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Sample records for crystal x-ray crystallography

  1. X-ray Crystallography Facility

    Science.gov (United States)

    2000-01-01

    Edward Snell, a National Research Council research fellow at NASA's Marshall Space Flight Center (MSFC), prepares a protein crystal for analysis by x-ray crystallography as part of NASA's structural biology program. The small, individual crystals are bombarded with x-rays to produce diffraction patterns, a map of the intensity of the x-rays as they reflect through the crystal.

  2. Crystals x-rays and proteins comprehensive protein crystallography

    CERN Document Server

    Sherwood, Dennis

    2011-01-01

    Information derived from X-ray crystal structures of biological molecules allows us to explain their functions in living organisms and to develop drugs to treat disease. This book describes the principles and practice of X-ray diffraction as a key technique at the forefront of new discoveries in biology and medicine.

  3. X-ray crystallography

    Science.gov (United States)

    2001-01-01

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

  4. Visualization of X-ray Beam Using CdWO4 Crystal for Macromolecular Crystallography

    Directory of Open Access Journals (Sweden)

    Kazimierz J. Gofron

    2011-12-01

    Full Text Available In synchrotron diffraction experiments, it is typically assumed that the X-ray beam at the sample position is uniform, stable and has dimensions that are controlled by the focus and slits settings. As might be expected, this process is much more complex. We present here an investigation of the properties of a synchrotron X-ray beam at the sample position. The X-ray beam is visualized with a single crystal scintillator that converts X-ray photons into visible light photons, which can be imaged using Structure Biology Center (SBC on-axis and off-axis microscope optics. The X-ray penetration is dependent on the composition of the scintillator (especially the effective Z, and X-ray energy. Several scintillators have been used to visualize X-ray beams. Here we compare CdWO4, PbWO4, Bi4Ge3O12, Y3Al5O12:Ce (YAG:Ce, and Gd2O2S:Tb (phosphor. We determined that scintillator crystals made of CdWO4 and similar high-Z materials are best suited for the energy range (7–20 keV and are most suitable for beam visualization for macromolecular crystallography applications. These scintillators show excellent absorption, optical, and mechanical properties.

  5. Visualization of X-ray Beam Using CdWO4 Crystal for Macromolecular Crystallography

    Directory of Open Access Journals (Sweden)

    Kazimierz J. Gofron

    2011-12-01

    Full Text Available In synchrotron diffraction experiments, it is typically assumed that the X-ray beam at the sample position is uniform, stable and has dimensions that are controlled by the focus and slits settings. As might be expected, this process is much more complex. We present here an investigation of the properties of a synchrotron X-ray beam at the sample position. The X-ray beam is visualized with a single crystal scintillator that converts X-ray photons into visible light photons, which can be imaged using Structure Biology Center (SBC on-axis and off-axis microscope optics. The X-ray penetration is dependent on the composition of the scintillator (especially the effective Z, and X-ray energy. Several scintillators have been used to visualize X-ray beams. Here we compare CdWO4, PbWO4, Bi4Ge3O12, Y3Al5O12:Ce (YAG:Ce, and Gd2O2S:Tb (phosphor. We determined that scintillator crystals made of CdWO4 and similar high-Z materials are best suited for the energy range (7–20 keV and are most suitable for beam visualization for macromolecular crystallography applications. These scintillators show excellent absorption, optical, and mechanical properties.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-20

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

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

    Science.gov (United States)

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

    2005-07-01

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

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

    Science.gov (United States)

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

    2005-01-01

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

  9. X-Ray Crystallography Reagent

    Science.gov (United States)

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

    2003-01-01

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

  10. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1977-01-01

    Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

  11. Protein structure validation and analysis with X-ray crystallography.

    Science.gov (United States)

    Papageorgiou, Anastassios C; Mattsson, Jesse

    2014-01-01

    X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.

  12. X-ray Damage to the Mn4Ca Complex in Single Crystals ofPhotosystem II: A Case Study for Metalloprotein Crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Yano, Junko; Kern, Jan; Irrgang, Klaus-Dieter; Latimer, Matthew; Bergmann, Uwe; Glatzel, Pieter; Pushkar, Yulia; Biesiadka, Jacek; Loll,Bernhard; Sauer, Kenneth; Messinger, Johannes; Zouni, Athina; Yachandra,Vittal K.

    2005-06-21

    X-ray absorption spectroscopy was used to measure the damage caused by exposure to X-rays to the Mn4Ca active site in single crystals of photosystem II, as a function of dose and energy of X-rays, temperature, and time. These studies reveal that the conditions used for structure determination by X-ray crystallography cause serious damage specifically to the metal-site structure. The X-ray absorption spectra show that the structure changes from one that is characteristic of a high-valent Mn4(III2,IV2) oxo-bridged Mn4Ca cluster, to that of Mn(II) in aqueous solution. This damage to the metal site occurs at a dose that is more than an order of magnitude lower than that resulting in loss of diffractivity, and commonly considered safe for protein crystallography. These results establish the first quantitative X-ray dose parameters applicable to redox-active metallo-proteins. This case study shows that a careful evaluation of the structural intactness of the active sites by spectroscopic techniques can validate structures derived from crystallography, and it can be a valuable complementary method before structure-function correlations of metallo-proteins can be made on the basis of high resolution X-ray crystal structures.

  13. X-ray damage to the Mn4Ca complex in single crystals of photosystem II: a case study for metalloprotein crystallography.

    Science.gov (United States)

    Yano, Junko; Kern, Jan; Irrgang, Klaus-Dieter; Latimer, Matthew J; Bergmann, Uwe; Glatzel, Pieter; Pushkar, Yulia; Biesiadka, Jacek; Loll, Bernhard; Sauer, Kenneth; Messinger, Johannes; Zouni, Athina; Yachandra, Vittal K

    2005-08-23

    X-ray absorption spectroscopy was used to measure the damage caused by exposure to x-rays to the Mn(4)Ca active site in single crystals of photosystem II as a function of dose and energy of x-rays, temperature, and time. These studies reveal that the conditions used for structure determination by x-ray crystallography cause serious damage specifically to the metal-site structure. The x-ray absorption spectra show that the structure changes from one that is characteristic of a high-valent Mn(4)(III(2),IV(2)) oxo-bridged Mn(4)Ca cluster to that of Mn(II) in aqueous solution. This damage to the metal site occurs at a dose that is more than one order of magnitude lower than the dose that results in loss of diffractivity and is commonly considered safe for protein crystallography. These results establish quantitative x-ray dose parameters that are applicable to redox-active metalloproteins. This case study shows that a careful evaluation of the structural intactness of the active site(s) by spectroscopic techniques can validate structures derived from crystallography and that it can be a valuable complementary method before structure-function correlations of metalloproteins can be made on the basis of high-resolution x-ray crystal structures.

  14. 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.

  15. Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil.

    Science.gov (United States)

    Pöppler, Ann Christin; Corlett, Emily K; Pearce, Harriet; Seymour, Mark P; Reid, Matthew; Montgomery, Mark G; Brown, Steven P

    2017-03-01

    A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile-4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental (1)H and (13)C chemical shifts are determined from two-dimensional (1)H-(13)C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C-H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a (1)H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the (1)H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N-H...O and C-H...O hydrogen bonding, while changes of -2.7 and -1.5 ppm are due to ring current effects associated with C-H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.

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

    Directory of Open Access Journals (Sweden)

    Michael Heymann

    2014-09-01

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

  17. X-ray crystallography facility for the international space station

    Science.gov (United States)

    McDdonald, William T.; Lewis, Johanna L.; Smith, Craig D.; Delucas, Lawrence J.

    1997-01-01

    Directed by NASA's Office of Space Access and Technology (OSAT), the University of Alabama at Birmingham (UAB) Center for Macromolecular Crystallography (CMC) recently completed a Design Feasibility Study for the X-ray Crystallography Facility (XCF) for the International Space Station (ISS). The XCF is a facility for growing macromolecular protein crystals; harvesting, selecting, and mounting sample crystals, and snap-freezing the samples, if necessary; performing x-ray diffraction; and downlinking the diffraction data to the ground. Knowledge of the structure of protein molecules is essential for the development of pharmaceuticals by structure-based drug design techniques. Currently, x-ray diffraction of high quality protein crystals is the only method of determining the structure of these macromolecules. High quality protein crystals have been grown in microgravity onboard the Space Shuttle Orbiter for more than 10 years, but these crystals always have been returned to Earth for x-ray diffraction. The XCF will allow crystal growth, harvesting, mounting, and x-ray diffraction onboard the ISS, maximizing diffraction data quality and timeliness. This paper presents the XCF design concept, describing key feasibility issues for the ISS application and advanced technologies and operational features which resolve those issues. The conclusion is that the XCF design is feasible and can be operational onboard the ISS by early in 2002.

  18. Combining X-ray and neutron crystallography with spectroscopy

    Science.gov (United States)

    Smith, Oliver

    2017-01-01

    X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H+ ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal. By using single-crystal spectrophotometry, reactions taking place in the crystal can be monitored, either to trap intermediates or follow photoreduction during X-ray data collection. By using neutron crystallography, the positions of H atoms can be located, as it is the nuclei rather than the electrons that scatter neutrons, and the scattering length is not determined by the atomic number. Combining the two techniques allows much greater insight into both reaction mechanism and X-ray-induced photoreduction. PMID:28177310

  19. A glimpse of structural biology through X-ray crystallography.

    Science.gov (United States)

    Shi, Yigong

    2014-11-20

    Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.

  20. The 100th Anniversary of X-Ray Crystallography

    Directory of Open Access Journals (Sweden)

    Kojić-Prodić, B.

    2013-07-01

    Full Text Available The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them.W. L. BraggThe 100th anniversary of X-ray crystallography dates back to the first X-ray diffraction experiment on a crystal of copper sulphate pentahydrate. Max von Laue designed the theoretical background of the experiment, which was performed by German physicists W. Friedrich and P. Knipping in 1912. At that time, the mathematical formulation of the phenomenon and the fundamental concepts of crystallography were subjects of mineralogy. Altogether, they facilitated the development of methods for determination of the structure of matter at the atomic level. In 1913, father and son Bragg started to develop X-ray structure analysis for determination of crystal structures of simple molecules. Historic examples of structure determination starting from rock salt to complex, biologically important (macromolecules, such as globular proteins haemoglobin and myoglobin, DNA, vitamin B12 and the recent discovery of ribozyme, illustrate the development of X-ray structural analysis. The determination of 3D structures of these molecules by X-ray diffraction had opened new areas of scientific research, such as molecular biophysics, molecular genetics, structural molecular biology, bioinorganic chemistry, organometallic chemistry, and many others. The discovery and development of X-ray crystallography revolutionised our understanding of natural sciences – physics, chemistry, biology, and also science of materials. The scientific community recognised these fundamental achievements (including the discovery of X-rays by awarding twenty-eight Nobel prizes to thirty-nine men and two women. The explosive growth of science and technology in the 20th and 21st centuries had been founded on the detailed knowledge of the three-dimensional structure of molecules, which was the basis for explaining and predicting the physical, chemical, biological and

  1. A Compact X-Ray System for Macromolecular Crystallography. 5

    Science.gov (United States)

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

    2000-01-01

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

  2. A Compact X-Ray System for Macromolecular Crystallography

    Science.gov (United States)

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

    2000-01-01

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

  3. A Compact X-Ray System for Support of High Throughput Crystallography

    Science.gov (United States)

    Ciszak, Ewa; Gubarev, Mikhail; Gibson, Walter M.; Joy, Marshall K.; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Standard x-ray systems for crystallography rely on massive generators coupled with optics that guide X-ray beams onto the crystal sample. Optics for single-crystal diffractometry include total reflection mirrors, polycapillary optics or graded multilayer monochromators. The benefit of using polycapillary optic is that it can collect x-rays over tile greatest solid angle, and thus most efficiently, utilize the greatest portion of X-rays emitted from the Source, The x-ray generator has to have a small anode spot, and thus its size and power requirements can be substantially reduced We present the design and results from the first high flux x-ray system for crystallography that combine's a microfocus X-ray generator (40microns FWHM Spot size at a power of 45 W) and a collimating, polycapillary optic. Diffraction data collected from small test crystals with cell dimensions up to 160A (lysozyme and thaumatin) are of high quality. For example, diffraction data collected from a lysozyme crystal at RT yielded R=5.0% for data extending to 1.70A. We compare these results with measurements taken from standard crystallographic systems. Our current microfocus X-ray diffraction system is attractive for supporting crystal growth research in the standard crystallography laboratory as well as in remote, automated crystal growth laboratory. Its small volume, light-weight, and low power requirements are sufficient to have it installed in unique environments, i.e.. on-board International Space Station.

  4. 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…

  5. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

    Directory of Open Access Journals (Sweden)

    Matthew P. Blakeley

    2015-07-01

    Full Text Available The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden and Sirius (Brazil under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å, for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59% were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+ remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place

  6. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

    Science.gov (United States)

    Blakeley, Matthew P; Hasnain, Samar S; Antonyuk, Svetlana V

    2015-07-01

    The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron

  7. Metalloprotein active site structure determination: synergy between X-ray absorption spectroscopy and X-ray crystallography.

    Science.gov (United States)

    Cotelesage, Julien J H; Pushie, M Jake; Grochulski, Pawel; Pickering, Ingrid J; George, Graham N

    2012-10-01

    Structures of metalloprotein active sites derived from X-ray crystallography frequently contain chemical anomalies such as unexpected atomic geometries or elongated bond-lengths. Such anomalies are expected from the known errors inherent in macromolecular crystallography (ca. 0.1-0.2Å) and from the lack of appropriate restraints for metal sites which are often without precedent in the small molecule structure literature. Here we review the potential of X-ray absorption spectroscopy to provide information and perspective which could aid in improving the accuracy of metalloprotein crystal structure solutions. We also review the potential problem areas in analysis of the extended X-ray absorption fine structure (EXAFS) and discuss the use of density functional theory as another possible source of geometrical restraints for crystal structure analysis of metalloprotein active sites.

  8. 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

  9. Exploring ribozyme conformational changes with X-ray crystallography.

    Science.gov (United States)

    Spitale, Robert C; Wedekind, Joseph E

    2009-10-01

    Relating three-dimensional fold to function is a central challenge in RNA structural biology. Toward this goal, X-ray crystallography has long been considered the "gold standard" for structure determinations at atomic resolution, although NMR spectroscopy has become a powerhouse in this arena as well. In the area of dynamics, NMR remains the dominant technique to probe the magnitude and timescales of molecular motion. Although the latter area remains largely unassailable by conventional crystallographic methods, inroads have been made on proteins using Laue radiation on timescales of ms to ns. Proposed 'fourth generation' radiation sources, such as free-electron X-ray lasers, promise ps- to fs-timescale resolution, and credible evidence is emerging that supports the feasibility of single molecule imaging. At present however, the preponderance of RNA structural information has been derived from timescale and motion insensitive crystallographic techniques. Importantly, developments in computing, automation and high-flux synchrotron sources have propelled the rapidity of 'conventional' RNA crystal structure determinations to timeframes of hours once a suitable set of phases is obtained. With a sufficient number of crystal structures, it is possible to create a structural ensemble that can provide insight into global and local molecular motion characteristics that are relevant to biological function. Here we describe techniques to explore conformational changes in the hairpin ribozyme, a representative non-protein-coding RNA catalyst. The approaches discussed include: (i) construct choice and design using prior knowledge to improve X-ray diffraction; (ii) recognition of long-range conformational changes and (iii) use of single-base or single-atom changes to create ensembles. The methods are broadly applicable to other RNA systems.

