pulses offer a way to outrun radiation damage. XFELs are powerful enough to obliterate most samples in a single pulse. While this allows for a "diffract and destroy" methodology, it also requires instrumentation that can position microscopic particles into the X-ray beam (which may also be microscopic), continuously renew the sample after each pulse, and maintain sample viability during data collection. Typically these experiments have used liquid microjets to continuously renew sample. The high flow rate associated with liquid microjets requires large amounts of sample, most of which runs to waste between pulses. An injector designed to stream a viscous gel-like material called lipidic cubic phase (LCP) was developed to address this problem. LCP, commonly used as a growth medium for membrane protein crystals, lends itself to low flow rate jetting and so reduces the amount of sample wasted significantly. This work discusses sample delivery and injection for XFEL experiments. It reviews the liquid microjet method extensively, and presents the LCP injector as a novel device for serial crystallography, including detailed protocols for the LCP injector and anti-settler operation.

Crystal glass and barite used for x ray and gamma radiation shielding

International Nuclear Information System (INIS)

Antonio Filho, Joao

2008-01-01

Full text: Crystal glass, barite plaster and barite concrete has been widely used as shielding material in gamma radiation sources as well as x-ray generating equipment to replace the plumbiferous glass and in the wall covering, in order to minimize exposure to individuals. However, properties of the radiation attenuation of crystal glass commercially available in Brazil, for the different types of energy are not known. For this reason, this work was carried out aiming to determine the radiation attenuation, transmission curves and Half Value Layer. In this work, ten plates of crystal glass, with dimensions of 20 cm x 20 cm and range of thicknesses from 0.5 to 2.0 cm, and ten plates of barite plaster and five plates of barite concrete, with dimensions of 20 x 20 cm 2 and range of thicknesses from 1,0 to 5,0 cm, were used. The plates were X-ray irradiated with potential constants of 60, 80, 110, 150 kV and gamma radiation of 60 Co. Analysis in the properties of the 60 Co radiation attenuation of barite plaster and barite concrete commercially available in Brazil were also carried out. The curves of attenuation and of transmission were obtained for crystal glass, barite plaster and barite concrete (mGy/m A.min) at 1 meter as a function of thickness. The thickness equivalent of a half value layer and deci value layer of crystal glass for all types of radiation and energies studied was also determined. Although their use permits the dimensioning of the armor covering for external x-radiation whit precision and safety without elevating the cost of protection. (author)

A high resolution reflecting crystal spectrometer to measure 3 keV pionic hydrogen and deuterium X-rays

International Nuclear Information System (INIS)

Badertscher, A.; Bogdan, M.; Goudsmit, P.F.A.; Knecht, L.; Leisi, H.J.; Schroeder, H.C.; Sigg, D.; Zhao, Z.G.; Chatellard, D.; Egger, J.P.; Jeannet, E.; Aschenauer, E.C.; Gabathuler, K.; Simons, L.M.; Rusi El Hassani, A.J.

1993-01-01

A reflecting crystal spectrometer consisting of three cylindrically bent quartz (110) crystals is described. It was designed to measure the 3 keV K β X-rays from pionic hydrogen and deuterium. Charge coupled devices (CCDs) were used as X-ray detectors. Projecting the reflexes of all three crystals on one common focus, an instrumental energy resolution below 1 eV was obtained at an energy of 2.9 keV. (orig.)

X-ray absorption spectroscopy investigation of structurally modified lithium niobate crystals

Energy Technology Data Exchange (ETDEWEB)

Vitova, Tonya

2008-02-15

The type and concentration of impurity centers in different valence states are crucial for tuning the photorefractive properties of doped Lithium Niobate (LN) crystals. X-ray Absorption Spectroscopy (XAS) is an appropriate tool for studying the local structure of impurity centers. XAS combined with absorption in UV/VIS/IR and High Resolution X-ray Emission Spectroscopy (HRXES) provide information about the valence state of the dopant ions in as-grown, reduced or oxidized doped LN crystals. Cu (Cu{sup 1+} and Cu{sup 2+}) and Fe (Fe{sup 2+} and Fe{sup 3+}) atoms are found in two different valence states, whereas there are indications for a third Mn valency, in addition to Mn{sup 2+} and Mn{sup 3+} in manganese-doped LN crystals. One of the charge compensation mechanisms during reduction of copper- doped LN crystals is outgassing of oxygen atoms. Cu ions in the reduced crystals have at least two different site symmetries: twofold (Cu{sup 1+}) and sixfold (Cu{sup 2+}) coordinated by O atoms. Fe and Mn atoms are coordinated by six O atoms. Cu and Fe ions are found to occupy only Li sites, whereas Mn ions are also incorporated into Li and Nb sites. The refractive index change in LN crystals irradiated with {sup 3}He{sup 2+} ions is caused by structurally disordered centers, where Nb atoms are displaced from normal crystallographic sites and Li or/and O vacancies are present. (orig.)

Crystallization and preliminary X-ray characterization of full-length Chlamydomonas reinhardtii centrin

International Nuclear Information System (INIS)

Alfaro, Elisa; Valle Sosa, Liliana del; Sanoguet, Zuleika; Pastrana-Ríos, Belinda; Schreiter, Eric R.

2008-01-01

C. reinhardtii centrin, an EF-hand calcium-binding protein localized to the microtubule-organizing center of eukaryotic organisms, has been crystallized in the presence of the model peptide melittin. X-ray diffraction data were collected to 2.2 Å resolution. Chlamydomonas reinhardtii centrin is a member of the EF-hand calcium-binding superfamily. It is found in the basal body complex and is important for flagellar motility. Like other members of the EF-hand family, centrin interacts with and modulates the function of other proteins in a calcium-dependent manner. To understand how C. reinhardtii centrin interacts with its protein targets, it has been crystallized in the presence of the model peptide melittin and X-ray diffraction data have been collected to 2.2 Å resolution. The crystals are orthorhombic, with unit-cell parameters a = 52.1, b = 114.4, c = 34.8 Å, and are likely to belong to space group P2 1 2 1 2

Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures

International Nuclear Information System (INIS)

Joseph, Raji E.; Ginder, Nathaniel D.; Hoy, Julie A.; Nix, Jay C.; Fulton, D. Bruce; Honzatko, Richard B.; Andreotti, Amy H.

2012-01-01

The interleukin-2 tyrosine kinase Src homology 2 domain was crystallized and its structure was solved to 2.35 Å resolution. The structure reveals a domain-swapped dimer that is related to other dimeric SH2 domains solved previously. The cis–trans-prolyl isomerization that is evident from solution studies of Itk SH2 cannot be observed in the crystal structure. The crystal structure of the interleukin-2 tyrosine kinase Src homology domain (Itk SH2) is described and it is found that unlike in studies of this domain using NMR spectroscopy, cis–trans-prolyl isomerization is not readily detected in the crystal structure. Based on similarities between the Itk SH2 crystal form and the cis form of the Itk SH2 NMR structure, it is concluded that it is likely that the prolyl imide bond at least in part adopts the cis conformation in the crystal form. However, the lack of high-resolution data and the dynamic nature of the proline-containing loop mean that the precise imide-bond conformation cannot be determined and prolyl cis–trans isomerization in the crystal cannot be ruled out. Given the preponderance of structures that have been solved by X-ray crystallography in the Protein Data Bank, this result supports the notion that prolyl isomerization in folded proteins has been underestimated among known structures. Interestingly, while the precise status of the proline residue is ambiguous, Itk SH2 crystallizes as a domain-swapped dimer. The domain-swapped structure of Itk SH2 is similar to the domain-swapped SH2 domains of Grb2 and Nck, with domain swapping occurring at the β-meander region of all three SH2 domains. Thus, for Itk SH2 structural analysis by NMR spectroscopy and X-ray crystallography revealed very different structural features: proline isomerization versus domain-swapped dimerization, respectively

Multiple wavelength X-ray monochromators

International Nuclear Information System (INIS)

Steinmeyer, P.A.

1992-01-01

An improved apparatus and method is provided for separating input x-ray radiation containing first and second x-ray wavelengths into spatially separate first and second output radiation which contain the first and second x-ray wavelengths, respectively. The apparatus includes a crystalline diffractor which includes a first set of parallel crystal planes, where each of the planes is spaced a predetermined first distance from one another. The crystalline diffractor also includes a second set of parallel crystal planes inclined at an angle with respect to the first set of crystal planes where each of the planes of the second set of parallel crystal planes is spaced a predetermined second distance from one another. In one embodiment, the crystalline diffractor is comprised of a single crystal. In a second embodiment, the crystalline diffractor is comprised of a stack of two crystals. In a third embodiment, the crystalline diffractor includes a single crystal that is bent for focusing the separate first and second output x-ray radiation wavelengths into separate focal points. 3 figs

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.

Science.gov (United States)

Gardberg, Anna S; Del Castillo, Alexis Rae; Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew P; Myles, Dean A A

2010-05-01

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

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.

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.

Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum

Energy Technology Data Exchange (ETDEWEB)

Nithianantham, Stanley [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States); Xu, Minghua [Department of Biological Sciences, School of Dentistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905 (United States); Wu, Nan [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States); Han, Yiping W., E-mail: ywh2@case.edu [Department of Biological Sciences, School of Dentistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905 (United States); Department of Pathology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Shoham, Menachem, E-mail: ywh2@case.edu [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States)

2006-12-01

The FadA adhesin from F. nucleatum, which is involved in bacterial attachment and invasion of human oral epithelial cells, has been crystallized in space group P6{sub 1} or P6{sub 5}, and X-ray data have been collected to 1.9 Å resolution. Fusobacterium nucleatum is a Gram-negative anaerobe prevalent in the oral cavity that is associated with periodontal disease, preterm birth and infections in other parts of the human body. The bacteria attach to and invade epithelial and endothelial cells in the gum tissue and elsewhere via a 13.7 kDa adhesin protein FadA (Fusobacterium adhesin A). FadA exists in two forms: the intact form (pre-FadA), consisting of 129 amino acids, and the mature form (mFadA), which lacks an 18-residue signal sequence. Both forms have been expressed in Escherichia coli and purified. mFadA has been crystallized. The crystals belong to the hexagonal space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 59.3, c = 125.7 Å and one molecule per asymmetric unit. The crystals exhibit an unusually high solvent content of 74%. Synchrotron X-ray data have been collected to 1.9 Å. The crystals are suitable for X-ray structure determination. The crystal structure of FadA may provide a basis for the development of therapeutic agents to combat periodontal disease and other infections associated with F. nucleatum.

Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum

International Nuclear Information System (INIS)

Nithianantham, Stanley; Xu, Minghua; Wu, Nan; Han, Yiping W.; Shoham, Menachem

2006-01-01

The FadA adhesin from F. nucleatum, which is involved in bacterial attachment and invasion of human oral epithelial cells, has been crystallized in space group P6 1 or P6 5 , and X-ray data have been collected to 1.9 Å resolution. Fusobacterium nucleatum is a Gram-negative anaerobe prevalent in the oral cavity that is associated with periodontal disease, preterm birth and infections in other parts of the human body. The bacteria attach to and invade epithelial and endothelial cells in the gum tissue and elsewhere via a 13.7 kDa adhesin protein FadA (Fusobacterium adhesin A). FadA exists in two forms: the intact form (pre-FadA), consisting of 129 amino acids, and the mature form (mFadA), which lacks an 18-residue signal sequence. Both forms have been expressed in Escherichia coli and purified. mFadA has been crystallized. The crystals belong to the hexagonal space group P6 1 or P6 5 , with unit-cell parameters a = b = 59.3, c = 125.7 Å and one molecule per asymmetric unit. The crystals exhibit an unusually high solvent content of 74%. Synchrotron X-ray data have been collected to 1.9 Å. The crystals are suitable for X-ray structure determination. The crystal structure of FadA may provide a basis for the development of therapeutic agents to combat periodontal disease and other infections associated with F. nucleatum

Epitaxial Ge-crystal arrays for X-ray detection

International Nuclear Information System (INIS)

Kreiliger, T; Falub, C V; Müller, E; Känel, H von; Isa, F; Isella, G; Chrastina, D; Bergamaschini, R; Marzegalli, A; Miglio, L; Kaufmann, R; Niedermann, P; Neels, A; Dommann, A; Meduňa, M

2014-01-01

Monolithic integration of an X-ray absorber layer on a Si CMOS chip might be a potentially attractive way to improve detector performance at acceptable costs. In practice this requires, however, the epitaxial growth of highly mismatched layers on a Si-substrate, both in terms of lattice parameters and thermal expansion coefficients. The generation of extended crystal defects, wafer bowing and layer cracking have so far made it impossible to put the simple concept into practice. Here we present a way in which the difficulties of fabricating very thick, defect-free epitaxial layers may be overcome. It consists of an array of densely packed, three-dimensional Ge-crystals on a patterned Si(001) substrate. The finite gap between neighboring micron-sized crystals prevents layer cracking and substrate bowing, while extended defects are driven to the crystal sidewalls. We show that the Ge-crystals are indeed defect-free, despite the lattice misfit of 4.2%. The electrical characteristics of individual Ge/Si heterojunction diodes are obtained from in-situ measurements inside a scanning electron microscope. The fabrication of monolithically integrated detectors is shown to be compatible with Si-CMOS processing

Wavelength dispersive X-ray absorption fine structure imaging by parametric X-ray radiation

International Nuclear Information System (INIS)

Inagaki, Manabu; Sakai, Takeshi; Sato, Isamu; Hayakawa, Yasushi; Nogami, Kyoko; Tanaka, Toshinari; Hayakawa, Ken; Nakao, Keisuke

2008-01-01

The parametric X-ray radiation (PXR) generator system at Laboratory for Electron Beam Research and Application (LEBRA) in Nihon University is a monochromatic and coherent X-ray source with horizontal wavelength dispersion. The energy definition of the X-rays, which depends on the horizontal size of the incident electron beam on the generator target crystal, has been investigated experimentally by measuring the X-ray absorption near edge structure (XANES) spectra on Cu and CuO associated with conventional X-ray absorption imaging technique. The result demonstrated the controllability of the spectrum resolution of XANES by adjusting of the horizontal electron beam size on the target crystal. The XANES spectra were obtained with energy resolution of several eV at the narrowest case, which is in qualitative agreement with the energy definition of the PXR X-rays evaluated from geometrical consideration. The result also suggested that the wavelength dispersive X-ray absorption fine structure measurement associated with imaging technique is one of the promising applications of PXR. (author)

Biological X-ray absorption spectroscopy (BioXAS): a valuable tool for the study of trace elements in the life sciences.