  10. SPINE-compatible `carboloops': a new microshaped vitreous carbon sample mount for X-ray and neutron crystallography.

    Science.gov (United States)

    Romoli, Filippo; Mossou, Estelle; Cuypers, Maxime; van der Linden, Peter; Carpentier, Philippe; Mason, Sax A; Forsyth, V Trevor; McSweeney, Sean

    2014-05-01

    A novel vitreous carbon mount for macromolecular crystallography, suitable for neutron and X-ray crystallographic studies, has been developed. The technology described here is compatible both with X-ray and neutron cryo-crystallography. The mounts have low density and low background scattering for both neutrons and X-rays. They are prepared by laser cutting, allowing high standards of production quality, the ability to custom-design the mount to specific crystal sizes and large-scale production.

  11. 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.

  12. A readout system for X-ray powder crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Loukas, D. E-mail: loukas@inplab.ariadne-t.gr; Haralabidis, N.; Pavlidis, A.; Karvelas, E.; Psycharis, K.; Misiakos, V.; Mousa, J.; Dre, Ch

    2000-06-11

    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.

  13. Temperature-dependent macromolecular X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Weik, Martin, E-mail: martin.weik@ibs.fr; Colletier, Jacques-Philippe [CEA, IBS, Laboratoire de Biophysique Moléculaire, F-38054 Grenoble (France); CNRS, UMR5075, F-38027 Grenoble (France); Université Joseph Fourier, F-38000 Grenoble (France)

    2010-04-01

    The dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.

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

    Science.gov (United States)

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

    2016-01-01

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

  15. Locating and Visualizing Crystals for X-Ray Diffraction Experiments.

    Science.gov (United States)

    Becker, Michael; Kissick, David J; Ogata, Craig M

    2017-01-01

    Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.

  16. First Results from a Microfocus X-Ray System for Macromolecular Crystallography

    Science.gov (United States)

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

    1999-01-01

    The design and performance of a 40 Watt laboratory crystallography system optimized for the structure determination of small protein crystals are described. This system combines a microfocus x-ray generator (40 microns FWHM spot size at a power level of 40 Watts) and a short focal length (F = 2.6 mm) polycapillary collimating optic, and produces a small diameter quasi-parallel x-ray beam. Measurements of x-ray flux, divergence and spectral purity of the resulting x-ray beam are presented. The x-ray flux in a 250 microns diameter aperture produced by the microfocus system is 14.7 times higher .than that from a 3.15 kW rotating anode generator equipped with graphite monochromator. Crystallography data taken with the microfocus system are presented, and indicate that the divergence and spectral purity of the x-ray are sufficient to refine the diffraction data using a standard crystallographic software. Significant additional improvements in flux and beam divergence are possible, and plans for achieving these coals are discussed.

  17. Performance of detectors for x-ray crystallography

    Science.gov (United States)

    Stanton, Martin J.; Phillips, Walter C.

    1993-12-01

    The performance of a detector can be characterized by its efficiency for measuring individual x-rays or for measuring Bragg peak intensities. The performance for detecting individual x- rays or for measuring Bragg peak intensities. The performance for detecting individual x-rays is well modeled by the DQE. The performance for measuring Bragg peak intensities in the presence of an x-ray background can be modeled by an expanded definition of the DQE which allows inclusion of experimental constraints, the XDCE. These constraints include the observation that by increasing the crystal-to-detector distance and using a larger detector, Bragg peaks can be better resolved and the x-ray background reduced. Calculation of the XDCE for a detector consisting of a fiberoptic taper with a phosphor x-ray convertor deposited on the large end and a CCD bonded to the small end demonstrate the need to make the detector area relatively large, possibly at the expense of a decrease in the DQE.

  18. 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.

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

    Science.gov (United States)

    Tsujino, Soichiro; Tomizaki, Takashi

    2016-05-06

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

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

    Science.gov (United States)

    Tsujino, Soichiro; Tomizaki, Takashi

    2016-05-01

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

  1. X-ray powder crystallography with vertex instrumentation

    Energy Technology Data Exchange (ETDEWEB)

    Chatzisotiriou, V. [NCSR Demokritos, X-Ray Lab., Institute of Material Science, 15310 Aghia Paraskevi (Greece); Christofis, I. [General Machining S.A., 183 46 Moshato Attiki (Greece); Dimitriou, N.; Karvelas, S.; Karydas, A.G.; Loukas, D.; Pavlidis, A.; Spirou, S. [NCSR Demokritos, Institute of Nuclear Physics, 15310 Aghia Paraskevi (Greece); Dre, C. [Intracom S.A., 19002 Peania Attika (Greece); Haralabidis, N.; Misiakos, K.; Tsoi, E. [NCSR Demokritos, Institute of Microelectronics, 15310 Aghia Paraskevi (Greece); Perdikatsis, V. [Institute of Geology and Mineral Exploration, 115 27 Athens (Greece); Psycharis, V.; Terzis, A. [NCSR Demokritos, X-Ray Lab., Institute of Material Science, 15310 Aghia Paraskevi (Greece); Turchetta, R. [LEPSI, 67037 Strasbourg (France)

    1998-11-21

    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.)

  2. X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.

    Science.gov (United States)

    Büttner, Felix Michael; Renner-Schneck, Michaela; Stehle, Thilo

    2015-02-01

    The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding.

  3. Holographic methods in X-ray crystallography. Pt. 4. A fast algorithm and its application to macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Somoza, J.R. [California Univ., Berkeley (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States); Szoeke, H. [Lawrence Livermore National Lab., CA (United States); Goodman, D.M. [Lawrence Livermore National Lab., CA (United States); Beran, P. [Lawrence Livermore National Lab., CA (United States); Truckses, D. [Wisconsin Univ., Madison, WI (United States). Dept. of Biochemistry; Kim, S.H. [California Univ., Berkeley (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States); Szoeke, A. [Lawrence Livermore National Lab., CA (United States)

    1995-09-01

    The holographic method makes use of partially modeled electron density and experimentally measured structure-factor amplitudes to recover electron density corresponding to the unmodeled part of a crystal structure. This paper describes a fast algorithm that makes it possible to apply the holographic method to sizable crystallographic problems. The algorithm uses positivity constraints on the electron density and can incorporate a `target` electron density, making it similar to solvent flattening. The potential for applying the holographic method to macromolecular X-ray crystallography is assessed using both synthetic and experimental data. (orig.).

  4. Beamline X29: a novel undulator source for X-ray crystallography.

    Science.gov (United States)

    Shi, Wuxian; Robinson, Howard; Sullivan, Michael; Abel, Don; Toomey, John; Berman, Lonny E; Lynch, Don; Rosenbaum, Gerd; Rakowsky, George; Rock, Larry; Nolan, Bill; Shea-McCarthy, Grace; Schneider, Dieter; Johnson, Erik; Sweet, Robert M; Chance, Mark R

    2006-09-01

    A high-flux insertion device and beamline for macromolecular crystallography has been built at the National Synchrotron Light Source (NSLS) that employs a mini-gap undulator source developed by the NSLS. The mini-gap undulator at beamline X29 is a hybrid-magnet device of period 12.5 mm operating at proven gaps of 3.3-10 mm. The beamline provides hard X-rays for macromolecular crystallography experiments from the second and third harmonics over an energy range of 5-15 keV. The X-ray optics is designed to deliver intense and highly collimated X-rays. Horizontal focusing is achieved by a cryogenically cooled sagittally focusing double-crystal monochromator with approximately 4.1:1 demagnification. A vertical focusing mirror downstream of the monochromator is used for harmonic rejection and vertical focusing. The experimental station hosts an Area Detector Systems Quantum 315 CCD detector with 2.2 s readout time between exposures and Crystal Logic goniostat for crystal rotation and detector positioning. An auto-mounter crystal changer has been installed to facilitate the high-throughput data collection required by the major users, which includes structural genomics projects and the Macromolecular Crystallography Research Resource mail-in program. X29 is 10(3) times brighter than any existing bending-magnet beamline at NSLS with an actual flux of 2.5 x 10(11) photons s(-1) through a 0.12 mm square aperture at 11.271 keV.

  5. X-ray diffraction and the beginnings of X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Juretschke, H.J. [Polytechnic Univ., Brooklyn, NY (United States)

    1995-12-31

    A retelling of the discovery of X-ray diffraction in Munich in 1912, and an overview of its rapidity spreading applications to crystal structure determination. The early work by Laue`s group and by approaches and different instrumentation, soon set two basic patterns of investigations in this field, with Ewald offering a grand theoretical framework for encompassing both. Some of the successes, problems, and interplays of these trends are reviewed, also as reflected in the stimulation and response by other early participants in structural research, as well as by the interruptions caused by the first World War.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, Kalyaneswar; Pentelute, Brad L.; Tereshko, Valentina; Kossiakoff, Anthony A.; Kent, Stephen B.H.; (UC)

    2009-04-08

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

  7. Watching proteins function with time-resolved x-ray crystallography

    Science.gov (United States)

    Šrajer, Vukica; Schmidt, Marius

    2017-09-01

    Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron x-ray sources. An expansive database of more than 100 000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al 2005a Methods Mol. Biol. 305 115-54, Schmidt 2008 Ultrashort Laser Pulses in Biology and Medicine (Berlin: Springer) pp 201-41, Neutze and Moffat 2012 Curr. Opin. Struct. Biol. 22 651-9, Šrajer 2014 The Future of Dynamic Structural Science (Berlin: Springer) pp 237-51). In this approach, short and intense x-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron x-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard x-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond x-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al 2014 Science 346 1242-6, Barends et al 2015 Science 350 445-50, Pande et al 2016 Science 352 725-9). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline

  8. Watching proteins function with time-resolved x-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Šrajer, Vukica; Schmidt, Marius

    2017-08-22

    Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron x-ray sources. An expansive database of more than 100 000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al 2005a Methods Mol. Biol. 305 115–54, Schmidt 2008 Ultrashort Laser Pulses in Biology and Medicine (Berlin: Springer) pp 201–41, Neutze and Moffat 2012 Curr. Opin. Struct. Biol. 22 651–9, Šrajer 2014 The Future of Dynamic Structural Science (Berlin: Springer) pp 237–51). In this approach, short and intense x-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron x-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard x-rays (XFELs; 5–20 keV), which provide exceptionally intense, femtosecond x-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al 2014 Science 346 1242–6, Barends et al 2015 Science 350 445–50, Pande et al 2016 Science 352 725–9). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We

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

    Science.gov (United States)

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

    2014-07-17

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

  10. 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.

  11. Splendid Century of X-ray Crystallography%X射线晶体学的百年辉煌

    Institute of Scientific and Technical Information of China (English)

    马礼敦

    2014-01-01

    It has been more than one century since Max von Laue discovered the X-ray diffraction by copper sulfate crystal and W. L. Bragg pioneered the X-ray Crystallography. This has been one of the major milestones in the progress of modern sciences, in particular in the sciences and technologies of microstructures. In the past 100 years, the X-ray Crystallography has developed rapidly with significant scientific achievements. In this review article, the history of the X-ray Crystallography is highlighted from four distinct stages for the X-ray crystallographic experimental techniques. In each of the ma jor stages, the developments of the X-ray Crystallography in terms of the sin-gle crystal diffraction, powder diffraction, and X-ray spectroscopy are presented. Furthermore, the profound impacts of the X-ray Crystallography on not only basic sciences such as Physics, Crystallography, Chemistry and Biology, but also applied sciences such as Materials, Medicine, Pharmacology, Environments and so on, are described. The future challenges and opportuni-ties for the X-ray Crystallography, including several scientific frontiers such as the giant X-ray source-hard X-ray free electron laser, multi-dimensional crystallography, electron crystallography, mathematical crystallography, and three-dimensional X-ray diffraction microscopy etc will be dis-cussed. It is believed that as much as has been achieved in the last century, even more will be expected in the next 100 years.%自1912年劳厄发现X射线晶体衍射现象,小布拉格开创X射线晶体学以来,已经过去了100年。这一发现,对人类科学的发展,特别是微观结构科学的影响至为巨大,具有里程碑的意义。在这100年中,X射线晶体学发展迅速,成果累累。本文按主要实验技术的特点将100年大致分为四个阶段,从单晶体衍射、多晶体衍射和X射线光谱三个方面简述其主要进展和成果。并简单概括了她对物理学、晶体学、

  12. Dynamic X-ray diffraction sampling for protein crystal positioning.

    Science.gov (United States)

    Scarborough, Nicole M; Godaliyadda, G M Dilshan P; Ye, Dong Hye; Kissick, David J; Zhang, Shijie; Newman, Justin A; Sheedlo, Michael J; Chowdhury, Azhad U; Fischetti, Robert F; Das, Chittaranjan; Buzzard, Gregery T; Bouman, Charles A; Simpson, Garth J

    2017-01-01

    A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by

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

    Science.gov (United States)

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

    2016-05-01

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

  14. 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.…

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

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Chia-Ying [Trinity College, Dublin (Ireland); Olieric, Vincent [Paul Scherrer Institute, CH-5232 Villigen (Switzerland); Ma, Pikyee [Trinity College, Dublin (Ireland); Panepucci, Ezequiel [Paul Scherrer Institute, CH-5232 Villigen (Switzerland); Diederichs, Kay [Universität Konstanz, M647, D-78457 Konstanz (Germany); Wang, Meitian, E-mail: meitian.wang@psi.ch [Paul Scherrer Institute, CH-5232 Villigen (Switzerland); Caffrey, Martin, E-mail: meitian.wang@psi.ch [Trinity College, Dublin (Ireland)

    2015-05-14

    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{sub 2}-adrenoreceptor–G{sub s} protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at

  16. 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.

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

    Science.gov (United States)

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

    2015-06-01

    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 β2-adrenoreceptor-Gs 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 crystallography synchrotron beamlines worldwide. Because of its simplicity and effectiveness, the IMISX approach is likely to supplant existing in meso crystallization protocols. It should prove particularly attractive in the area of ligand screening for drug discovery and development.

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

    Science.gov (United States)

    Atac, Muzaffer; McKay, Timothy

    1999-01-01

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

  19. 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 wavefunctio

  20. Optimizing the spatial distribution of dose in X-ray macromolecular crystallography.

    Science.gov (United States)

    Zeldin, Oliver B; Gerstel, Markus; Garman, Elspeth F

    2013-01-01

    X-ray data collection for macromolecular crystallography can lead to highly inhomogeneous distributions of dose within the crystal volume for cases when the crystal is larger than the beam or when the beam is non-uniform (gaussian-like), particularly when crystal rotation is fully taken into account. Here the spatial distribution of dose is quantitatively modelled in order to compare the effectiveness of two dose-spreading data-collection protocols: helical scanning and translational collection. Their effectiveness in reducing the peak dose per unit diffraction is investigated via simulations for four common crystal shapes (cube, plate, long and short needles) and beams with a wide range of full width half maximum values. By inspection of the chosen metric, it is concluded that the optimum strategy is always to use as flat (top-hat) a beam as possible and to either match the beam size in both dimensions to the crystal, or to perform a helical scan with a beam which is narrow along the rotation axis and matched to the crystal size along the perpendicular axis. For crystal shapes where this is not possible, the reduction in peak dose per unit diffraction achieved through dose spreading is quantified and tabulated as a reference for experimenters.