Science.gov (United States)

Strange, Richard W; Feiters, Martin C

2008-10-01

Using X-ray absorption spectroscopy (XAS) the binding modes (type and number of ligands, distances and geometry) and oxidation states of metals and other trace elements in crystalline as well as non-crystalline samples can be revealed. The method may be applied to biological systems as a 'stand-alone' technique, but it is particularly powerful when used alongside other X-ray and spectroscopic techniques and computational approaches. In this review, we highlight how biological XAS is being used in concert with crystallography, spectroscopy and computational chemistry to study metalloproteins in crystals, and report recent applications on relatively rare trace elements utilised by living organisms and metals involved in neurodegenerative diseases.

Observation of dislocations in crystals using X-ray and electron transmission

International Nuclear Information System (INIS)

Morlevat, J.P.

1965-10-01

Two approaches of the dynamical theory of diffraction (EWALD's and AUTHIER's) are recalled briefly. In the light of these theories, one then considers what information concerning the dislocations existing in a crystal can be obtained by X-Ray as well as electron diffraction. (author) [fr

Fully convergent chemical synthesis of ester insulin: determination of the high resolution X-ray structure by racemic protein crystallography.

Science.gov (United States)

Avital-Shmilovici, Michal; Mandal, Kalyaneswar; Gates, Zachary P; Phillips, Nelson B; Weiss, Michael A; Kent, Stephen B H

2013-02-27

Efficient total synthesis of insulin is important to enable the application of medicinal chemistry to the optimization of the properties of this important protein molecule. Recently we described "ester insulin"--a novel form of insulin in which the function of the 35 residue C-peptide of proinsulin is replaced by a single covalent bond--as a key intermediate for the efficient total synthesis of insulin. Here we describe a fully convergent synthetic route to the ester insulin molecule from three unprotected peptide segments of approximately equal size. The synthetic ester insulin polypeptide chain folded much more rapidly than proinsulin, and at physiological pH. Both the D-protein and L-protein enantiomers of monomeric DKP ester insulin (i.e., [Asp(B10), Lys(B28), Pro(B29)]ester insulin) were prepared by total chemical synthesis. The atomic structure of the synthetic ester insulin molecule was determined by racemic protein X-ray crystallography to a resolution of 1.6 Å. Diffraction quality crystals were readily obtained from the racemic mixture of {D-DKP ester insulin + L-DKP ester insulin}, whereas crystals were not obtained from the L-ester insulin alone even after extensive trials. Both the D-protein and L-protein enantiomers of monomeric DKP ester insulin were assayed for receptor binding and in diabetic rats, before and after conversion by saponification to the corresponding DKP insulin enantiomers. L-DKP ester insulin bound weakly to the insulin receptor, while synthetic L-DKP insulin derived from the L-DKP ester insulin intermediate was fully active in binding to the insulin receptor. The D- and L-DKP ester insulins and D-DKP insulin were inactive in lowering blood glucose in diabetic rats, while synthetic L-DKP insulin was fully active in this biological assay. The structural basis of the lack of biological activity of ester insulin is discussed.

High resolution monochromatic X-ray imaging system based on spherically bent crystals

International Nuclear Information System (INIS)

Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C.M.; Seely, J.; Feldman, U.; Holland, G.

1997-01-01

We have developed a new X-ray imaging system based on spherically curved crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser [1,2]. The imaging system is used for plasma diagnostics of the main target and for characterization of potential backlighters. A spherically curved quartz crystal (2d=6.687 Angstrom, R=200mm) is used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the X-ray optical system is 3 endash 4 μm. Time resolved backlit monochromatic images of CH planar targets driven by the Nike facility have been obtained with 6 endash 7 μm spatial resolution. copyright 1997 American Institute of Physics

Crystallization and preliminary X-ray analysis of the TetR-like efflux pump regulator SimR

International Nuclear Information System (INIS)

Le, Tung B. K.; Stevenson, Clare E. M.; Buttner, Mark J.; Lawson, David M.

2011-01-01

Crystals of SimR, a TetR-like efflux pump repressor from S. antibioticus, were obtained and X-ray data were recorded to a resolution of 2.3 Å. Crystals of SimR were grown by vapour diffusion. The protein crystallized with trigonal symmetry and X-ray data were recorded to a resolution of 2.3 Å from a single crystal at the synchrotron. SimR belongs to the TetR family of bacterial transcriptional regulators. In the absence of the antibiotic simocyclinone, SimR represses the transcription of a divergently transcribed gene encoding the simocyclinone efflux pump SimX in Streptomyces antibioticus by binding to operators in the simR–simX intergenic region. Simocyclinone binding causes SimR to dissociate from its operators, leading to expression of the SimX efflux pump. Thus, SimR represents an intimate link between the biosynthesis of simocyclinone and its export, which may also provide the mechanism of self-resistance to the antibiotic in the producer strain

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

X-ray diagnostics for TFTR

International Nuclear Information System (INIS)

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

1982-12-01

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

Where Water is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster from X-ray Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

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

2007-10-24

Light-driven oxidation of water to dioxygen in plants, algae and cyanobacteria iscatalyzed within photosystem II (PS II) by a Mn4Ca cluster. Although the cluster has been studied by many different methods, the structure and the mechanism have remained elusive. X-ray absorption and emission spectroscopy and EXAFS studies have been particularly useful in probing the electronic and geometric structure, and the mechanism of the water oxidation reaction. Recent progress, reviewed here, includes polarized X-ray absorption spectroscopy measurements of PS II single crystals. Analysis of those results has constrained the Mn4Ca cluster geometry to a setof three similar high-resolution structures. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 Angstrom-resolution X-ray structures or other previously proposed models. The differences between the models derived from X-rayspectroscopy and crystallography are predominantly because of damage to the Mn4Ca cluster by X-rays under the conditions used for structure determination by X-ray crystallography. X-ray spectroscopy studies are also used for studying the changes in the structure of the Mn4Ca catalytic center as it cycles through the five intermediate states known as the Si-states (i=0-4). The electronic structure of the Mn4Ca cluster has been studied more recently using resonant inelastic X-ray scattering spectroscopy (RIXS), in addition to the earlier X-ray absorption and emission spectroscopy methods. These studies are revealing that the assignment of formaloxidation states is overly simplistic. A more accurate description should consider the charge density on the Mn atoms that includes the covalency of the bonds and delocalization of the charge over the cluster. The geometric and electronic structure of the Mn4Ca cluster in the S-states derived from X-ray spectroscopy are leading to a detailed understanding of the mechanism of the O-O bond formation during the photosynthetic water

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 ...

Upgrades of imaging x-ray crystal spectrometers for high-resolution and high-temperature plasma diagnostics on EAST

Energy Technology Data Exchange (ETDEWEB)

Lyu, B., E-mail: blu@ipp.ac.cn; Wang, F. D.; Fu, J.; Li, Y. Y. [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Pan, X. Y.; Chen, J.; Wan, B. N. [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); Bitter, M.; Hill, K. W.; Delgado-Aparicio, L. F.; Pablant, N. [Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543-0451 (United States); Lee, S. G. [National Fusion Research Institute, 52 Eoeun-Dong, Yusung-Gu, Daejeon 305-333 (Korea, Republic of); Shi, Y. J. [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); WCI for Fusion Theory, National Fusion Research Institute, 52 Eoeun-Dong, Yusung-Gu, Daejeon 305-333 (Korea, Republic of); Ye, M. Y. [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China)

2014-11-15

Upgrade of the imaging X-ray crystal spectrometers continues in order to fulfill the high-performance diagnostics requirements on EAST. For the tangential spectrometer, a new large pixelated two-dimensional detector was deployed on tokamaks for time-resolved X-ray imaging. This vacuum-compatible detector has an area of 83.8 × 325.3 mm{sup 2}, a framing rate over 150 Hz, and water-cooling capability for long-pulse discharges. To effectively extend the temperature limit, a double-crystal assembly was designed to replace the previous single crystals for He-like argon line measurement. The tangential spectrometer employed two crystal slices attached to a common substrate and part of He- and H-like Ar spectra could be recorded on the same detector when crystals were chosen to have similar Bragg angles. This setup cannot only extend the measurable Te up to 10 keV in the core region, but also extend the spatial coverage since He-like argon ions will be present in the outer plasma region. Similarly, crystal slices for He-like iron and argon spectra were adopted on the poloidal spectrometer. Wavelength calibration for absolute rotation velocity measurement will be studied using cadmium characteristic L-shell X-ray lines excited by plasma radiation. A Cd foil is placed before the crystal and can be inserted and retracted for in situ wavelength calibration. The Geant4 code was used to estimate X-ray fluorescence yield and optimize the thickness of the foil.