  1. Adenovirus Structure as Revealed by X-Ray Crystallography, Electron Microscopy, and Difference Imaging

    Science.gov (United States)

    Stewart, Phoebe L.; Burnett, Roger M.

    1993-03-01

    The three-dimensional structure of human type 2 adenovirus was studied by combining X-ray crystallography and electron microscopy in a novel way. The 2.9 Å crystal structure of the major capsid protein, hexon, was positioned into a three-dimensional image reconstruction of the intact virus that was derived from cryo-electron micrographs. A three-dimensional difference map was generated by subtracting 240 copies of the crystallographic hexon from the density of the intact virus. This map revealed several minor structural proteins acting as “cement” to stabilize the assembly. The current state of structural knowledge concerning the location of the polypeptide components and the viral DNA is presented.

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

    Science.gov (United States)

    Clegg, William

    2004-01-01

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

  3. 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 procedu...

  4. Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography.

    Science.gov (United States)

    Yu, B; Blaber, M; Gronenborn, A M; Clore, G M; Caspar, D L

    1999-01-05

    Water in the hydrophobic cavity of human interleukin 1beta, which was detected by NMR spectroscopy but was invisible by high resolution x-ray crystallography, has been mapped quantitatively by measurement and phasing of all of the low resolution x-ray diffraction data from a single crystal. Phases for the low resolution data were refined by iterative density modification of an initial flat solvent model outside the envelope of the atomic model. The refinement was restrained by the condition that the map of the difference between the electron density distribution in the full unit cell and that of the atomic model be flat within the envelope of the well ordered protein structure. Care was taken to avoid overfitting the diffraction data by maintaining phases for the high resolution data from the atomic model and by a resolution-dependent damping of the structure factor differences between data and model. The cavity region in the protein could accommodate up to four water molecules. The refined solvent difference map indicates that there are about two water molecules in the cavity region. This map is compatible with an atomic model of the water distribution refined by using XPLOR. About 70% of the time, there appears to be a water dimer in the central hydrophobic cavity, which is connected to the outside by two constricted channels occupied by single water molecules approximately 40% of the time on one side and approximately 10% on the other.

  5. X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery

    Science.gov (United States)

    Cooper, David R.; Porebski, Przemyslaw J.; Chruszcz, Maksymilian; Minor, Wladek

    2011-01-01

    Introduction Crystallography is the key initial component for structure-based and fragment-based drug design and can often generate leads that can be developed into high potency drugs. Therefore, huge sums of money are committed based on the outcome of crystallography experiments and their interpretation. Areas covered This review discusses how to evaluate the correctness of an X-ray structure, focusing on the validation of small molecule-protein complexes. Various types of inaccuracies found within the PDB are identified and the ramifications of these errors are discussed. The reader will gain an understanding of the key parameters that need to be inspected before a structure can be used in drug discovery efforts, as well as an appreciation of the difficulties of correctly interpreting electron density for small molecules. The reader will also be introduced to methods for validating small molecules within the context of a macromolecular structure. Expert opinion One of the reasons that ligand identification and positioning, within a macromolecular crystal structure, is so difficult is that the quality of small molecules widely varies in the PDB. For this reason, the PDB can not always be considered a reliable repository of structural information pertaining to small molecules, and this makes the derivation of general principles that govern small molecule-protein interactions more difficult. PMID:21779303

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

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan; Kick, Leonhard M.; Gati, Cornelius; Nelson, Garrett; Deupi, Xavier; Standfuss, Jörg; Schertler, Gebhard; Panneels, Valérie, E-mail: valerie.panneels@psi.ch [Paul Scherrer Institute, OFLC/103, 5232 Villigen-PSI (Switzerland)

    2015-06-27

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

  7. Au₂₅(SEt)₁₈, a nearly naked thiolate-protected Au₂₅ cluster: structural analysis by single crystal X-ray crystallography and electron nuclear double resonance.

    Science.gov (United States)

    Dainese, Tiziano; Antonello, Sabrina; Gascón, José A; Pan, Fangfang; Perera, Neranjan V; Ruzzi, Marco; Venzo, Alfonso; Zoleo, Alfonso; Rissanen, Kari; Maran, Flavio

    2014-04-22

    X-ray crystallography has been fundamental in discovering fine structural features of ultrasmall gold clusters capped by thiolated ligands. For still unknown structures, however, new tools capable of providing relevant structural information are sought. We prepared a 25-gold atom nanocluster protected by the smallest ligand ever used, ethanethiol. This cluster displays the electrochemistry, mass spectrometry, and UV-vis absorption spectroscopy features of similar Au25 clusters protected by 18 thiolated ligands. The anionic and the neutral form of Au25(SEt)18 were fully characterized by (1)H and (13)C NMR spectroscopy, which confirmed the monolayer's properties and the paramagnetism of neutral Au25(SEt)18(0). X-ray crystallography analysis of the latter provided the first known structure of a gold cluster protected by a simple, linear alkanethiolate. Here, we also report the direct observation by electron nuclear double resonance (ENDOR) of hyperfine interactions between a surface-delocalized unpaired electron and the gold atoms of a nanocluster. The advantages of knowing the exact molecular structure and having used such a small ligand allowed us to compare the experimental values of hyperfine couplings with DFT calculations unaffected by structure's approximations or omissions.

  8. Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laser.

    Science.gov (United States)

    Tono, Kensuke; Nango, Eriko; Sugahara, Michihiro; Song, Changyong; Park, Jaehyun; Tanaka, Tomoyuki; Tanaka, Rie; Joti, Yasumasa; Kameshima, Takashi; Ono, Shun; Hatsui, Takaki; Mizohata, Eiichi; Suzuki, Mamoru; Shimamura, Tatsuro; Tanaka, Yoshiki; Iwata, So; Yabashi, Makina

    2015-05-01

    An experimental system for serial femtosecond crystallography using an X-ray free-electron laser (XFEL) has been developed. It basically consists of a sample chamber, fluid injectors and a two-dimensional detector. The chamber and the injectors are operated under helium atmosphere at 1 atm. The ambient pressure operation facilitates applications to fluid samples. Three kinds of injectors are employed to feed randomly oriented crystals in aqueous solution or highly viscous fluid. Experiments on lysozyme crystals were performed by using the 10 keV XFEL of the SPring-8 Angstrom Compact free-electron LAser (SACLA). The structure of model protein lysozyme from 1 µm crystals at a resolution of 2.4 Å was obtained.

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

    Science.gov (United States)

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

    2016-03-01

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

  10. 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.

  11. Long-Wavelength X-Ray Diffraction and Its Applications in Macromolecular Crystallography.

    Science.gov (United States)

    Weiss, Manfred S

    2017-01-01

    For many years, diffraction experiments in macromolecular crystallography at X-ray wavelengths longer than that of Cu-K α (1.54 Å) have been largely underappreciated. Effects caused by increased X-ray absorption result in the fact that these experiments are more difficult than the standard diffraction experiments at short wavelengths. However, due to the also increased anomalous scattering of many biologically relevant atoms, important additional structural information can be obtained. This information, in turn, can be used for phase determination, for substructure identification, in molecular replacement approaches, as well as in structure refinement. This chapter reviews the possibilities and the difficulties associated with such experiments, and it provides a short description of two macromolecular crystallography synchrotron beam lines dedicated to long-wavelength X-ray diffraction experiments.

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

    Science.gov (United States)

    Perry, J Jefferson P; Tainer, John A

    2013-03-01

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

  13. Radiation-damage-free quantum crystallography and resolution-enhanced x-ray imaging techniques using quantum multipath interference of thermal light

    CERN Document Server

    Li, Zheng; Medvedev, Nikita; Wang, Fenglin; Chapman, Henry N; Shih, Yanhua

    2016-01-01

    Using higher order coherence of thermal light sources, we can achieve enhancement of resolution of standard x-ray imaging techniques, such as x-ray diffraction and phase contrast imaging. The cost of implementing such schemes is minimal comparing to the schemes using entangled two-photon pairs. The proposed diffractive quan- tum crystallography using multipath interference of thermal light can be eventually free of radiation damage, because the diffraction pattern could be formed by using low energy photons of optical wavelength. Thus it is promising to apply the proposed quantum crystallography scheme to nanocrystalline or non-crystalline samples that are too difficult to be crystallized.

  14. 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.

  15. Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR.

    Science.gov (United States)

    Lengyel, Jeffrey; Hnath, Eric; Storms, Marc; Wohlfarth, Thomas

    2014-09-01

    Cryo-transmission electron microscopy (Cryo-TEM) and particularly single particle analysis is rapidly becoming the premier method for determining the three-dimensional structure of protein complexes, and viruses. In the last several years there have been dramatic technological improvements in Cryo-TEM, such as advancements in automation and use of improved detectors, as well as improved image processing techniques. While Cryo-TEM was once thought of as a low resolution structural technique, the method is currently capable of generating nearly atomic resolution structures on a routine basis. Moreover, the combination of Cryo-TEM and other methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular dynamics modeling are allowing researchers to address scientific questions previously thought intractable. Future technological developments are widely believed to further enhance the method and it is not inconceivable that Cryo-TEM could become as routine as X-ray crystallography for protein structure determination.

  16. An exponential modeling algorithm for protein structure completion by X-ray crystallography.

    Science.gov (United States)

    Shneerson, V L; Wild, D L; Saldin, D K

    2001-03-01

    An exponential modeling algorithm is developed for protein structure completion by X-ray crystallography and tested on experimental data from a 59-residue protein. An initial noisy difference Fourier map of missing residues of up to half of the protein is transformed by the algorithm into one that allows easy identification of the continuous tube of electron density associated with that polypeptide chain. The method incorporates the paradigm of phase hypothesis generation and cross validation within an automated scheme.

  17. 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.

  18. Dose, exposure time, and resolution in Serial X-ray Crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Starodub, D; Rez, P; Hembree, G; Howells, M; Shapiro, D; Chapman, H N; Fromme, P; Schmidt, K; Weierstall, U; Doak, R B; Spence, J C

    2007-03-22

    Using detailed simulation and analytical models, the exposure time is estimated for serial crystallography, where hydrated laser-aligned proteins are sprayed across a continuous synchrotron beam. The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available fluxes of molecules and X-rays. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of a density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 7 {angstrom} should be possible with short (below 100 s) exposures.

  19. X-Ray Imaging Crystal Spectrometer for Extended X-Ray Sources

    Energy Technology Data Exchange (ETDEWEB)

    Bitter, Manfred L.; Fraekel, Benjamin; Gorman, James L.; Hill, Kenneth W.; Roquemore, Lane A.; Stodiek, Wolfgang; Goeler, Schweickhard von

    1999-05-01

    Spherically or toroidally curved, double focusing crystals are used in a spectrometer for X-ray diagnostics of an extended X-ray source such as a hot plasma produced in a tokamak fusion experiment to provide spatially and temporally resolved data on plasma parameters such as ion temperature, toroidal and poloidal rotation, electron temperature, impurity ion charge-state distributions, and impurity transport. The imaging properties of these spherically or toroidally curved crystals provide both spectrally and spatially resolved X-ray data from the plasma using only one small spherically or toroidally curved crystal, thus eliminating the requirement for a large array of crystal spectrometers and the need to cross-calibrate the various crystals.

  20. Using Two-Dimensional Colloidal Crystals to Understand Crystallography

    Science.gov (United States)

    Bosse, Stephanie A.; Loening, Nikolaus M.

    2008-01-01

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

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

    Science.gov (United States)

    Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan; Kick, Leonhard M; Gati, Cornelius; Nelson, Garrett; Deupi, Xavier; Standfuss, Jörg; Schertler, Gebhard; Panneels, Valérie

    2015-07-01

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

  2. Large area high-resolution CCD-based X-ray detector for macromolecular crystallography

    CERN Document Server

    Pokric, M; Jorden, A R; Cox, M P; Marshall, A; Long, P G; Moon, K; Jerram, P A; Pool, P; Nave, C; Derbyshire, G E; Helliwell, J R

    2002-01-01

    An X-ray detector system for macromolecular crystallography based on a large area charge-coupled device (CCD) sensor has been developed as part of a large research and development programme for advanced X-ray sensor technology, funded by industry and the Particle Physics and Astronomy Research Council (PPARC) in the UK. The prototype detector consists of two large area three-sides buttable charge-coupled devices (CCD 46-62 EEV), where the single CCD area is 55.3 mmx41.5 mm. Overall detector imaging area is easily extendable to 85 mmx110 mm. The detector consists of an optically coupled X-ray sensitive phosphor, skewed fibre-optic studs and CCDs. The crystallographic measurement requirements at synchrotron sources are met through a high spatial resolution (2048x1536 pixel array), high dynamic range (approx 10 sup 5), a fast readout (approx 1 s), low noise (<10e sup -) and much reduced parallax error. Additionally, the prototype detector system has been optimised by increasing its efficiency at low X-ray ene...

  3. The Mn₄Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser.

    Science.gov (United States)

    Tran, Rosalie; Kern, Jan; Hattne, Johan; Koroidov, Sergey; Hellmich, Julia; Alonso-Mori, Roberto; Sauter, Nicholas K; Bergmann, Uwe; Messinger, Johannes; Zouni, Athina; Yano, Junko; Yachandra, Vittal K

    2014-07-17

    The structure of photosystem II and the catalytic intermediate states of the Mn₄CaO₅ cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.

  4. Preparation, X-ray crystallography, and thermal decomposition of some transition metal perchlorate complexes of hexamethylenetetramine.

    Science.gov (United States)

    Singh, Gurdip; Baranwal, B P; Kapoor, I P S; Kumar, Dinesh; Fröhlich, Roland

    2007-12-20

    The perchlorate complexes of manganese, nickel, and zinc with hexamethylenetetramine (HMTA) of the general formula [M(H2O-HMTA-H2O)2(H2O-ClO4)2(H2O)2] (where M=Mn, Ni, and Zn) have been prepared and characterized by X-ray crystallography. Thermal studies were undertaken using thermogravimetry (TG), differential thermal analysis (DTA), and explosion delay (DE) measurements. The kinetics of thermal decomposition of these complexes was investigated using isothermal TG data by applying isoconversional method. The decomposition pathways of the complexes have also been proposed. These were found to explode when subjected to higher temperatures.

  5. Stig Sundell at the bent crystal X-ray spectrometer for the X-ray shift experiment.

    CERN Multimedia

    1976-01-01

    The bent crystal X-ray spectrometer is being used to measure small shifts in the frequencies of X-rays emitted from the lower electron energy levels, in order to learn about the size of the nuclei concerned

  6. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

    OpenAIRE

    2015-01-01

    G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveal...

  7. Analysis of urinary stone composition in Eastern India by X-ray diffraction crystallography

    Directory of Open Access Journals (Sweden)

    Tarun Jindal

    2014-01-01

    Full Text Available Background: Stones in the urinary system are common in our country. This study was done to assess the composition of the urinary stones in eastern part of India. Materials and Methods: A prospective study was done over a period of thirty months. A total of 90 stones were analyzed in this time period by using X-ray diffraction crystallography. Results: Of the 90 stones analyzed, 77 were renal stones, 12 were ureteric stones and one was a bladder stone. Six stones (all renal did not have properties to be represented by X-ray diffraction crystallography. The overall prevalence of the oxalate containing stones was 85.7% with calcium oxalate monohydrate (COM being the major constituent. Calcium oxalate dihydrate (COD was the next most common constituent. Struvite stones constituted 9.5% of the stones analyzed. Pure calcium phosphate stones were found in 4.7% of the cases. Conclusion: Our study reveals that the stone composition in the eastern part of India is different from that in other parts of the country. We have a comparatively lower prevalence of oxalate stones while a higher prevalence of phosphate and struvite stones.