New Paradigm for Macromolecular Crystallography Experiments at SSRL: Automated Crystal Screening And Remote Data Collection

International Nuclear Information System (INIS)

Soltis, S.M.; Cohen, A.E.; Deacon, A.; Eriksson, T.; Gonzalez, A.; McPhillips, S.; Chui, H.; Dunten, P.; Hollenbeck, M.; Mathews, I.; Miller, M.; Moorhead, P.; Phizackerley, R.P.; Smith, C.; Song, J.; Bedem, H. van dem; Ellis, P.; Kuhn, P.; McPhillips, T.; Sauter, N.; Sharp, K.

2009-01-01

Complete automation of the macromolecular crystallography experiment has been achieved at Stanford Synchrotron Radiation Lightsource (SSRL) through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled crystallography experiments to be carried out from the researchers' home institutions and other remote locations while retaining complete control over even the most challenging systems. A breakthrough component of the system, the Stanford Auto-Mounter (SAM), has enabled the efficient mounting of cryocooled samples without human intervention. Taking advantage of this automation, researchers have successfully screened more than 200 000 samples to select the crystals with the best diffraction quality for data collection as well as to determine optimal crystallization and cryocooling conditions. These systems, which have been deployed on all SSRL macromolecular crystallography beamlines and several beamlines worldwide, are used by more than 80 research groups in remote locations, establishing a new paradigm for macromolecular crystallography experimentation.

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.

X-ray imaging crystal spectroscopy for use in plasma transport research

Science.gov (United States)

Reinke, M. L.; Podpaly, Y. A.; Bitter, M.; Hutchinson, I. H.; Rice, J. E.; Delgado-Aparicio, L.; Gao, C.; Greenwald, M.; Hill, K.; Howard, N. T.; Hubbard, A.; Hughes, J. W.; Pablant, N.; White, A. E.; Wolfe, S. M.

2012-11-01

This research describes advancements in the spectral analysis and error propagation techniques associated with x-ray imaging crystal spectroscopy (XICS) that have enabled this diagnostic to be used to accurately constrain particle, momentum, and heat transport studies in a tokamak for the first time. Doppler tomography techniques have been extended to include propagation of statistical uncertainty due to photon noise, the effect of non-uniform instrumental broadening as well as flux surface variations in impurity density. These methods have been deployed as a suite of modeling and analysis tools, written in interactive data language (IDL) and designed for general use on tokamaks. Its application to the Alcator C-Mod XICS is discussed, along with novel spectral and spatial calibration techniques. Example ion temperature and radial electric field profiles from recent I-mode plasmas are shown, and the impact of poloidally asymmetric impurity density and natural line broadening is discussed in the context of the planned ITER x-ray crystal spectrometer.

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

International Nuclear Information System (INIS)

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

2005-01-01

Human agmatinase (Ala36–Val352) was overexpressed and crystallized, and X-ray diffraction data were collected to 2.49 Å. Agmatine, which results from the decarboxylation of l-arginine by arginine decarboxylase, is a metabolic intermediate in the biosynthesis of putresine and higher polyamines (spermidine and spermine). Recent studies indicate that agmatine can have several important biochemical effects in humans, ranging from effects on the central nervous system to cell proliferation in cancer and viral replication. Agmatinase catalyses the hydrolysis of agmatine to putresine and urea and is a major target for drug action and development. The human agmatinase gene encodes a 352-residue protein with a putative mitochondrial targeting sequence at the N-terminus. Human agmatinase (residues Ala36–Val352) has been overexpressed as a fusion with both N- and C-terminal purification tags in Escherichia coli and crystallized in the presence of Mn 2+ and 1,6-diaminohexane at 297 K using polyethylene glycol 4000 as a precipitant. X-ray diffraction data were collected at 100 K to 2.49 Å from a flash-frozen crystal. The crystals are tetragonal, belonging to space group P4 2 , with unit-cell parameters a = b = 114.54, c = 125.65 Å, α = β = γ = 90°. Three monomers are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (V M ) of 3.66 Å 3 Da −1 and a solvent content of 66.4%

A versatile, highly-efficient, high-resolution von Hamos Bragg crystal x-ray spectrometer

International Nuclear Information System (INIS)

Vane, C.R.; Smith, M.S.; Raman, S.

1988-01-01

An efficient, high-resolution, vertical-focusing, Bragg crystal x-ray spectrometer has been specifically designed and constructed for use in measurements of x rays produced in collisions of energetic heavy ions. In this report the design and resulting operational characteristics of the final instrument are fully described. A wide variety of sample data is also included to illustrate the utility of this device in several areas of research. 14 refs., 38 figs

Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy.

Directory of Open Access Journals (Sweden)

Simon Meyer

2009-10-01

Full Text Available MnmE, which is involved in the modification of the wobble position of certain tRNAs, belongs to the expanding class of G proteins activated by nucleotide-dependent dimerization (GADs. Previous models suggested the protein to be a multidomain protein whose G domains contact each other in a nucleotide dependent manner. Here we employ a combined approach of X-ray crystallography and pulse electron paramagnetic resonance (EPR spectroscopy to show that large domain movements are coupled to the G protein cycle of MnmE. The X-ray structures show MnmE to be a constitutive homodimer where the highly mobile G domains face each other in various orientations but are not in close contact as suggested by the GDP-AlF(x structure of the isolated domains. Distance measurements by pulse double electron-electron resonance (DEER spectroscopy show that the G domains adopt an open conformation in the nucleotide free/GDP-bound and an open/closed two-state equilibrium in the GTP-bound state, with maximal distance variations of 18 A. With GDP and AlF(x, which mimic the transition state of the phosphoryl transfer reaction, only the closed conformation is observed. Dimerization of the active sites with GDP-AlF(x requires the presence of specific monovalent cations, thus reflecting the requirements for the GTPase reaction of MnmE. Our results directly demonstrate the nature of the conformational changes MnmE was previously suggested to undergo during its GTPase cycle. They show the nucleotide-dependent dynamic movements of the G domains around two swivel positions relative to the rest of the protein, and they are of crucial importance for understanding the mechanistic principles of this GAD.