  8. Crystallization and Preliminary X-ray Diffraction Analysis of Salmonella typhi PilS

    Energy Technology Data Exchange (ETDEWEB)

    Balakrishna,A.; Tan, Y.; Mok, H.; Saxena, A.; Swaminathan, K.

    2006-01-01

    The structure determination of PilS, a type IV pilin, by X-ray crystallography is reported. The recombinant protein from Salmonella typhi was overexpressed, purified and crystallized. The crystals belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 77.88, b = 114.53, c = 31.75 {angstrom}. The selenomethionine derivative of the PilS protein was overexpressed, purified and crystallized in the same space group. Data sets have been collected to 2.1 {angstrom} resolution from the selenomethionine-derivative crystal using synchrotron radiation for multiwavelength anomalous dispersion (MAD) phasing.

  9. 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.

  10. X-ray Scintillation in Lead Halide Perovskite Crystals

    OpenAIRE

    Birowosuto, M. D.; Cortecchia, D.; Drozdowski, W.; K. Brylew; Łachmański, W.; A. Bruno; Soci, C.

    2016-01-01

    Current technologies for X-ray detection rely on scintillation from expensive inorganic crystals grown at high-temperature, which so far has hindered the development of large-area scintillator arrays. Thanks to the presence of heavy atoms, solution-grown hybrid lead halide perovskite single crystals exhibit short X-ray absorption length and excellent detection efficiency. Here we compare X-ray scintillator characteristics of three-dimensional (3D) MAPbI3 and MAPbBr3 and two-dimensional (2D) (...

  11. 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...

  12. On-line optical and X-ray spectroscopies with crystallography: an integrated approach for determining metalloprotein structures in functionally well defined states.

    Science.gov (United States)

    Ellis, Mark J; Buffey, Steven G; Hough, Michael A; Hasnain, S Samar

    2008-09-01

    X-ray-induced redox changes can lead to incorrect assignments of the functional states of metals in metalloprotein crystals. The need for on-line monitoring of the status of metal ions (and other chromophores) during protein crystallography experiments is of growing importance with the use of intense synchrotron X-ray beams. Significant efforts are therefore being made worldwide to combine different spectroscopies in parallel with X-ray crystallographic data collection. Here the implementation and utilization of optical and X-ray absorption spectroscopies on the modern macromolecular crystallography (MX) beamline 10, at the SRS, Daresbury Laboratory, is described. This beamline is equipped with a dedicated monolithic energy-dispersive X-ray fluorescence detector, allowing X-ray absorption spectroscopy (XAS) measurements to be made in situ on the same crystal used to record the diffraction data. In addition, an optical microspectrophotometer has been incorporated on the beamline, thus facilitating combined MX, XAS and optical spectroscopic measurements. By uniting these techniques it is also possible to monitor the status of optically active and optically silent metal centres present in a crystal at the same time. This unique capability has been applied to observe the results of crystallographic data collection on crystals of nitrite reductase from Alcaligenes xylosoxidans, which contains both type-1 and type-2 Cu centres. It is found that the type-1 Cu centre photoreduces quickly, resulting in the loss of the 595 nm peak in the optical spectrum, while the type-2 Cu centre remains in the oxidized state over a much longer time period, for which independent confirmation is provided by XAS data as this centre has an optical spectrum which is barely detectable using microspectrophotometry. This example clearly demonstrates the importance of using two on-line methods, spectroscopy and XAS, for identifying well defined redox states of metalloproteins during

  13. X-ray Crystallography of A Metalloprotein: A Reaction Intermediate of Heme Oxygenase

    Science.gov (United States)

    Unno, Masaki; Matsui, Toshitaka; Ikeda-Saito, Masao

    X-ray crystallographic analysis of a metalloprotein requires knowing the electronic state of the metal center, if one wants to elucidate the exact function and/or reaction mechanism. As an example, we show our recent structural analysis of the heme oxygenase reaction intermediate which is involved in the third step of the heme degradation reaction. The reaction intermediate was crystallized under anaerobic condition, and the obtained crystals were frozen into liquid nitrogen. The absorption spectra of the single crystal before and after X-ray irradiation were compared with that of the frozen solution in 100 K cold nitrogen stream. The determined structure offers the first solid evidence for the presence of a water cluster in the distal pocket of this catalytically critical intermediate. This structure combined with the QM/MM calculation supports our proposal that the biliverdin is produced via Fe-OOH verdoheme intermediate.

  14. Crystallization and preliminary X-ray diffraction data of alpha-galactosidase from Saccharomyces cerevisiae.

    Science.gov (United States)

    Fernández-Leiro, Rafael; Pereira-Rodríguez, Angel; Cerdán, M Esperanza; Becerra, Manuel; Sanz-Aparicio, Juliana

    2010-01-01

    Saccharomyces cerevisiae alpha-galactosidase is a highly glycosylated extracellular protein that catalyzes the hydrolysis of alpha-galactosidic linkages in various glucids. Its enzymatic activity is of interest in many food-related industries and has biotechnological applications. Glycosylated and in vitro deglycosylated protein samples were both assayed for crystallization, but only the latter gave good-quality crystals that were suitable for X-ray crystallography. The crystals belonged to space group P42(1)2, with unit-cell parameters a = b = 101.24, c = 111.52 A. A complete diffraction data set was collected to 1.95 A resolution using a synchrotron source.

  15. X-ray crystallography over the past decade for novel drug discovery – where are we heading next?

    Science.gov (United States)

    Zheng, Heping; Handing, Katarzyna B; Zimmerman, Matthew D; Shabalin, Ivan G; Almo, Steven C; Minor, Wladek

    2015-01-01

    Introduction Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. Areas covered This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. Expert opinion X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible. PMID:26177814

  16. Crystal growth and crystallography

    Science.gov (United States)

    Chernov, A. A.

    1998-01-01

    Selected topics that may be of interest for both crystal-structure and crystal-growth communities are overviewed. The growth of protein crystals, along with that of some other compounds, is one of the topics, and recent insights into related phenomena are considered as examples of applications of general principles. The relationship between crystal growth shape and structure is reviewed and an attempt to introduce semiquantitative characterization of binding for proteins is made. The concept of kinks for complex structures is briefly discussed. Even at sufficiently low supersaturations, the fluctuation of steps may not be sufficient to implement the Gibbs-Thomson law if the kink density is low enough. Subsurface ordering of liquids and growth of rough interfaces from melts is discussed. Crystals growing in microgravity from solution should be more perfect if they preferentially trap stress-inducing impurities, thus creating an impurity-depleted zone around themselves. Evidently, such a zone is developed only around the crystals growing in the absence of convection. Under terrestrial conditions, the self-purified depleted zone is destroyed by convection, the crystal traps more impurity and grows stressed. The stress relief causes mosaicity. In systems containing stress-inducing but poorly trapped impurities, the crystals grown in the absence of convection should be worse than those of their terrestrial counterparts.

  17. 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...

  18. Large-volume protein crystal growth for neutron macromolecular crystallography.

    Science.gov (United States)

    Ng, Joseph D; Baird, James K; Coates, Leighton; Garcia-Ruiz, Juan M; Hodge, Teresa A; Huang, Sijay

    2015-04-01

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

  19. 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...

  20. X-Ray structural investigation of VAS-393 crystals

    CERN Document Server

    Martirosian, A H; Harurtjunian, V S

    2001-01-01

    X-ray structural study of VAS-393 crystals was performed. Investigations were carried out with the use of the Weissenberg rotating and powder (employing the Bjornstrem diagrams) methods. The lattice constants ''c'' and ''a''are calculated. The crystal is shown to belong to the trigonal syngony (medium category)

  1. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals

    Directory of Open Access Journals (Sweden)

    E. Han Dao

    2015-07-01

    Full Text Available In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.

  2. 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.

  3. X-ray Scintillation in Lead Halide Perovskite Crystals

    CERN Document Server

    Birowosuto, M D; Drozdowski, W; Brylew, K; Lachmanski, W; Bruno, A; Soci, C

    2016-01-01

    Current technologies for X-ray detection rely on scintillation from expensive inorganic crystals grown at high-temperature, which so far has hindered the development of large-area scintillator arrays. Thanks to the presence of heavy atoms, solution-grown hybrid lead halide perovskite single crystals exhibit short X-ray absorption length and excellent detection efficiency. Here we compare X-ray scintillator characteristics of three-dimensional (3D) MAPbI3 and MAPbBr3 and two-dimensional (2D) (EDBE)PbCl4 hybrid perovskite crystals. X-ray excited thermoluminescence measurements indicate the absence of deep traps and a very small density of shallow trap states, which lessens after-glow effects. All perovskite single crystals exhibit high X-ray excited luminescence yields of >120,000 photons/MeV at low temperature. Although thermal quenching is significant at room temperature, the large exciton binding energy of 2D (EDBE)PbCl4 significantly reduces thermal effects compared to 3D perovskites, and moderate light yie...

  4. X-ray Scintillation in Lead Halide Perovskite Crystals

    Science.gov (United States)

    Birowosuto, M. D.; Cortecchia, D.; Drozdowski, W.; Brylew, K.; Lachmanski, W.; Bruno, A.; Soci, C.

    2016-11-01

    Current technologies for X-ray detection rely on scintillation from expensive inorganic crystals grown at high-temperature, which so far has hindered the development of large-area scintillator arrays. Thanks to the presence of heavy atoms, solution-grown hybrid lead halide perovskite single crystals exhibit short X-ray absorption length and excellent detection efficiency. Here we compare X-ray scintillator characteristics of three-dimensional (3D) MAPbI3 and MAPbBr3 and two-dimensional (2D) (EDBE)PbCl4 hybrid perovskite crystals. X-ray excited thermoluminescence measurements indicate the absence of deep traps and a very small density of shallow trap states, which lessens after-glow effects. All perovskite single crystals exhibit high X-ray excited luminescence yields of >120,000 photons/MeV at low temperature. Although thermal quenching is significant at room temperature, the large exciton binding energy of 2D (EDBE)PbCl4 significantly reduces thermal effects compared to 3D perovskites, and moderate light yield of 9,000 photons/MeV can be achieved even at room temperature. This highlights the potential of 2D metal halide perovskites for large-area and low-cost scintillator devices for medical, security and scientific applications.

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

    Energy Technology Data Exchange (ETDEWEB)

    Sutton, Kristin A. [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States); Black, Paul J.; Mercer, Kermit R. [University of Rochester Medical Center, Rochester, NY 14642 (United States); Garman, Elspeth F. [University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QU (United Kingdom); Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Snell, Edward H., E-mail: esnell@hwi.buffalo.edu [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States); SUNY Buffalo Medical School, 700 Ellicott Street, Buffalo, NY 14203 (United States); Bernhard, William A. [University of Rochester Medical Center, Rochester, NY 14642 (United States); Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States)

    2013-12-01

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

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

    Science.gov (United States)

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

    2012-04-27

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

  7. 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.

  8. Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII.

    Science.gov (United States)

    Chernev, Petko; Zaharieva, Ivelina; Rossini, Emanuele; Galstyan, Artur; Dau, Holger; Knapp, Ernst-Walter

    2016-10-12

    Structural data of the oxygen-evolving complex (OEC) in photosystem II (PSII) determined by X-ray crystallography, quantum chemistry (QC), and extended X-ray absorption fine structure (EXAFS) analyses are presently inconsistent. Therefore, a detailed study of what information can be gained about the OEC through a comparison of QC and crystallographic structure information combined with the information from range-extended EXAFS spectra was undertaken. An analysis for determining the precision of the atomic coordinates of the OEC by QC is carried out. OEC model structures based on crystallographic data that are obtained by QC from different research groups are compared with one another and with structures obtained by high-resolution crystallography. The theory of EXAFS spectra is summarized, and the application of EXAFS spectra to the experimental determination of the structure of the OEC is detailed. We discriminate three types of parameters entering the formula for the EXAFS spectrum: (1) model-independent, predefined, and fixed; (2) model-dependent that can be computed or adjusted; and (3) model-dependent that must be adjusted. The information content of EXAFS spectra is estimated and is related to the precision of atomic coordinates and resolution power to discriminate different atom-pair distances of the OEC. It is demonstrated how a precise adjustment of atomic coordinates can yield a nearly perfect representation of the experimental OEC EXAFS spectrum, but at the expense of overfitting and losing the knowledge of the initial OEC model structure. Introducing a novel type of penalty function, it is shown that moderate adjustment of atomic coordinates to the EXAFS spectrum limited by constraints avoids overfitting and can be used to validate different OEC model structures. This technique is used to identify the OEC model structures whose computed OEC EXAFS spectra agree best with the measured spectrum. In this way, the most likely S-state and protonation pattern

  9. Two crystal x-ray spectrometers for OMEGA experiments

    Science.gov (United States)

    Reverdin, C.; Casner, A.; Girard, F.; Lecherbourg, L.; Loupias, B.; Tassin, V.; Philippe, F.

    2016-11-01

    Two x-ray spectrometers have been built for x-ray spectroscopy of laser-produced plasmas on OMEGA at the Laboratory for Laser Energetics (LLE) by Commissariat a ̀ l'Energie Atomique et aux énergies alternatives (CEA). The accessible photon energy range is from 1.5 to 20 keV. The first spectrometer, called X-ray CEA Crystal Spectrometer with a Charge-Injection Device (XCCS-CID), records three spectra with three crystals coupled to a time integrated CID camera. The second one, called X-ray CEA Crystal Spectrometer (XCCS) with a framing camera, is time resolved and records four spectra with two crystals on the four frames of a framing camera. Cylindrical crystals are used in Johan geometry. Each spectrometer is positioned with a ten-inch manipulator inside the OMEGA target chamber. In each experiment, after choosing a spectral window, a specific configuration is designed and concave crystals are precisely positioned on a board with angled wedges and spacers. Slits on snouts enable 1D spatial resolution to distinguish spectra emitted from different parts of the target.

  10. Crystal quality analysis and improvement using x-ray topography

    Science.gov (United States)

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

    2008-08-01

    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.

  11. Crystal quality analysis and improvement using x-ray topography.

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  12. Photonic crystals at visible, x-ray, and terahertz frequencies

    Science.gov (United States)

    Prasad, Tushar

    Photonic crystals are artificial structures with a periodically varying refractive index. This property allows photonic crystals to control the propagation of photons, making them desirable components for novel photonic devices. Photonic crystals are also termed as "semiconductors of light", since they control the flow of electromagnetic radiation similar to the way electrons are excited in a semiconductor crystal. The scale of periodicity in the refractive index determines the frequency (or wavelength) of the electromagnetic waves that can be manipulated. This thesis presents a detailed analysis of photonic crystals at visible, x-ray, and terahertz frequencies. Self-assembly and spin-coating methods are used to fabricate colloidal photonic crystals at visible frequencies. Their dispersion characteristics are examined through theoretical as well as experimental studies. Based on their peculiar dispersion property called the superprism effect, a sensor that can detect small quantities of chemical substances is designed. A photonic crystal that can manipulate x-rays is fabricated by using crystals of a non-toxic plant virus as templates. Calculations show that these metallized three-dimensional crystals can find utility in x-ray optical systems. Terahertz photonic crystal slabs are fabricated by standard lithographic and etching techniques. In-plane superprism effect and out-of-plane guided resonances are studied by terahertz time-domain spectroscopy, and verified by numerical simulations.

  13. Ultrafast x-ray diffraction of laser-irradiated crystals

    Science.gov (United States)

    Heimann, P. A.; Larsson, J.; Chang, Z.; Lindenberg, A.; Schuck, P. J.; Judd, E.; Padmore, H. A.; Bucksbaum, P. H.; Lee, R. W.; Murnane, M.; Kapteyn, H.; Wark, J. S.; Falcone, R. W.

    1997-07-01

    An apparatus has been developed for measuring time-dependent x-ray diffraction. X-ray pulses from an Advanced Light Source bend magnet are diffracted by a sagittally-focusing Si (111) crystal and then by a sample crystal, presently InSb (111). Laser pulses with 100 fs duration and a repetition rate of 1 KHz irradiate the sample inducing a phase transition. Two types of detectors are being employed: an x-ray streak camera and an avalanche photodiode. The streak camera is driven by a photoconductive switch and has a 2 ps temporal resolution determined by trigger jitter. The avalanche photodiode has high quantum efficiency and sufficient time resolution to detect single x-ray pulses in ALS two bunch or `camshaft' operation. A beamline is under construction dedicated for time resolved and micro-diffraction experiments. In the new beamline a toroidal mirror collects 3 mrad horizontally and makes a 1:1 image of the bend magnet source in the x-ray hutch. A laser induced phase transition has been observed in InSb occurring within 70 ps.

  14. Revised stereochemistry of ceramide-trafficking inhibitor HPA-12 by X-ray crystallography analysis.

    Science.gov (United States)

    Ueno, Masaharu; Huang, Yi-Yong; Yamano, Akihito; Kobayashi, Shū

    2013-06-07

    In response to Berkeš's report revising the stereochemistry of HPA-12, an important ceramide-trafficking inhibitor that was discovered and synthesized and its stereochemistry determined in 2001, the synthesis and the stereochemistry were reinvestigated. A large-scale synthetic method for HPA-12 based on a Zn-catalyzed asymmetric Mannich-type reaction in water was developed. Single crystals of HPA-12 for X-ray crystallographic analysis were obtained from ethyl propionate/n-hexane, and the stereochemistry was definitely determined to be 1R,3S, consistent with Berkeš's revised structure.

  15. Crystallization and preliminary X-ray analysis of the NKX2.5 homeodomain in complex with DNA.

    Science.gov (United States)

    Genis, Caroli; Scone, Peyton; Kasahara, Hideko; Nam, Hyun Joo

    2008-11-01

    As part of an effort to elucidate the molecular basis for the pathogenesis of NKX2.5 mutations in congenital heart disease using X-ray crystallography, the NKX2.5 homeodomain has been crystallized in complex with a specific DNA element, the -242 promoter region of atrial natriuretic factor. Crystals of the homeodomain-DNA complex diffracted X-rays to 1.7 A resolution and belonged to space group P6(5), with unit-cell parameters a = b = 71.5, c = 94.3 A. The asymmetric unit contained two molecules of the NKX2.5 homeodomain and one double-stranded oligonucleotide.

  16. Spatiotemporal Response of Crystals in X-ray Bragg Diffraction

    CERN Document Server

    Shvyd'ko, Yuri

    2012-01-01

    The spatiotemporal response of crystals in x-ray Bragg diffraction resulting from excitation by an ultra-short, laterally confined x-ray pulse is studied theoretically. The theory presents an extension of the analysis in symmetric reflection geometry [1] to the generic case, which includes Bragg diffraction both in reflection (Bragg) and transmission (Laue) asymmetric scattering geometries. The spatiotemporal response is presented as a product of a crystal-intrinsic plane wave spatiotemporal response function and an envelope function defined by the crystal-independent transverse profile of the incident beam and the scattering geometry. The diffracted wavefields exhibit amplitude modulation perpendicular to the propagation direction due to both angular dispersion and the dispersion due to Bragg's law. The characteristic measure of the spatiotemporal response is expressed in terms of a few parameters: the extinction length, crystal thickness, Bragg angle, asymmetry angle, and the speed of light. Applications to...

  17. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  18. X-Ray Line Measurements with High Efficiency Bragg Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Pak, A; Gregori, G; Knight, J; Campbell, K; Landen, O; Glenzer, S

    2004-04-01

    We have studied the focusing properties of two highly oriented pyrolitic graphite (HOPG) spectrometers, which differ in the degree of the mosaic spread: ZYA with a low mosaic spread ({gamma}=0.4 degrees) and ZYH with a large mosaic spread ({gamma}=3.5 degrees). In order to assess the crystal performance for a variety of different experiments, various K{alpha} and K{beta} x-ray lines have been produced using a high-intensity ({approx}>10{sup 17} W/cm{sup 2}) short-pulse ({approx} 100 fs) laser beam focused onto Ti, V, Zn, and Cu foils. The measured spectral resolution of the HOPG crystals in both first and second order diffraction has been compared with theoretical predictions. Using known values for the peak reflectivity of HOPG crystals, we have also computed K{alpha} x-ray conversion efficiencies of Ti, V, Zn, and Cu. These results are important to estimate the optimal conditions under which different types of HOPG monochromators can be used for the detection of weak x-ray signals as the one encountered in x-ray Thomson/Compton scattering experiments.

  19. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  20. -2,4-Dichlorobenzoyl phosphoric triamides: Synthesis, spectroscopic and X-ray crystallography studies

    Indian Academy of Sciences (India)

    Khodayar Gholivand; Nasrin Oroujzadeh; Zahra Shariatinia

    2010-07-01

    New phosphoric triamides 1-9 were synthesized by the reaction of -2,4-dichlorobenzoyl phosphoramidic dichloride with various cyclic aliphatic amines and the products were characterized by 1H, 13C, 31P NMR, IR spectroscopy and elemental analysis. Surprisingly, the 1H NMR spectrum of 2 indicated long range 6 (P, H) coupling constant = 1.3, 1.4 Hz and those of molecules 3, 4, 6-8 display longrange 4 (H, H) coupling constants (1.8-1.9 Hz) for the coupling of aromatic protons in 2,4-dichlorophenyl rings. 1H NMR spectra indicated 3 (PNCH) for enantiotopic and diastereotopic benzylic CH2 protons in compounds 7 and 8. The spectroscopic data of newly synthesized compounds were compared with those related -benzoyl derivatives. The structures of compounds 5, 8 and 10 (2,4-Cl2-C6H3C(O)NHP(O)[NCH2CH(CH3)2]2) have been determined by X-ray crystallography. The structures form centrosymmetric dimers through intermolecular strong -P=O…H-N-hydrogen bonds. The dimers connect to each other via rather strong and weak C-H…O plus weak C-H…Cl H-bonds to produce a 1-D network for 5 while 3-D polymeric chains for 8 and 10.

  1. 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

  2. A versatile three/four crystal X-ray diffractometer for X-ray optical elements: Performance and applications

    DEFF Research Database (Denmark)

    Christensen, Finn Erland; Hornstrup, Allan; Jacobsen, E.;

    1987-01-01

    A versatile X-ray diffractometer for the study of X-ray optical elements such as grazing incidence mirrors, crystals and X-ray gratings has been built and put into operation at the Danish Space Research Institute. The diffractrometer is built on a 1.5 m long granite bench with the X-ray source...... located at one end of the bench where it can be rotated around a fixed vertical axis. The beam defining elements are perfect crystals of Si, Ge or quartz. With these it is possible to define a highly collimated beam of a few arcsec fwhm in the scattering plane. Examples of measurements on various X-ray...

  3. The use of X-ray crystallography to determine absolute configuration.

    Science.gov (United States)

    Flack, H D; Bernardinelli, G

    2008-05-15

    Essential background on the determination of absolute configuration by way of single-crystal X-ray diffraction (XRD) is presented. The use and limitations of an internal chiral reference are described. The physical model underlying the Flack parameter is explained. Absolute structure and absolute configuration are defined and their similarities and differences are highlighted. The necessary conditions on the Flack parameter for satisfactory absolute-structure determination are detailed. The symmetry and purity conditions for absolute-configuration determination are discussed. The physical basis of resonant scattering is briefly presented and the insights obtained from a complete derivation of a Bijvoet intensity ratio by way of the mean-square Friedel difference are exposed. The requirements on least-squares refinement are emphasized. The topics of right-handed axes, XRD intensity measurement, software, crystal-structure evaluation, errors in crystal structures, and compatibility of data in their relation to absolute-configuration determination are described. Characterization of the compounds and crystals by the physicochemical measurement of optical rotation, CD spectra, and enantioselective chromatography are presented. Some simple and some complex examples of absolute-configuration determination using combined XRD and CD measurements, using XRD and enantioselective chromatography, and in multiply-twinned crystals clarify the technique. The review concludes with comments on absolute-configuration determination from light-atom structures.

  4. Crystallization of prostaglandin-H synthase for X-ray structure analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jahnke, K.; Degen, G.H.; Buehner, M. (Univ. of Wuerzburg (West Germany))

    1990-08-01

    Prostaglandin-H (PGH) synthase from ram seminal vesicles is a dimeric integral membrane protein of molecular weight 140 kDa. PGH synthase is a key enzyme in the biosynthesis of prostaglandins, has cyclooxygenase and peroxidase activities, and contains heme as a coenzyme. In the peroxidation step of its reaction, PGH synthase can use xenobiotics as co-substrates and can catalyze the metabolic activation of carcinogens such as diethylstilbestrol. To gain a detailed understanding of the inner workings of PGH synthase, the authors are investigating its three-dimensional structure by X-ray crystallography. A purification procedure was established that yields stable homogeneous PGH synthase that is at least 80% holoenzyme. Manipulation of these crystals is very difficult due to the small volume of the growth phase. The crystals dissolved rapidly in all aqueous media into which they were transferred for mounting in X-ray capillaries. Therefore, the authors have not yet been able to demonstrate their true X-ray scattering power. A crystal provisionally dry mounted diffracted to about 8 {angstrom} resolution.

  5. 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.

  6. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

    Science.gov (United States)

    Keedy, Daniel A; Fraser, James S; van den Bedem, Henry

    2015-10-01

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the "flap" regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  7. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

    Directory of Open Access Journals (Sweden)

    Daniel A Keedy

    2015-10-01

    Full Text Available Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the "flap" regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  8. Recent Results with Crystal X-ray Generators

    Science.gov (United States)

    Brownridge, James; Shafroth, Stephen

    1999-11-01

    Thermally stimulated small crystalsfootnote J. D. Brownridge and S. Raboy, J. Appl. Phys. 86, 640 (1999) of LiTaO3 and LiNbO3 (0.1 cm^3) in mtorr environments are viable alternatives to ^55Fe, ^57Co,^109Cd or ^241Am excitation sources in X-ray Fluorescence (XRF) analysis. Several different types of crystal x-ray generators have been built for use in teachingfootnote S.M. Shafroth and J.D. Brownridge, AIP Conference Proceedings 475, 1100 (1998) and research in physics, biology and environmental studies. These XRF sources can be designed to meet safety standards so no license is required.. They can generate characteristic X-rays of most elements at specified intensities. The design, construction and performance of several units will be discussed. Electrons of energies greater than 50 keV and currents of 10 nA or more can be produced for from several minutes to several hours using these crystals. Some unexpected new results will be presented.

  9. 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.

  10. 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 CaMn4O5 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 O2 evolution. The structure of the dark-stable S1 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 S1 state. However, the atom positions in this crystal

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

    Science.gov (United States)

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

    2015-02-01

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

  12. Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.

    Science.gov (United States)

    Peters, Justin P; Kowal, Ewa A; Pallan, Pradeep S; Egli, Martin; Maher, L James

    2017-09-04

    Leveraging structural biology tools, we report the results of experiments seeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from 'electrostatic' or 'base stacking' influences without considering the larger context of altered helical geometry. Circular dichroism spectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of I⋅C pairs. X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight I⋅C and two A⋅T pairs) revealed an A-tract-like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1'-exo (southeastern) conformation. This contrasts with the standard B-DNA geometry with C2'-endo sugar puckers (south conformation). In contrast, the crystal structure of a decamer with only four I⋅C pairs has a geometry similar to that of the reference duplex with eight G⋅C and two A⋅T pairs. The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signature in solution and the altered mechanical properties of some inosine-containing DNAs.

  13. Crystallization and preliminary X-ray diffraction analysis of apolipoprotein E-containing lipoprotein particles

    Energy Technology Data Exchange (ETDEWEB)

    Newhouse, Yvonne [Gladstone Institutes of Cardiovascular and Neurological Disease, University of California, San Francisco, CA 94158 (United States); Peters-Libeu, Clare [Gladstone Institutes of Cardiovascular and Neurological Disease, University of California, San Francisco, CA 94158 (United States); Cardiovascular Research Institute, University of California, San Francisco, CA 94158 (United States); Weisgraber, Karl H., E-mail: kweisgraber@gladstone.ucsf.edu [Gladstone Institutes of Cardiovascular and Neurological Disease, University of California, San Francisco, CA 94158 (United States); Cardiovascular Research Institute, University of California, San Francisco, CA 94158 (United States); Department of Pathology, University of California, San Francisco, CA 94158 (United States)

    2005-11-01

    Further understanding of the structure and function of plasma apolipoproteins requires the determination of their high-resolution structures when complexed with lipids. In these studies, the production of homogeneous, biologically active lipoprotein particles of apolipoprotein E complexed with dipalmitoylphosphatidylcholine and their crystallization and X-ray diffraction are demonstrated. High-resolution structural information is available for several soluble plasma apolipoproteins (apos) in a lipid-free state. However, this information provides limited insight into structure–function relationships, as this class of proteins primarily performs its functions of lipid transport and modulation of lipid metabolism in a lipid-bound state on lipoprotein particles. Here, the possibility of generating homogeneous lipoprotein particles that could be crystallized was explored, opening the possibility of obtaining high-resolution structural information by X-ray crystallography. To test this possibility, apoE4 complexed with the phospholipid dipalmitoylphosphatidylcholine was chosen. Uniform particles containing 50% lipid and 50% apoE4 were obtained and crystallized using the hanging-drop method. Two crystal forms diffract to beyond 8 Å resolution.

  14. 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.

  15. Expression, Purification, Crystallization And Preliminary X-Ray Studies of Histamine Dehydrogenase From Nocardioides Simplex

    Energy Technology Data Exchange (ETDEWEB)

    Reed, T.M.; Hirakawa, H.; Mure, M.; Scott, E.E.; Limburg, J.

    2009-05-21

    Histamine dehydrogenase (HADH) from Nocardioides simplex catalyzes the oxidative deamination of histamine to produce imidazole acetaldehyde and an ammonium ion. HADH is functionally related to trimethylamine dehydrogenase (TMADH), but HADH has strict substrate specificity towards histamine. HADH is a homodimer, with each 76 kDa subunit containing two redox cofactors: a [4Fe-4S] cluster and an unusual covalently bound flavin mononucleotide, 6-S-cysteinyl-FMN. In order to understand the substrate specificity of HADH, it was sought to determine its structure by X-ray crystallography. This enzyme has been expressed recombinantly in Escherichia coli and successfully crystallized in two forms. Diffraction data were collected to 2.7 {angstrom} resolution at the SSRL synchrotron with 99.7% completeness. The crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 101.14, b = 107.03, c = 153.35 {angstrom}.