Advanced x-ray stress analysis method for a single crystal using different diffraction plane families

International Nuclear Information System (INIS)

Imafuku, Muneyuki; Suzuki, Hiroshi; Sueyoshi, Kazuyuki; Akita, Koichi; Ohya, Shin-ichi

2008-01-01

Generalized formula of the x-ray stress analysis for a single crystal with unknown stress-free lattice parameter was proposed. This method enables us to evaluate the plane stress states with any combination of diffraction planes. We can choose and combine the appropriate x-ray sources and diffraction plane families, depending on the sample orientation and the apparatus, whenever diffraction condition is satisfied. The analysis of plane stress distributions in an iron single crystal was demonstrated combining with the diffraction data for Fe{211} and Fe{310} plane families

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

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

Flash X-ray

International Nuclear Information System (INIS)

Sato, Eiichi

2003-01-01

Generation of quasi-monochromatic X-ray by production of weakly ionized line plasma (flash X-ray), high-speed imaging by the X-ray and high-contrast imaging by the characteristic X-ray absorption are described. The equipment for the X-ray is consisted from the high-voltage power supply and condenser, turbo molecular pump, and plasma X-ray tube. The tube has a long linear anticathode to produce the line plasma and flash X-ray at 20 kA current at maximum. X-ray spectrum is measured by the imaging plate equipped in the computed radiography system after diffracted by a LiF single crystal bender. Cu anticathode generates sharp peaks of K X-ray series. The tissue images are presented for vertebra, rabbit ear and heart, and dog heart by X-ray fluoroscopy with Ce anticathode. Generation of K-orbit characteristic X-ray with extremely low bremsstrahung is to be attempted for medical use. (N.I.)

High-pressure crystallography

Science.gov (United States)

Katrusiak, A.

2008-01-01

The history and development of high-pressure crystallography are briefly described and examples of structural transformations in compressed compounds are given. The review is focused on the diamond-anvil cell, celebrating its 50th anniversary this year, the principles of its operation and the impact it has had on high-pressure X-ray diffraction.

High-resolution monochromatic x-ray imaging system based on spherically bent crystals

International Nuclear Information System (INIS)

Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C.M.; Seely, J.; Feldman, U.; Holland, G.

1998-01-01

We have developed an improved x-ray imaging system based on spherically curve crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser. A spherically curved quartz crystal (2d=6.687 Angstrom, R=200 mm) has been used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the x-ray optical system is 1.7 μm in selected places and 2 - 3 μm over a larger area. Time-resolved backlit monochromatic images of polystyrene planar targets driven by the Nike facility have been obtained with a spatial resolution of 2.5 μm in selected places and 5 μm over the focal spot of the Nike laser. copyright 1998 Optical Society of America

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

Science.gov (United States)

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

2014-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Navarro, Marcos Vicente de A. S.; Vierira, Débora F. [Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador Sãocarlense 400, CEP 13560-970, São Carlos, SP (Brazil); Nagem, Ronaldo A. P. [Biochemistry and Immunology Department, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Antônio Carlos 6627, Caixa Postal 486, CEP 31270-901, Belo Horizonte, MG (Brazil); Araújo, Ana Paula U. de [Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador Sãocarlense 400, CEP 13560-970, São Carlos, SP (Brazil); Oliva, Maria Luiza V. [Universidade Federal de São Paulo, Escola Paulista de Medicina, Rua Três de Maio 100, CEP 04044-020, São Paulo, SP (Brazil); Garratt, Richard C., E-mail: richard@if.sc.usp.br [Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador Sãocarlense 400, CEP 13560-970, São Carlos, SP (Brazil)

2005-10-01

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{sub 1}2{sub 1}2{sub 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{sub M} = 2.5 Å{sup 3} Da{sup −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.

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.

Crystal nucleation in metallic alloys using x-ray radiography and machine learning

Science.gov (United States)

Arteta, Carlos; Lempitsky, Victor

2018-01-01

The crystallization of solidifying Al-Cu alloys over a wide range of conditions was studied in situ by synchrotron x-ray radiography, and the data were analyzed using a computer vision algorithm trained using machine learning. The effect of cooling rate and solute concentration on nucleation undercooling, crystal formation rate, and crystal growth rate was measured automatically for thousands of separate crystals, which was impossible to achieve manually. Nucleation undercooling distributions confirmed the efficiency of extrinsic grain refiners and gave support to the widely assumed free growth model of heterogeneous nucleation. We show that crystallization occurred in temporal and spatial bursts associated with a solute-suppressed nucleation zone. PMID:29662954

Models of protein–ligand crystal structures: trust, but verify

Science.gov (United States)

Deller, Marc C.

2015-01-01

X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575

Models of protein-ligand crystal structures: trust, but verify.

Science.gov (United States)

Deller, Marc C; Rupp, Bernhard

2015-09-01

X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

Performance characteristics needed for protein crystal diffraction x-ray detectors

International Nuclear Information System (INIS)

Westbrook, E. M.

1999-01-01

During the 1990's, macromolecular crystallography became progressively more dependent on synchrotrons X-ray sources for diffraction data collection. Detectors of this diffraction data at synchrotrons beamlines have evolved over the decade, from film to image phosphor plates, and then to CCD systems. These changes have been driven by the data quality and quantity improvements each newer detector technology provided. The improvements have been significant. It is likely that newer detector technologies will be adopted at synchrotron beamlines for crystallographic diffraction data collection in the future, but these technologies will have to compete with existing CCD detector systems which are already excellent and are getting incrementally better in terms of size, speed, efficiency, and resolving power. Detector development for this application at synchrotrons must concentrate on making systems which are bigger and faster than CCDs and which can capture weak data more efficiently. And there is a need for excellent detectors which are less expensive than CCD systems

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 ...

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

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

Comparing pharmacophore models derived from crystallography and NMR ensembles

Science.gov (United States)

Ghanakota, Phani; Carlson, Heather A.

2017-11-01

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225-8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the "extra" pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.

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.

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.

Analysis and implementation of a space resolving spherical crystal spectrometer for x-ray Thomson scattering experiments.

Science.gov (United States)

Harding, E C; Ao, T; Bailey, J E; Loisel, G; Sinars, D B; Geissel, M; Rochau, G A; Smith, I C

2015-04-01

The application of a space-resolving spectrometer to X-ray Thomson Scattering (XRTS) experiments has the potential to advance the study of warm dense matter. This has motivated the design of a spherical crystal spectrometer, which is a doubly focusing geometry with an overall high sensitivity and the capability of providing high-resolution, space-resolved spectra. A detailed analysis of the image fluence and crystal throughput in this geometry is carried out and analytical estimates of these quantities are presented. This analysis informed the design of a new spectrometer intended for future XRTS experiments on the Z-machine. The new spectrometer collects 6 keV x-rays with a spherically bent Ge (422) crystal and focuses the collected x-rays onto the Rowland circle. The spectrometer was built and then tested with a foam target. The resulting high-quality spectra prove that a spherical spectrometer is a viable diagnostic for XRTS experiments.

Synthesis, X-ray crystal structures, and phosphate ester cleavage properties of bis(2-pyridylmethyl)amine copper(II) complexes with guanidinium pendant groups.