  16. Developing small vacuum spark as an x-ray source for calibration of an x-ray focusing crystal spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Ghomeishi, Mostafa; Adikan, Faisal Rafiq Mahamd [Photonic Research Group, Department of Electrical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur (Malaysia); Karami, Mohammad [Department of Mechanical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur (Malaysia)

    2012-10-15

    A new technique of x-ray focusing crystal spectrometers' calibration is the desired result. For this purpose the spectrometer is designed to register radiated copper K{alpha} and K{beta} lines by using a flat {alpha}-quartz crystal. This experiment uses pre-breakdown x-ray emissions in low vacuum of about 2.5-3 mbar. At this pressure the pinch will not form so the plasma will not radiate. The anode material is copper and the capacity of the capacitor bank is 22.6 nF. This experiment designed and mounted a repetitive triggering system to save the operator time making hundreds of shots. This emission amount is good for calibration and geometrical adjustment of an optical crystal x-ray focusing spectrometer.

  17. Developing small vacuum spark as an x-ray source for calibration of an x-ray focusing crystal spectrometer.

    Science.gov (United States)

    Ghomeishi, Mostafa; Karami, Mohammad; Adikan, Faisal Rafiq Mahamd

    2012-10-01

    A new technique of x-ray focusing crystal spectrometers' calibration is the desired result. For this purpose the spectrometer is designed to register radiated copper Kα and Kβ lines by using a flat α-quartz crystal. This experiment uses pre-breakdown x-ray emissions in low vacuum of about 2.5-3 mbar. At this pressure the pinch will not form so the plasma will not radiate. The anode material is copper and the capacity of the capacitor bank is 22.6 nF. This experiment designed and mounted a repetitive triggering system to save the operator time making hundreds of shots. This emission amount is good for calibration and geometrical adjustment of an optical crystal x-ray focusing spectrometer.

  18. Study of the inclusion of the (R)- and (S)-camphor enantiomers in alpha-cyclodextrin by X-ray crystallography and molecular dynamics.

    Science.gov (United States)

    Kokkinou, Areti; Tsorteki, Frantzeska; Karpusas, Michael; Papakyriakou, Athanasios; Bethanis, Kostas; Mentzafos, Dimitris

    2010-05-27

    The inclusion of (R)- and (S)-camphor compounds in alpha-cyclodextrin has been studied by X-ray crystallography. The crystal structures of the complexes reveal that one guest molecule is accommodated inside the cavity formed by a head-to-head cyclodextrin dimer. In the crystal lattice, the dimers form layers which are successively shifted by half a dimer. In both (R)- and (S)-cases, the camphor molecule exhibits disorder and occupies three major sites with orientations that can be described as either 'polar' or 'equatorial'. Molecular dynamics simulations performed for the observed complexes indicate that although the carbonyl oxygen of both (R)- and (S)-camphor switches between different hydrogen bonding partners, it maintains the observed mode of 'polar' or 'equatorial' alignment.

  19. 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...... side as the three oxygen substituents. In addition to the glucosides, two amides, (1S,2S,3R,4R)-2,3-epoxy-1,4-dihydroxycyclopentane-1-carboxamide and (1S,4R)-1,4-dihydroxy-2-cyclopentene-1-carboxamide, were isolated from P. suberosa and characterized; the amides are probably artefacts...

  20. The renin-angiotensin system: an example of the study of linear peptides by x-ray crystallography.

    Science.gov (United States)

    Precigoux, G; Benkoulouche, M; Geoffre, S

    1989-01-01

    In order to get information on the bioactive conformations of the endogenic renin substrate, a few peptide segments of angiotensinogen, along with a pepstatin analogue, were studied in the solid state by x-ray crystallography. These results are compared with the conformations of acidic proteinase inhibitors observed at the level of the active site. Such a comparison allows us to point out some analogies and differences between the observed conformation for the peptide alone and the conformations on the active sites. The analysis of the results should be a good starting point for making hypotheses on the renin substrate bioactive conformation(s).

  1. 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.

  2. X-ray Structure of Snow Flea Antifreeze Protein Determined by Racemic Crystallization of Synthetic Protein Enantiomers

    Energy Technology Data Exchange (ETDEWEB)

    Pentelute, Brad L.; Gates, Zachary P.; Tereshko, Valentina; Dashnau, Jennifer L.; Vanderkooi, Jane M.; Kossiakoff, Anthony A.; Kent, Stephen B.H. (UPENN); (UC)

    2008-08-20

    Chemical protein synthesis and racemic protein crystallization were used to determine the X-ray structure of the snow flea antifreeze protein (sfAFP). Crystal formation from a racemic solution containing equal amounts of the chemically synthesized proteins d-sfAFP and l-sfAFP occurred much more readily than for l-sfAFP alone. More facile crystal formation also occurred from a quasi-racemic mixture of d-sfAFP and l-Se-sfAFP, a chemical protein analogue that contains an additional -SeCH2- moiety at one residue and thus differs slightly from the true enantiomer. Multiple wavelength anomalous dispersion (MAD) phasing from quasi-racemate crystals was then used to determine the X-ray structure of the sfAFP protein molecule. The resulting model was used to solve by molecular replacement the X-ray structure of l-sfAFP to a resolution of 0.98 {angstrom}. The l-sfAFP molecule is made up of six antiparallel left-handed PPII helixes, stacked in two sets of three, to form a compact brick-like structure with one hydrophilic face and one hydrophobic face. This is a novel experimental protein structure and closely resembles a structural model proposed for sfAFP. These results illustrate the utility of total chemical synthesis combined with racemic crystallization and X-ray crystallography for determining the unknown structure of a protein.

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

    Science.gov (United States)

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

    2016-09-01

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

  4. In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

    Directory of Open Access Journals (Sweden)

    Arjen J. Jakobi

    2016-03-01

    Full Text Available The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. The observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.

  5. Surface x-ray crystallography with alternating constraints in real and reciprocal space: the case of mixed domains

    Energy Technology Data Exchange (ETDEWEB)

    Saldin, D.K.; Harder, R.J.; Shneerson, V.L. [Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI (United States); Moritz, W. [Institute of Crystallography and Applied Mineralogy, University of Munich, Munich (Germany)

    2002-04-29

    A recently developed recursive algorithm for the direct recovery of the electron density of a surface unit cell from scattered x-ray intensities is adapted to crystal surfaces that may consist of mutually rotated domains. We examine the cases of both mutually coherent scattering from the domains and the more common case of mutually incoherent scattering. In each case we test the algorithms on simulated data calculated from a standard surface x-ray diffraction computer program. In both cases the iterative algorithm depends on satisfying data constraints in reciprocal space and non-negativity constraints on the electron density in real space. (author)

  6. High-pressure crystallography of periodic and aperiodic crystals.

    Science.gov (United States)

    Hejny, Clivia; Minkov, Vasily S

    2015-03-01

    More than five decades have passed since the first single-crystal X-ray diffraction experiments at high pressure were performed. These studies were applied historically to geochemical processes occurring in the Earth and other planets, but high-pressure crystallography has spread across different fields of science including chemistry, physics, biology, materials science and pharmacy. With each passing year, high-pressure studies have become more precise and comprehensive because of the development of instrumentation and software, and the systems investigated have also become more complicated. Starting with crystals of simple minerals and inorganic compounds, the interests of researchers have shifted to complicated metal-organic frameworks, aperiodic crystals and quasicrystals, molecular crystals, and even proteins and viruses. Inspired by contributions to the microsymposium 'High-Pressure Crystallography of Periodic and Aperiodic Crystals' presented at the 23rd IUCr Congress and General Assembly, the authors have tried to summarize certain recent results of single-crystal studies of molecular and aperiodic structures under high pressure. While the selected contributions do not cover the whole spectrum of high-pressure research, they demonstrate the broad diversity of novel and fascinating results and may awaken the reader's interest in this topic.

  7. High-pressure crystallography of periodic and aperiodic crystals

    Directory of Open Access Journals (Sweden)

    Clivia Hejny

    2015-03-01

    Full Text Available More than five decades have passed since the first single-crystal X-ray diffraction experiments at high pressure were performed. These studies were applied historically to geochemical processes occurring in the Earth and other planets, but high-pressure crystallography has spread across different fields of science including chemistry, physics, biology, materials science and pharmacy. With each passing year, high-pressure studies have become more precise and comprehensive because of the development of instrumentation and software, and the systems investigated have also become more complicated. Starting with crystals of simple minerals and inorganic compounds, the interests of researchers have shifted to complicated metal–organic frameworks, aperiodic crystals and quasicrystals, molecular crystals, and even proteins and viruses. Inspired by contributions to the microsymposium `High-Pressure Crystallography of Periodic and Aperiodic Crystals' presented at the 23rd IUCr Congress and General Assembly, the authors have tried to summarize certain recent results of single-crystal studies of molecular and aperiodic structures under high pressure. While the selected contributions do not cover the whole spectrum of high-pressure research, they demonstrate the broad diversity of novel and fascinating results and may awaken the reader's interest in this topic.

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

    Energy Technology Data Exchange (ETDEWEB)

    Higashiura, Akifumi, E-mail: hgsur-a@protein.osaka-u.ac.jp [Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Ohta, Kazunori; Masaki, Mika; Sato, Masaru [Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505 (Japan); Inaka, Koji [Maruwa Foods and Biosciences Inc., Nara 639-1123 (Japan); Tanaka, Hiroaki [Confocal Science Inc., Tokyo 101-0032 (Japan); Nakagawa, Atsushi [Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan)

    2013-11-01

    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.

  9. Crystallography using synchrotron radiation X-ray. Application of Weissenberg and time resolved Laue methods to macromolecular structure analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sakabe, Noriyoshi [National Lab. for High Energy Physics, Tsukuba, Ibaraki (Japan)

    1994-12-31

    The three-dimensional structures of macromolecules under static and dynamic conditions are very important for the study of molecular biology. X-ray crystallography is the most powerful tool to obtain the three-dimensional structures of the macromolecules of especially large size, for which synchrotron radiation X-ray is used, The collection of diffraction data is the first, most important step for crystalline structure analysis. Efforts have been exerted to establish the data collection system using monochromatic synchrotron radiation X-ray (SRX). The diffraction intensity data collection system combined with a newly developed Weissenberg camera for macromolecules and an image plate (IP) using SRX has been established at the Photon Factory. Many important biological structures by high resolution have already come out with this data collection system, which is used also for the study on enzymatic reaction mechanism. A time resolved Laue camera has been designed, and the preliminary experiment has been carried out in the Photon Factory. These systems are reported. (K.I.).

  10. 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...

  11. Structure of the Lassa virus nucleoprotein revealed by X-ray crystallography, small-angle X-ray scattering, and electron microscopy.

    Science.gov (United States)

    Brunotte, Linda; Kerber, Romy; Shang, Weifeng; Hauer, Florian; Hass, Meike; Gabriel, Martin; Lelke, Michaela; Busch, Carola; Stark, Holger; Svergun, Dmitri I; Betzel, Christian; Perbandt, Markus; Günther, Stephan

    2011-11-04

    The nucleoprotein (NP) of Lassa virus (LASV) strain AV was expressed in a recombinant baculovirus system. The crystal structure of full-length NP was solved at a resolution of 2.45 Å. The overall fold corresponds to that of NP of LASV strain Josiah (Qi, X., Lan, S., Wang, W., Schelde, L. M., Dong, H., Wallat, G. D., Ly, H., Liang, Y., and Dong, C. (2010) Nature 468, 779-783) with a root mean square deviation of 0.67 Å for all atoms (6.3% difference in primary sequence). As the packing in the crystal offers two different trimer architectures for the biological assembly, the quaternary structure of NP in solution was determined by small-angle x-ray scattering and EM. After classification and averaging of >6000 EM raw images, trimeric centrosymmetric structures were obtained, which correspond in size and shape to one trimer in the crystal structure formed around a crystallographic 3-fold rotation axis (symmetric trimer). The symmetric trimer is also a good model for the small-angle x-ray scattering data and could be well embedded into the ab initio model. The N-terminal domain of NP contains a deep nucleotide-binding cavity that has been proposed to bind cellular cap structures for priming viral mRNA synthesis. All residues implicated in m(7)GpppN binding were exchanged, and the transcription/replication phenotype of the NP mutant was tested using a LASV replicon system. None of the mutants showed a specific defect in mRNA expression; most were globally defective in RNA synthesis. In conclusion, we describe the full-length crystal structure and the quaternary structure in solution of LASV NP. The nucleotide-binding pocket of NP could not be assigned a specific role in viral mRNA synthesis.

  12. X-ray wavefront modeling of Bragg diffraction from crystals

    Science.gov (United States)

    Sutter, John P.

    2011-09-01

    The diffraction of an X-ray wavefront from a slightly distorted crystal can be modeled by the Takagi-Taupin theory, an extension of the well-known dynamical diffraction theory for perfect crystals. Maxwell's equations applied to a perturbed periodic medium yield two coupled differential equations in the incident and diffracted amplitude. These equations are discretized for numerical calculation into the determination of the two amplitudes on the points of an integration mesh, beginning with the incident amplitudes at the crystal's top surface. The result is a set of diffracted amplitudes on the top surface (in the Bragg geometry) or the bottom surface (in the Laue geometry), forming a wavefront that in turn can be propagated through free space using the Fresnel- Huygens equations. The performance of the Diamond Light Source I20 dispersive spectrometer has here been simulated using this method. Methods are shown for transforming displacements calculated by finite element analysis into local lattice distortions, and for efficiently performing 3-D linear interpolations from these onto the Takagi-Taupin integration mesh, allowing this method to be extended to crystals under thermal load or novel mechanical bender designs.

  13. Hard x-ray single crystal bi-mirror.

    Science.gov (United States)

    Lyubomirskiy, M; Snigireva, I; Kuznetsov, S; Yunkin, V; Snigirev, A

    2015-05-15

    We report a novel hard x-ray interferometer consisting of two parallel channels manufactured in a single Si crystal by means of microfabrication technology. The sidewall surfaces of the channels, similar to mirrors, scatter at very small incident angles, acting equivalently to narrow micrometer size slits as in the Young double-slit interferometer. Experimental tests of the interferometer were performed at the ESRF ID06 beamline in the energy range from 12 to 16 keV. The interference patterns at different grazing incidence angles were recorded in the near- and far-field. Evaluation of the influence of the channel surface roughness on the visibility of interference fringes was performed. The proposed interferometer design allows the arrangement of mirrors at different split distances.

  14. High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K.

    Science.gov (United States)

    Chatake, Toshiyuki; Ishikawa, Takuya; Yanagisawa, Yasuhide; Yamada, Taro; Tanaka, Ichiro; Fujiwara, Satoru; Morimoro, Yukio

    2011-11-01

    Deuteration of macromolecules is an important technique in neutron protein crystallography. Solvent deuteration of protein crystals is carried out by replacing water (H(2)O) with heavy water (D(2)O) prior to neutron diffraction experiments in order to diminish background noise. The effects of solvent deuteration on the crystallization of proteinase K (PK) with polyethylene glycol as a precipitant were investigated using high-resolution X-ray crystallography. In previous studies, eight NO(3)(-) anions were included in the PK crystal unit cell grown in NaNO(3) solution. In this study, however, the PK crystal structure did not contain NO(3)(-) anions; consequently, distortions of amino acids arising from the presence of NO(3)(-) anions were avoided in the present crystal structures. High-resolution (1.1 Å) X-ray diffraction studies showed that the degradation of PK crystals induced by solvent deuteration was so small that this degradation would be negligible for the purpose of neutron protein crystallography experiments at medium resolution. Comparison of the nonhydrogen structures of nondeuterated and deuterated crystal structures demonstrated very small structural differences. Moreover, a positive correlation between the root-mean-squared differences and B factors indicated that no systematic difference existed.