Science.gov (United States)

Belousoff, Matthew J; Tjioe, Linda; Graham, Bim; Spiccia, Leone

2008-10-06

Three new derivatives of bis(2-pyridylmethyl)amine (DPA) featuring ethylguanidinium (L (1)), propylguanidinium (L (2)), or butylguanidinium (L (3)) pendant groups have been prepared by the reaction of N, N- bis(2-pyridylmethyl)alkane-alpha,omega-diamines with 1 H-pyrazole-1-carboxamidine hydrochloride. The corresponding mononuclear copper(II) complexes were prepared by reacting the ligands with copper(II) nitrate and were isolated as [Cu(LH (+))(OH 2)](ClO 4) 3. xNaClO 4. yH 2O ( C1: L = L (1), x = 2, y = 3; C2: L = L (2), x = 2, y = 4; C3: L = L (3), x = 1, y = 0) following cation exchange purification. Recrystallization yielded crystals of composition [Cu(LH (+))(X)](ClO 4) 3.X ( C1': L = L (1), X = MeOH; C2': L = L (2), X = H 2O; C3': L = L (3), X = H 2O), which were suitable for X-ray crystallography. The crystal structures of C1', C2', and C3' indicate that the DPA moieties of the ligands coordinate to the copper(II) centers in a meridional fashion, with a water or methanol molecule occupying the fourth basal position. Weakly bound perchlorate anions located in the axial positions complete the distorted octahedral coordination spheres. The noncoordinating, monoprotonated guanidinium groups project away from the Cu(II)-DPA units and are involved in extensive charge-assisted hydrogen-bonding interactions with cocrystallized water/methanol molecules and perchlorate anions within the crystal lattices. The copper(II) complexes were tested for their ability to promote the cleavage of two model phosphodiesters, bis( p-nitrophenyl)phosphate (BNPP) and uridine-3'- p-nitrophenylphosphate (UpNP), as well as supercoiled plasmid DNA (pBR 322). While the presence of the guanidine pendants was found to be detrimental to BNPP cleavage efficiency, the functionalized complexes were found to cleave plasmid DNA and, in some cases, the model ribose phosphate diester, UpNP, at a faster rate than the parent copper(II) complex of DPA.

Expression, purification, crystallization and preliminary X-ray analysis of two arginine-biosynthetic enzymes from Mycobacterium tuberculosis

International Nuclear Information System (INIS)

Moradian, Fatemeh; Garen, Craig; Cherney, Leonid; Cherney, Maia; James, Michael N. G.

2006-01-01

Two enzymes responsible for arginine biosynthesis in M. tuberculosis were expressed in Escherichia coli, then purified to homogeneity. Preliminary X-ray analysis of diffraction-quality crystals grown from each enzyme are reported. The gene products of two open reading frames from Mycobacterium tuberculosis (Mtb) have been crystallized using the sitting-drop vapour-diffusion method. Rv1652 encodes a putative N-acetyl-γ-glutamyl-phosphate reductase (MtbAGPR), while the Rv1656 gene product is annotated as ornithine carbamoyltransferase (MtbOTC). Both MtbAGPR and MtbOTC were expressed in Escherichia coli, purified to homogeneity and crystallized. Native data for each crystal were collected to resolutions of 2.15 and 2.80 Å, respectively. Preliminary X-ray data are presented for both enzymes

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.

Crystallization and preliminary X-ray analysis of Chandipura virus glycoprotein G

International Nuclear Information System (INIS)

Baquero, Eduard; Buonocore, Linda; Rose, John K.; Bressanelli, Stéphane; Gaudin, Yves; Albertini, Aurélie A.

2012-01-01

Chandipura virus glycoprotein ectodomain (Gth) was purified and crystallized at pH 7.5. X-ray diffraction data set was collected to a resolution of 3.1 Å. Fusion in members of the Rhabdoviridae virus family is mediated by the G glycoprotein. At low pH, the G glycoprotein catalyzes fusion between viral and endosomal membranes by undergoing a major conformational change from a pre-fusion trimer to a post-fusion trimer. The structure of the G glycoprotein from vesicular stomatitis virus (VSV G), the prototype of Vesiculovirus, has recently been solved in its trimeric pre-fusion and post-fusion conformations; however, little is known about the structural details of the transition. In this work, a soluble form of the ectodomain of Chandipura virus G glycoprotein (CHAV G th ) was purified using limited proteolysis of purified virus; this soluble ectodomain was also crystallized. This protein shares 41% amino-acid identity with VSV G and thus its structure could provide further clues about the structural transition of rhabdoviral glycoproteins induced by low pH. Crystals of CHAV G th obtained at pH 7.5 diffracted X-rays to 3.1 Å resolution. These crystals belonged to the orthorhombic space group P2 1 2 1 2, with unit-cell parameters a = 150.3, b = 228.2, c = 78.8 Å. Preliminary analysis of the data based on the space group and the self-rotation function indicated that there was no trimeric association of the protomers. This unusual oligomeric status could result from the presence of fusion intermediates in the crystal

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

Energy Technology Data Exchange (ETDEWEB)

Kim, Kyoung Hoon; Ahn, Hyung Jun; Kim, Do Jin; Lee, Hyung Ho; Ha, Jun-Yong; Kim, Hye-Kyung; Yoon, Hye-Jin; Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742 (Korea, Republic of)

2005-10-01

Human agmatinase (Ala36–Val352) was overexpressed and crystallized, and X-ray diffraction data were collected to 2.49 Å. Agmatine, which results from the decarboxylation of l-arginine by arginine decarboxylase, is a metabolic intermediate in the biosynthesis of putresine and higher polyamines (spermidine and spermine). Recent studies indicate that agmatine can have several important biochemical effects in humans, ranging from effects on the central nervous system to cell proliferation in cancer and viral replication. Agmatinase catalyses the hydrolysis of agmatine to putresine and urea and is a major target for drug action and development. The human agmatinase gene encodes a 352-residue protein with a putative mitochondrial targeting sequence at the N-terminus. Human agmatinase (residues Ala36–Val352) has been overexpressed as a fusion with both N- and C-terminal purification tags in Escherichia coli and crystallized in the presence of Mn{sup 2+} and 1,6-diaminohexane at 297 K using polyethylene glycol 4000 as a precipitant. X-ray diffraction data were collected at 100 K to 2.49 Å from a flash-frozen crystal. The crystals are tetragonal, belonging to space group P4{sub 2}, with unit-cell parameters a = b = 114.54, c = 125.65 Å, α = β = γ = 90°. Three monomers are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (V{sub M}) of 3.66 Å{sup 3} Da{sup −1} and a solvent content of 66.4%.

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.)

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.

Influence of UV Photo-Transfer on Post Irradiated Double Sulphate Poly-Crystals By Gamma And X-rays

International Nuclear Information System (INIS)

El-kolaly, M.A.

2000-01-01

Solid state thermoluminescence (TL) dosimetry has for many years been the pre-eminent method for quantifying ionizing radiation dose. In this work, thermoluminescence characteristics of the double sulphate (Li Cs So 4 ) poly-crystals have been studied after exposure to different doses from X and gamma radiation. The glue curves showed TL response of three peaks at 75,125,250 degree. The structure of the glue peaks due to X-rays is quite different from that due to gamma rays. UV exposure yields a regeneration of the TL peaks for the post irradiated samples for X or gamma radiation with some changes in the peaks structure especially the third peak. For the post X-ray irradiated crystals, the area under the third glow peak (III) increased linearly with the integrated time of UV exposures till about 30 min. after which no changes were observed; while , for the post gamma-irradiated crystals two linear regions were observed

The Ferrara hard X-ray facility for testing/calibrating hard X-ray focusing telescopes

Science.gov (United States)

Loffredo, Gianluca; Frontera, Filippo; Pellicciotta, Damiano; Pisa, Alessandro; Carassiti, Vito; Chiozzi, Stefano; Evangelisti, Federico; Landi, Luca; Melchiorri, Michele; Squerzanti, Stefano

2005-12-01

We will report on the current configuration of the X-ray facility of the University of Ferrara recently used to perform reflectivity tests of mosaic crystals and to calibrate the experiment JEM X aboard Integral. The facility is now located in the technological campus of the University of Ferrara in a new building (named LARIX laboratory= LARge Italian X-ray facility) that includes a tunnel 100 m long with, on the sides, two large experimental rooms. The facility is being improved for determining the optical axis of mosaic crystals in Laue configuration, for calibrating Laue lenses and hard X-ray mirror prototypes.