  15. The founding and development of X-ray crystallography%X射线晶体学的创立与发展

    Institute of Scientific and Technical Information of China (English)

    麦振洪

    2014-01-01

    2014 is the centennial of X-ray crystallography. Crystals have played an impor-tant role in our lives and in the development of society throughout these 100 years. In July 2012 the 66th General Assembly of the United Nations declared 2014 to be the official International Year of Crystallography (IYCr2014). The discovery of X-ray diffraction by crystals has had a profound impact on science and tech-nology worldwide. It provides for us a distinct image of the arrangement of atoms or/and molecules in crystals. The development of X-ray spectroscopy has made it possible for us to understand the laws of atomic structure, and thus to identify the elements in all kinds of matter. In this article the greatest events in the history of X-ray crystallography, including the development of X-ray sources, detectors, experimental data analysis, and experimental methods are reviewed to commemorate the pioneers who made such important contributions to science and technology.%2014年,正值X射线晶体学诞生100周年,100年来,晶体对社会发展及人类生活起着重要的作用,它塑造了当今的世界,支撑着今天的科学。鉴于此,2012年7月举行的第66届联合国大会宣布,将2014年作为国际晶体学年(IYCr2014)。晶体X射线衍射的发现对自然科学的影响是深远的,它给人们提供了原子、分子在晶体中的微观排列图像;而X射线光谱学的发展,使人们认识原子结构的规律性,为原子结构理论提供了直接的实验佐证,也使辨别物质的元素成为可能,从而创立了X射线晶体学。X射线的应用,促进了X射线晶体学的发展,使物理学的研究从宏观进入微观,从经典过渡到现代,从而开拓了现代化学、现代生物学和医学的先河,使科学技术产生划时代的进展。文章回顾了X射线晶体学的创立与发展的历程,纵览了X射线晶体学重要的实验元素:光源、探测器、分析软件与晶体学数

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

    Science.gov (United States)

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

    2016-07-01

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

  17. X-ray instrumentation for SR beamlines

    CERN Document Server

    Kovalchuk, M V; Zheludeva, S I; Aleshko-Ozhevsky, O P; Arutynyan, E H; Kheiker, D M; Kreines, A Y; Lider, V V; Pashaev, E M; Shilina, N Y; Shishkov, V A

    2000-01-01

    The main possibilities and parameters of experimental X-ray stations are presented: 'Protein crystallography', 'X-ray structure analysis', 'High-precision X-ray optics', 'X-ray crystallography and material science', 'X-ray topography', 'Photoelectron X-ray standing wave' that are being installed at Kurchatov SR source by A.V. Shubnikov Institute of Crystallography.

  18. 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.

  19. 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.

  20. A novel inert crystal delivery medium for serial femtosecond crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; Hunter, Mark S.; Koglin, Jason E.; Kupitz, Christopher; Nelson, Garrett; Subramanian, Ganesh; White, Thomas A.; Zhao, Yun; Zook, James; Boutet, Sébastien; Cherezov, Vadim; Spence, John C. H.; Fromme, Raimund; Weierstall, Uwe; Fromme, Petra

    2015-06-30

    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 2.5Å resolution using 300µg 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.

  1. 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.

  2. 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...... 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...

  3. Crystallization and X-ray diffraction of crystals formed in water-plasticized amorphous lactose.

    Science.gov (United States)

    Jouppila, K; Kansikas, J; Roos, Y H

    1998-01-01

    Effects of storage time and relative humidity on crystallization and crystal forms produced from amorphous lactose were investigated. Crystallization was observed from time-dependent loss of sorbed water and increasing intensities of peaks in X-ray diffraction patterns. The rate of crystallization increased with increasing storage relative humidity. Lactose crystallized mainly as alpha-lactose monohydrate and anhydrous crystals with alpha- and beta-lactose in a molar ratio of 5:3. The results suggested that the crystal form was defined by the early nucleation process. The crystallization data are important in modeling of crystallization phenomena and prediction of stability of lactose-containing food and pharmaceutical materials.

  4. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    Science.gov (United States)

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

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

    Science.gov (United States)

    Sutton, Kristin A; Black, Paul J; Mercer, Kermit R; Garman, Elspeth F; Owen, Robin L; Snell, Edward H; Bernhard, William A

    2013-12-01

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

  6. Observation of unphosphorylated STAT3 core protein binding to target dsDNA by PEMSA and X-ray crystallography.

    Science.gov (United States)

    Nkansah, Edwin; Shah, Rahi; Collie, Gavin W; Parkinson, Gary N; Palmer, Jonathan; Rahman, Khondaker M; Bui, Tam T; Drake, Alex F; Husby, Jarmila; Neidle, Stephen; Zinzalla, Giovanna; Thurston, David E; Wilderspin, Andrew F

    2013-04-02

    The STAT3 transcription factor plays a central role in a wide range of cancer types where it is over-expressed. Previously, phosphorylation of this protein was thought to be a prerequisite for direct binding to DNA. However, we have now shown complete binding of a purified unphosphorylated STAT3 (uSTAT3) core directly to M67 DNA, the high affinity STAT3 target DNA sequence, by a protein electrophoretic mobility shift assay (PEMSA). Binding to M67 DNA was inhibited by addition of increasing concentrations of a phosphotyrosyl peptide. X-ray crystallography demonstrates one mode of binding that is similar to that known for the STAT3 core phosphorylated at Y705.

  7. Synthesis, X-ray crystallography, thermal studies, spectroscopic and electrochemistry investigations of uranyl Schiff base complexes.

    Science.gov (United States)

    Asadi, Zahra; Shorkaei, Mohammad Ranjkesh

    2013-03-15

    Some tetradentate salen type Schiff bases and their uranyl complexes were synthesized and characterized by UV-Vis, NMR, IR, TG, C.H.N. and X-ray crystallographic studies. From these investigations it is confirmed that a solvent molecule occupied the fifth position of the equatorial plane of the distorted pentagonal bipyramidal structure. Also, the kinetics of complex decomposition by using thermo gravimetric methods (TG) was studied. The thermal decomposition reactions are first order for the studied complexes. To examine the properties of uranyl complexes according to the substitutional groups, we have carried out the electrochemical studies. The electrochemical reactions of uranyl Schiff base complexes in acetonitrile were reversible.

  8. Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

    Science.gov (United States)

    Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

    2013-01-01

    Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

  9. X-ray crystal structure of N-6 adenine deoxyribose nucleic acid methyltransferase from Streptococcus pneumoniae

    Science.gov (United States)

    Tran, Phidung Hong

    X-ray diffraction by using resonant anomalous scattering has become a popular tool for solving crystal structures in the last ten years with the expanded availability of tunable synchrotron radiation for protein crystallography. Mercury atoms were used for phasing. The crystal structure of N-6 deoxyribose nucleic acid methyltransferase from Streptoccocus pneumoniae (DpnM) was solved by using the Multiple Anomalous Diffraction technique. The crystal structure reveals the formation of mercaptide between the mercury ion and the thiol group on the cysteine amino acid in a hydrophobic environment. The crystal structure contains the bound ligand, S- adenosyl-l-methionine on the surface of the concave opening. The direction of the β-strands on the beta sheets are identical to other solved methyltransferases. The highly conserved motifs, DPPY and the FxGxG, are found to be important in ligand binding and possibly in methyl group transfer. The structure has a concave cleft with an opening on the order of 30 Å that can accommodate a DNA duplex. By molecular modelling coupled to sequence alignment, two other highly conserved residues Arg21 and Gly19 are found to be important in catalysis.

  10. 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.

  11. Sensitive X-ray detectors made of methylammonium lead tribromide perovskite single crystals

    NARCIS (Netherlands)

    Wei, Haotong; Fang, Yanjun; Mulligan, Padhraic; Chuirazzi, William; Fang, Hong-Hua; Wang, Congcong; Ecker, Benjamin R.; Gao, Yongli; Loi, Maria Antonietta; Cao, Lei; Huang, Jinsong

    2016-01-01

    The large mobilities and carrier lifetimes of hybrid perovskite single crystals and the high atomic numbers of Pb, I and Br make them ideal for X-ray and gamma-ray detection. Here, we report a sensitive X-ray detector made of methylammonium lead bromide perovskite single crystals. A record-high mobi

  12. Sensitive X-ray detectors made of methylammonium lead tribromide perovskite single crystals

    NARCIS (Netherlands)

    Wei, Haotong; Fang, Yanjun; Mulligan, Padhraic; Chuirazzi, William; Fang, Hong-Hua; Wang, Congcong; Ecker, Benjamin R.; Gao, Yongli; Loi, Maria Antonietta; Cao, Lei; Huang, Jinsong

    2016-01-01

    The large mobilities and carrier lifetimes of hybrid perovskite single crystals and the high atomic numbers of Pb, I and Br make them ideal for X-ray and gamma-ray detection. Here, we report a sensitive X-ray detector made of methylammonium lead bromide perovskite single crystals. A record-high mobi

  13. Purification, crystallization and preliminary X-ray analysis of struthiocalcin 1 from ostrich (Struthio camelus) eggshell

    Energy Technology Data Exchange (ETDEWEB)

    Reyes-Grajeda, Juan Pablo [Unidad de Proteómica Médica, Instituto Nacional de Medicina Genómica, Mexico City (Mexico); Marín-García, Liliana [Instituto de Química, Universidad Nacional Autónoma de México (Mexico); Stojanoff, Vivian [Brookhaven National Laboratories, NSLS, Upton, New York (United States); Moreno, Abel, E-mail: carcamo@servidor.unam.mx [Instituto de Química, Universidad Nacional Autónoma de México (Mexico); Unidad de Proteómica Médica, Instituto Nacional de Medicina Genómica, Mexico City (Mexico)

    2007-11-01

    The purification, crystallization and preliminary X-ray diffraction data of the protein struthiocalcin 1 isolated from ostrich eggshell are reported. The purification, crystallization and preliminary X-ray analysis of struthiocalcin 1 (SCA-1), a protein obtained from the intramineral part of ostrich (Struthio camelus) eggshell, is reported.

  14. New insight into the dynamic properties and the active site architecture of H-Ras p21 revealed by X-ray crystallography at very high resolution

    Directory of Open Access Journals (Sweden)

    Klink Björn U

    2010-10-01

    Full Text Available Abstract Background In kinetic crystallography, the usually static method of X-ray diffraction is expanded to allow time-resolved analysis of conformational rearrangements in protein structures. To achieve this, reactions have to be triggered within the protein crystals of interest, and optical spectroscopy can be used to monitor the reaction state. For this approach, a modified form of H-Ras p21 was designed which allows reaction initiation and fluorescence readout of the initiated GTPase reaction within the crystalline state. Rearrangements within the crystallized protein due to the progressing reaction and associated heterogeneity in the protein conformations have to be considered in the subsequent refinement processes. Results X-ray diffraction experiments on H-Ras p21 in different states along the reaction pathway provide detailed information about the kinetics and mechanism of the GTPase reaction. In addition, a very high data quality of up to 1.0 Å resolution allowed distinguishing two discrete subconformations of H-Ras p21, expanding the knowledge about the intrinsic flexibility of Ras-like proteins, which is important for their function. In a complex of H-Ras•GppNHp (guanosine-5'-(β,γ-imido-triphosphate, a second Mg2+ ion was found to be coordinated to the γ-phosphate group of GppNHp, which positions the hydrolytically active water molecule very close to the attacked γ-phosphorous atom. Conclusion For the structural analysis of very high-resolution data we have used a new 'two-chain-isotropic-refinement' strategy. This refinement provides an alternative and easy to interpret strategy to reflect the conformational variability within crystal structures of biological macromolecules. The presented fluorescent form of H-Ras p21 will be advantageous for fluorescence studies on H-Ras p21 in which the use of fluorescent nucleotides is not feasible.

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

    Science.gov (United States)

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

    2015-04-17

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

  16. Numerical Modeling on Thermal Loading of Diamond Crystal in X-ray FEL Oscillator

    CERN Document Server

    Song, Meiqi; Guo, Yuhang; Li, Kai; Deng, Haixiao

    2015-01-01

    Due to high reflectivity and high resolution to X-ray pulse, diamond is one of the most popular Bragg crystals serving as the reflecting mirror and mono-chromator in the next generation free electrons lasers (FELs). The energy deposition of X-rays will result in thermal heating, and thus lattice expanding of diamond crystal, which may degrade the performance of X-ray FELs. In this paper, the thermal loading effect of diamond crystal for X-ray FEL oscillator has been systematically studied by the combined simulation of Geant4 and ANSYS, and its dependence on the environment temperature, crystal size, X-ray pulse repetition rate and pulse energy are presented.

  17. Phase Sensitive X-Ray Diffraction Imaging Study of Protein Crystals

    Science.gov (United States)

    Hu, Z. W.

    2003-01-01

    The study of defects and growth of protein crystals is of importance in providing a fundamental understanding of this important category of systems and the rationale for crystallization of better ordered crystals for structural determination and drug design. Yet, as a result of the extremely weak scattering power of x-rays in protein and other biological macromolecular crystals, the extinction lengths for those crystals are extremely large and, roughly speaking, of the order of millimeters on average compared to the scale of micrometers for most small molecular crystals. This has significant implication for x-ray diffraction and imaging study of protein crystals, and presents an interesting challenge to currently available x-ray analytical techniques. We proposed that coherence-based phase sensitive x-ray diffraction imaging could provide a way to augment defect contrast in x-ray diffraction images of weakly diffracting biological macromolecular crystals. I shall examine the principles and ideas behind this approach and compare it to other available x-ray topography and diffraction methods. I shall then present some recent experimental results in two model protein systems-cubic apofemtin and tetragonal lysozyme crystals to demonstrate the capability of the coherence-based imaging method in mapping point defects, dislocations, and the degree of perfection of biological macromolecular crystals with extreme sensitivity. While further work is under way, it is intended to show that the observed new features have yielded important information on protein crystal perfection and nucleation and growth mechanism otherwise unobtainable.

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

    Science.gov (United States)

    Meyer, Simon; Böhme, Sabine; Krüger, André; Steinhoff, Heinz-Jürgen; Klare, Johann P; Wittinghofer, Alfred

    2009-10-01

    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.

  19. 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.

  20. 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.

  1. Antiferroelectric surface layers in a liquid crystal as observed by synchrotron x-ray scattering

    DEFF Research Database (Denmark)

    Gramsbergen, E. F.; de Jeu, W. H.; Als-Nielsen, Jens Aage

    1986-01-01

    The X-ray reflectivity form the surface of a liquid crystal with terminally polar (cyano substituted) molecules has been studied using a high-resolution triple-axis X-ray spectrometer in combination with a synchrotron source. It is demonstrated that at the surface of the smectic Al phase a few...

  2. Crystal optics for hard-X-ray spectroscopy of highly charged ions

    OpenAIRE

    Beyer, H. F.; Attia, D.; Banas, D; Bigot, E. -O. Le; Bosch, F.; Dousse, Jean-Claude; Förster, E.; Gumberidze, A.; Hagmann, S.; Heß, S.; J. Hoszowska; Indelicato, P.; Jagodzinski, P.; Kozhuharov, Chr.; Krings, Th.