Characterization of barite and crystal glass as attenuators in X-ray and gamma radiation shieldings

International Nuclear Information System (INIS)

Almeida Junior, Airton Tavares de

2005-03-01

Aiming to determine the barium sulphate (BaSO 4 ) ore and crystal glass attenuation features, both utilized as shieldings against ionizing X and gamma radiations in radiographic installations, a study of attenuation using barite plaster and barite concrete was carried out, which are used, respectively, on wall coverings and in block buildings. The crystal glass is utilized in screens and in windows. To do so, ten plates of barite plaster and three of barite concrete with 900 cm 2 and with an average thickness ranging from 1 to 5 cm, and three plates of crystal glass with 323 cm 2 and with thicknesses of 1, 2 and 4 cm were analyzed. The samples were irradiated with X-rays with potentials of 60, 80, 110 and 150 kilovolts, and also with 60 Co gamma rays. Curves of attenuation were obtained for barite plaster and barite concrete (mGy/mA.min) and (mGy/h), both at 1 meter, as a function of thickness and curve of transmission through barite plaster and barite concrete as a function of the thickness. The equivalent thicknesses of half and tenth value layers for barite plaster, barite concrete and crystal glass for all X-Ray energies were also determined. (author)

Measurement of characteristic X-rays by positron impact

International Nuclear Information System (INIS)

Nagashima, Y.; Saito, F.; Itoh, Y.; Goto, A.; Hyodo, T.

2004-01-01

An X-ray detector with thin Si(Li) crystals has been fabricated and employed to detect the characteristic X-rays by positron impact. Use of thin detector crystals is essential for the measurements of the characteristic X-rays induced by positron impact. Otherwise the background produced in the crystals by the annihilation γ-rays is too large to isolate the X-ray peaks. The data has been analyzed to obtain the inner-shell ionization cross sections by positron impact. (orig.)

NSLS-II biomedical beamlines for micro-crystallography, FMX, and for highly automated crystallography, AMX: New opportunities for advanced data collection

Energy Technology Data Exchange (ETDEWEB)

Fuchs, Martin R., E-mail: mfuchs@bnl.gov; Bhogadi, Dileep K.; Jakoncic, Jean; Myers, Stuart; Sweet, Robert M.; Berman, Lonny E.; Skinner, John; Idir, Mourad; Chubar, Oleg; McSweeney, Sean; Schneider, Dieter K. [National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973 (United States)

2016-07-27

We present the final design of the x-ray optics and experimental stations of two macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source-II. The microfocusing FMX beamline will deliver a flux of ∼5×10{sup 12} ph/s at 1 Å into a 1 – 20 µm spot, its flux density surpassing current MX beamlines by up to two orders of magnitude. It covers an energy range from 5 – 30 keV. The highly automated AMX beamline is optimized for high throughput, with beam sizes from 4 – 100 µm, an energy range of 5 – 18 keV and a flux at 1 Å of ∼10{sup 13} ph/s. A focus in designing the beamlines lay on achieving high beam stability, for example by implementing a horizontal bounce double crystal monochromator at FMX. A combination of compound refractive lenses and bimorph mirror optics at FMX supports rapid beam size changes. Central components of the in-house developed experimental stations are horizontal axis goniometers with a target sphere of confusion of 100 nm, piezo-slits for dynamic beam size changes during diffraction experiments, dedicated secondary goniometers for data collection from specimen in crystallization plates, and next generation pixel array detectors. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and room temperature data collection of crystals in trays.

Design of an adaptive cooled first crystal for an X-ray monochromator

International Nuclear Information System (INIS)

Dezoret, D.; Marmoret, R.; Freund, A.K.; Kvick, AA.; Ravelet, R.

1994-01-01

We report here on the design of the first crystal in an x-ray monochromator for E.S.R.F. beam lines. This crystal is a thin silicon foil bonded to a cooled beryllium support. A system of piezoelectric actuators is used to counterbalance the deformations induced by synchrotron beams. This work was carried out by the C.E.A. in collaboration with the E.S.R.F. and the LASERDOT Company (Aerospatiale Group). (orig.)

Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima

International Nuclear Information System (INIS)

Lyashenko, Andrey V.; Zhukhlistova, Nadegda E.; Gabdoulkhakov, Azat G.; Zhukova, Yuliya N.; Voelter, Wolfang; Zaitsev, Viatcheslav N.; Bento, Isabel; Stepanova, Elena V.; Kachalova, Galina S.; Koroleva, Ol’ga V.; Cherkashyn, Evgeniy A.; Tishkov, Vladimir I.; Lamzin, Victor S.; Schirwitz, Katja; Morgunova, Ekaterina Yu.; Betzel, Christian; Lindley, Peter F.; Mikhailov, Al’bert M.

2006-01-01

The crystallization and preliminary X-ray structure at 1.9 Å resolution of the fungal laccase from C. maxima are presented. Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-ray data were collected to 1.9 Å resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccase structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 Å (R factor = 18.953%; R free = 23.835; r.m.s.d. bond lengths, 0.06 Å; r.m.s.d. bond angles, 1.07°) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002 ▶) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 Å X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO 2 substituents

Modern X-ray spectroscopy 3. X-ray fluorescence holography

International Nuclear Information System (INIS)

Hayashi, Kouichi

2008-01-01

X-ray fluorescence holography (XFH) provides three dimensional atomic images around specified elements. The XFH uses atoms as a wave source or monitor of interference field within a crystal sample, and therefore it can record both intensity and phase of scattered X-rays. Its current performance makes it possible to apply to ultra thin film, impurity and quasicrystal. In this article, I show the theory including solutions for twin image problem, advanced measuring system, data processing for reconstruction of the atomic images and for obtaining accurate atomic positions, applications using resonant X-ray scattering and X-ray excited optical luminescence, and an example of XFH result on the local structure around copper in silicon steal. (author)

Expression, crystallization and preliminary X-ray analysis of the phosphoribosylglycinamide formyltransferase from Streptococcus mutans

International Nuclear Information System (INIS)

Zhai, Fangli; Liu, Xiaojuan; Ruan, Jing; Li, Jing; Liu, Zhenlong; Hu, Yulin; Li, Shentao

2011-01-01

Phosphoribosylglycinamide formyltransferase (PurN) from Streptococcus mutans was expressed in E. coli, purified and studied crystallographically. Phosphoribosylglycinamide formyltransferase (PurN) from Streptococcus mutans was recombinantly expressed in Escherichia coli. An effective purification protocol was established. The purified protein, which had a purity of >95%, was identified by SDS–PAGE and MALDI–TOF MS. The protein was crystallized using the vapour-diffusion method in hanging-drop mode with PEG 3350 as the primary precipitant. X-ray diffraction data were collected to 2.1 Å resolution. Preliminary X-ray analysis indicated that the crystal belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 52.25, b = 63.29, c = 131.81 Å

X-ray detection capability of a Cs2ZnCl4 single-crystal scintillator

International Nuclear Information System (INIS)

Yahaba, Natsuna; Koshimizu, Masanori; Sun, Yan; Asai, Keisuke; Yanagida, Takayuki; Fujimoto, Yutaka; Haruki, Rie; Nishikido, Fumihiko; Kishimoto, Shunji

2014-01-01

The X-ray detection capability of a scintillation detector equipped with a Cs 2 ZnCl 4 single crystal was evaluated. The scintillation decay kinetics can be expressed as the sum of two exponential decay components. The fast decay component had a decay time constant of 1.8 ns, and its relative intensity was 95%. The total light output was 630 photons/MeV, and a subnanosecond timing resolution of 0.66 ns was obtained. The detection efficiency of 67.4 keV X-rays was 80% for a detector equipped with a 2.2-mm-thick Cs 2 ZnCl 4 crystal. Thus, excellent timing resolution and high detection efficiency were achieved simultaneously. (author)

Time-resolved pump-probe X-ray absorption fine structure spectroscopy of Gaq3

International Nuclear Information System (INIS)

Dicke, Benjamin

2013-01-01

of Gaq 3 was analyzed and presents one of the first time-resolved measurements at PETRA III. In addition to pump-probe XAFS spectroscopy, different phases of Gaq 3 and Alq 3 in form of powder, crystal, film and solution were analyzed by means of UV-VIS and fluorescence spectroscopy. Electronic and optical differences of the molecules related to the particular form could be revealed. Gaq 3 in benzyl alcohol solution and Gaq 3 in crystalline form exhibit very similar optical features, indicating similar structural properties. The various preparation techniques used to obtain the sample forms are presented in this thesis. Analyzing the differences among the diverse sample forms helps to answer the question on how the conclusions extracted from sample systems in liquid form can be transferred to the ones in crystal form or film form, the latter appearing in organic light emitting diodes. The future goal of this research project is the direct measurement of the excited state structure of Alq 3 as well as Gaq 3 , and similar sample systems by time-resolved X-ray crystallography. The sample crystals have to fulfill specific requirements especially for the laser induced photoexcitation process. In this thesis a newly developed preparation method for low roughness singe crystal slices is presented. These crystal slices can be used for future perspective time-resolved X-ray crystallography experiments.

A phase-contrast X-ray imaging system—with a 60×30 mm field of view—based on a skew-symmetric two-crystal X-ray interferometer

Science.gov (United States)

Yoneyama, Akio; Takeda, Tohoru; Tsuchiya, Yoshinori; Wu, Jin; Thet-Thet-Lwin; Koizumi, Aritaka; Hyodo, Kazuyuki; Itai, Yuji

2004-05-01

A phase-contrast X-ray imaging system—with a 60×30 mm field of view—for biomedical observations was developed. To extend the observation field of view, the system is fitted with a skew-symmetric two-crystal X-ray interferometer. To attain the required sub-nanoradian mechanical stability between the crystal blocks for precise operation, the interferometer was mounted on two extremely rigid positioning tables (one with a sleeve bearings) and was controlled by a feedback positioning system using phase-lock interferometry. The imaging system produced a 60×30 mm interference pattern with 60% visibility using 17.7 keV monochromatic synchrotron X-rays at the Photon Factory. It was then used to perform radiographic observation (i.e., phase mapping) of rat liver vessels. These results indicate that this imaging system can be used to perform observations of large and in vivo biological samples.

Lightweight and High-Resolution Single Crystal Silicon Optics for X-ray Astronomy

Science.gov (United States)

Zhang, William W.; Biskach, Michael P.; Chan, Kai-Wing; Mazzarella, James R.; McClelland, Ryan S.; Riveros, Raul E.; Saha, Timo T.; Solly, Peter M.

2016-01-01

We describe an approach to building mirror assemblies for next generation X-ray telescopes. It incorporates knowledge and lessons learned from building existing telescopes, including Chandra, XMM-Newton, Suzaku, and NuSTAR, as well as from our direct experience of the last 15 years developing mirror technology for the Constellation-X and International X-ray Observatory mission concepts. This approach combines single crystal silicon and precision polishing, thus has the potential of achieving the highest possible angular resolution with the least possible mass. Moreover, it is simple, consisting of several technical elements that can be developed independently in parallel. Lastly, it is highly amenable to mass production, therefore enabling the making of telescopes of very large photon collecting areas.

Discovery of x-rays and its impact on the development of physics

International Nuclear Information System (INIS)

Sirdeshmukh, D.B.

1996-01-01

Roentgen's discovery of x-rays is discussed. Roentgen's discovery was important not only for the property of transmission of x-rays, which immediately resulted in the new field of radiology, but also because it led to several experiments which had a great impact on the development of physics. Laue's discovery of x-ray diffraction in turn led to the development of x-ray crystallography and x-ray spectroscopy. The contributions of Barkla, Moseley and Siegbahn are discussed. The experiments of Duane and Hunt on continuous x-rays and Compton on scattering of x-rays lent support to the photon nature of radiation. In recent times, the line-widths of x-ray emission lines have given information about the band structure of solids. (author). 21 refs., 6 figs

Clear as Crystal: The Story of the Braggs--How X-Ray Crystallography Has Contributed to Science

Science.gov (United States)

George, Robert; Patterson, John

2014-01-01

Here is a brief history of the work of two of Australia's most famous scientists, Sir William Bragg and his son Sir Lawrence Bragg. Jointly awarded the Nobel Prize in 1915 for their groundbreaking research into the use of X-rays to study the chemical structure and function of molecules, they have contributed to our heritage and to science at an…

Crystallization and preliminary X-ray analysis of βC–S lyases from two oral streptococci

International Nuclear Information System (INIS)

Kezuka, Yuichiro; Yoshida, Yasuo; Nonaka, Takamasa

2009-01-01

The βC-S lyases from two oral bacteria, Streptococcus anginosus and S. gordonii, were cloned, overproduced, purified and crystallized. The obtained crystals were characterized by X-ray diffraction. Hydrogen sulfide, which causes oral malodour, is generally produced from l-cysteine by the action of βC–S lyase from oral bacteria. The βC–S lyases from two oral bacteria, Streptococcus anginosus and S. gordonii, have been cloned, overproduced, purified and crystallized. X-ray diffraction data were collected from the two types of crystals using synchrotron radiation. The crystal of S. anginosus βC–S lyase belonged to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 67.0, b = 111.1, c = 216.4 Å, and the crystal of S. gordonii βC–S lyase belonged to the same space group, with unit-cell parameters a = 58.0, b = 73.9. c = 187.6 Å. The structures of the βC–S lyases were solved by molecular-replacement techniques

Effect of impurities and post-experimental purification in SAD phasing with serial femtosecond crystallography data.

Science.gov (United States)

Zhang, Tao; Gu, Yuanxin; Fan, Haifu

2016-06-01

In serial crystallography (SX) with either an X-ray free-electron laser (XFEL) or synchrotron radiation as the light source, huge numbers of micrometre-sized crystals are used in diffraction data collection. For a SAD experiment using a derivative with introduced heavy atoms, it is difficult to completely exclude crystals of the native protein from the sample. In this paper, simulations were performed to study how the inclusion of native crystals in the derivative sample could affect the result of SAD phasing and how the post-experimental purification proposed by Zhang et al. [(2015), Acta Cryst. D71, 2513-2518] could be used to remove the impurities. A gadolinium derivative of lysozyme and the corresponding native protein were used in the test. Serial femtosecond crystallography (SFX) diffraction snapshots were generated by CrystFEL. SHELXC/D, Phaser, DM, ARP/wARP and REFMAC were used for automatic structure solution. It is shown that a small amount of impurities (snapshots from native crystals) in the set of derivative snapshots can strongly affect the SAD phasing results. On the other hand, post-experimental purification can efficiently remove the impurities, leading to results similar to those from a pure sample.