    2009-01-01

    A twin crystal-spectrometer assembly, operated in the focusing compensated asymmetric Laue geometry has been developed for accurate spectroscopy of fast highly charged heavy ions in the hard-X-ray region. Coupled to the focusing crystal optics is a specially developed two-dimensional position-sensitive X-ray detector which is necessary for retaining spectral resolution also for fast moving sources. We summarize the crystal optics and demonstrate the usefulness of the instrument for spectrosco...

  3. The rotating-crystal method in femtosecond X-ray diffraction.

    Science.gov (United States)

    Freyer, B; Stingl, J; Zamponi, F; Woerner, M; Elsaesser, T

    2011-08-01

    We report the first implementation of the rotating-crystal method in femtosecond X-ray diffraction. Applying a pump-probe scheme with 100 fs hard X-ray probe pulses from a laser-driven plasma source, the novel technique is demonstrated by mapping structural dynamics of a photoexcited bismuth crystal via changes of the diffracted intensity on a multitude of Bragg reflections. The method is compared to femtosecond powder diffraction and to Bragg diffraction from a crystal with stationary orientation.

  4. X-ray diffraction studies of NbTe2 single crystal

    Indian Academy of Sciences (India)

    Neha Bhatt; Rajiv Vaidya; S G Patel; A R Jani

    2004-02-01

    NbTe2 is a member of transition metal dichalcogenide (TMDC) group. Single crystals of niobium ditelluride (NbTe2) have been grown by a chemical vapour transport technique using iodine as transporting agent. 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 for a number of reflections has been calculated using Scherrer’s formula.

  5. Coherent-pulse 2D crystallography using a free-electron laser x-ray source.

    Science.gov (United States)

    Mancuso, A P; Schropp, A; Reime, B; Stadler, L-M; Singer, A; Gulden, J; Streit-Nierobisch, S; Gutt, C; Grübel, G; Feldhaus, J; Staier, F; Barth, R; Rosenhahn, A; Grunze, M; Nisius, T; Wilhein, T; Stickler, D; Stillrich, H; Frömter, R; Oepen, H-P; Martins, M; Pfau, B; Günther, C M; Könnecke, R; Eisebitt, S; Faatz, B; Guerassimova, N; Honkavaara, K; Kocharyan, V; Treusch, R; Saldin, E; Schreiber, S; Schneidmiller, E A; Yurkov, M V; Weckert, E; Vartanyants, I A

    2009-01-23

    Coherent diffractive imaging for the reconstruction of a two-dimensional (2D) finite crystal structure with a single pulse train of free-electron laser radiation at 7.97 nm wavelength is demonstrated. This measurement shows an advance on traditional coherent imaging techniques by applying it to a periodic structure. It is also significant that this approach paves the way for the imaging of the class of specimens which readily form 2D, but not three-dimensional crystals. We show that the structure is reconstructed to the detected resolution, given an adequate signal-to-noise ratio.

  6. Femtosecond X-ray diffraction from two-dimensional protein crystals.

    Science.gov (United States)

    Frank, Matthias; Carlson, David B; Hunter, Mark S; Williams, Garth J; Messerschmidt, Marc; Zatsepin, Nadia A; Barty, Anton; Benner, W Henry; Chu, Kaiqin; Graf, Alexander T; Hau-Riege, Stefan P; Kirian, Richard A; Padeste, Celestino; Pardini, Tommaso; Pedrini, Bill; Segelke, Brent; Seibert, M Marvin; Spence, John C H; Tsai, Ching-Ju; Lane, Stephen M; Li, Xiao-Dan; Schertler, Gebhard; Boutet, Sebastien; Coleman, Matthew; Evans, James E

    2014-03-01

    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.

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

    Science.gov (United States)

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

    2015-10-01

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

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

    Science.gov (United States)

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

    2014-05-16

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

  9. Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3, 4 domains of integrin α6β4

    Energy Technology Data Exchange (ETDEWEB)

    Alonso-García, Noelia [Consejo Superior de Investigaciones Científicas – University of Salamanca, Campus Unamuno, 37007 Salamanca (Spain); García-Rubio, Inés [ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich (Switzerland); Academia General Militar, Carretera de Huesca s/n, 50090 Zaragoza (Spain); Manso, José A. [Consejo Superior de Investigaciones Científicas – University of Salamanca, Campus Unamuno, 37007 Salamanca (Spain); Buey, Rubén M. [Consejo Superior de Investigaciones Científicas – University of Salamanca, Campus Unamuno, 37007 Salamanca (Spain); University of Salamanca, Campus Unamuno, 37007 Salamanca (Spain); Urien, Hector [Consejo Superior de Investigaciones Científicas – University of Salamanca, Campus Unamuno, 37007 Salamanca (Spain); Sonnenberg, Arnoud [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Jeschke, Gunnar [ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich (Switzerland); Pereda, José M. de, E-mail: pereda@usal.es [Consejo Superior de Investigaciones Científicas – University of Salamanca, Campus Unamuno, 37007 Salamanca (Spain)

    2015-04-01

    The structure of the FnIII-3, 4 region of integrin β4 was solved using a hybrid approach that combines crystallographic structures, SAXS, DEER and molecular modelling. The structure helps in understanding how integrin β4 might bind to other hemidesmosomal proteins and mediate signalling. Integrin α6β4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin α6β4 has also been implicated in cell proliferation and migration and in carcinoma progression. The third and fourth fibronectin type III domains (FnIII-3, 4) of integrin β4 mediate binding to the hemidesmosomal proteins BPAG1e and BPAG2, and participate in signalling. Here, it is demonstrated that X-ray crystallography, small-angle X-ray scattering and double electron–electron resonance (DEER) complement each other to solve the structure of the FnIII-3, 4 region. The crystal structures of the individual FnIII-3 and FnIII-4 domains were solved and the relative arrangement of the FnIII domains was elucidated by combining DEER with site-directed spin labelling. Multiple structures of the interdomain linker were modelled by Monte Carlo methods complying with DEER constraints, and the final structures were selected against experimental scattering data. FnIII-3, 4 has a compact and cambered flat structure with an evolutionary conserved surface that is likely to correspond to a protein-interaction site. Finally, this hybrid method is of general application for the study of other macromolecules and complexes.

  10. Epitope-dependent mechanisms of CD27 neutralization revealed by X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Obmolova, Galina; Teplyakov, Alexey; Malia, Thomas J.; Wunderler, Nicole; Kwok, Deborah; Barone, Linda; Sweet, Raymond; Ort, Tatiana; Scully, Michael; Gilliland, Gary L. (Janssen)

    2017-03-01

    CD27 is a T and B cell co-stimulatory protein of the TNF receptor superfamily dependent on the availability of the TNF-like ligand CD70. Two anti-CD27 neutralizing monoclonal antibodies were obtained from mouse hybridoma and subsequently humanized and optimized for binding the target. The two antibodies are similar in terms of their CD27-binding affinity and ability to block NF-κB signaling, however their clearance rates in monkeys are very different. The pharmacokinetics profiles could be epitope dependent. To identify the epitopes, we determined the crystal structure of the ternary complex between CD27 and the Fab fragments of these non-competing antibodies. The structure reveals the binding modes of the antibodies suggesting that their mechanisms of action are distinctly different and provides a possible explanation of the in vivo data.

  11. Nuclear fusion induced by X-rays in a crystal

    CERN Document Server

    Belyaev, V B; Otto, J; Rakityansky, S A

    2016-01-01

    The nuclei that constitute a crystalline lattice, oscillate relative to each other with a very low energy that is not sufficient to penetrate through the Coulomb barriers separating them. An additional energy, which is needed to tunnel through the barrier and fuse, can be supplied by external electromagnetic waves (X-rays or the synchrotron radiation). Exposing to the X-rays the solid compound LiD (lithium-deuteride) for the duration of 111 hours, we have detected 88 events of the nuclear fusion d+Li6 ---> Be8*. Our theoretical estimate agrees with what we observed. One of possible applications of the phenomenon we found, could be the measurements of the rates of various nuclear reactions (not necessarily fusion) at extremely low energies inaccessible in accelerator experiments.

  12. Preliminary results of absolute wavelength calibration of imaging X-ray crystal spectrometer on EAST

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Xiayun [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); University of Science and Technology of China, Hefei 230026 (China); Wang, Fudi [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Chen, Jun [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); University of Science and Technology of China, Hefei 230026 (China); Lyu, Bo, E-mail: blu@ipp.ac.cn [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Li, Yingying; Fu, Jia; Xu, Liqing [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Shi, Yuejiang [University of Science and Technology of China, Hefei 230026 (China); Department of Nuclear Engineering, Seoul National University, Seoul 151-742 (Korea, Republic of); Ye, Minyou [University of Science and Technology of China, Hefei 230026 (China); Wan, Baonian [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China)

    2015-10-15

    Highlights: • The absolute wavelength calibration method for X-ray crystal spectrometer using X-ray fluorescence of the appropriate materials was first tested on EAST, and the preliminary experimental results were obtained. • The experimental results were thoroughly discussed and suggestion for further improvements of the experimental arrangement was proposed. • Rotation calibration of X-ray crystal spectrometer on EAST using MHD frequency was presented when the absolute wavelength calibration method is unavailable currently. - Abstract: Imaging X-ray crystal spectrometers (XCS) are currently operating on several major tokamaks to provide profiles of ion temperature and rotation velocity. In order to acquire absolute rotation velocity, several indirect methods were pursued previously, however the direct and effective method is to use known X-ray lines for wavelength calibration. One way to produce standard spectral lines is X-ray fluorescence, which could be excited by X-rays from tokamak plasmas. As part of the upgrade of XCS system on EAST, wavelength calibration was studied using cadmium's L-shell lines, namely Lα{sub 1} line (3.9564 Å) and Lα{sub 2} line (3.9650 Å) as the reference wavelength. The Geant 4 code was used to optimize foil thickness to achieve a reasonable X-ray fluorescence intensity. The Cd foil was placed between the beryllium window and crystal and could be retracted to provide in situ wavelength calibration. The detailed arrangement and preliminary wavelength calibration results of imaging X-ray crystal spectrometer on EAST are presented, plus the calibration using MHD frequency.

  13. X-Ray Diffraction and Imaging Study of Imperfections of Crystallized Lysozyme with Coherent X-Rays

    Science.gov (United States)

    Hu, Zheng-Wei; Chu, Y. S.; Lai, B.; Cai, Z.; Thomas, B. R.; Chernov, A. A.

    2003-01-01

    Phase-sensitive x-ray diffraction imaging and high angular-resolution diffraction combined with phase contrast radiographic imaging are employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in symmetric Laue case. The fill width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal is approximately 16.7 arcseconds, and defects, which include point defects, line defects, and microscopic domains, have been clearly observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the growth front, and they have been found to originate mostly at a central growth area and occasionally at outer growth regions. Individual point defects trapped at a crystal nucleus are resolved in the images of high sensitivity to defects. Slow dehydration has led to the broadening of the 4 4 0 rocking curve by a factor of approximately 2.4. A significant change of the defect structure and configuration with drying has been revealed, which suggests the dehydration induced migration and evolution of dislocations and lattice rearrangements to reduce overall strain energy. The sufficient details of the observed defects shed light upon perfection, nucleation and growth, and properties of protein crystals.

  14. Type II Turn of Receptor-bound Salmon Calcitonin Revealed by X-ray Crystallography.

    Science.gov (United States)

    Johansson, Eva; Hansen, Jakob Lerche; Hansen, Ann Maria Kruse; Shaw, Allan Christian; Becker, Peter; Schäffer, Lauge; Reedtz-Runge, Steffen

    2016-06-24

    Calcitonin is a peptide hormone consisting of 32 amino acid residues and the calcitonin receptor is a Class B G protein-coupled receptor (GPCR). The crystal structure of the human calcitonin receptor ectodomain (CTR ECD) in complex with a truncated analogue of salmon calcitonin ([BrPhe(22)]sCT(8-32)) has been determined to 2.1-Å resolution. Parallel analysis of a series of peptide ligands showed that the rank order of binding of the CTR ECD is identical to the rank order of binding of the full-length CTR, confirming the structural integrity and relevance of the isolated CTR ECD. The structure of the CTR ECD is similar to other Class B GPCRs and the ligand binding site is similar to the binding site of the homologous receptors for the calcitonin gene-related peptide (CGRP) and adrenomedulin (AM) recently published (Booe, J. M., Walker, C. S., Barwell, J., Kuteyi, G., Simms, J., Jamaluddin, M. A., Warner, M. L., Bill, R. M., Harris, P. W., Brimble, M. A., Poyner, D. R., Hay, D. L., and Pioszak, A. A. (2015) Mol. Cell 58, 1040-1052). Interestingly the receptor-bound structure of the ligand [BrPhe(22)]sCT(8-32) differs from the receptor-bound structure of the homologous ligands CGRP and AM. They all adopt an extended conformation followed by a C-terminal β turn, however, [BrPhe(22)]sCT(8-32) adopts a type II turn (Gly(28)-Thr(31)), whereas CGRP and AM adopt type I turns. Our results suggest that a type II turn is the preferred conformation of calcitonin, whereas a type I turn is the preferred conformation of peptides that require RAMPs; CGRP, AM, and amylin. In addition the structure provides a detailed molecular explanation and hypothesis regarding ligand binding properties of CTR and the amylin receptors.

  15. Phase Sensitive X-Ray Diffraction Imaging of Defects in Biological Macromolecular Crystals

    Science.gov (United States)

    Hu, Z. W.; Lai, B.; Chu, Y. S.; Cai, Z.; Mancini, D. C.; Thomas, B. R.; Chernov, A. A.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    Characterization of defects and/or disorder in biological macromolecular crystals presents much greater challenges than in conventional small-molecule crystals. The lack of sufficient contrast of defects is often a limiting factor in x-ray diffraction topography of protein crystals. This has seriously hampered efforts to understand mechanisms and origins of formation of imperfections, and the role of defects as essential entities in the bulk of macromolecular crystals. In this report, we employ a phase sensitive x-ray diffraction imaging approach for augmenting the contrast of defects in protein crystals.

  16. 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

  17. The differences in binding 12-carbon aliphatic ligands by bovine β-lactoglobulin isoform A and B studied by isothermal titration calorimetry and X-ray crystallography.

    Science.gov (United States)

    Loch, Joanna I; Bonarek, Piotr; Polit, Agnieszka; Swiątek, Śylwia; Dziedzicka-Wasylewska, Marta; Lewiński, Krzysztof

    2013-08-01

    Isoforms A (LGB-A) and B (LGB-B) of bovine lactoglobulin, the milk protein, differ in positions 64 (D↔G) and 118 (V↔A). Interactions of LGB-A and LGB-B with sodium dodecyl sulfate (SDS), dodecyltrimethylammonium chloride (DTAC) and lauric acid (LA), 12-carbon ligands possessing differently charged polar groups, were investigated using isothermal titration calorimetry and X-ray crystallography, to study the proton linkage phenomenon and to distinguish between effects related to different isoforms and different ligand properties. The determined values of ΔS and ΔH revealed that for all ligands, binding is entropically driven. The contribution from enthalpy change is lower and shows strong dependence on type of buffer that indicates proton release from the protein varying with protein isoform and ligand type and involvement of LA and Asp64 (in isoform A) in this process. The ligand affinities for both isoforms were arranged in the same order, DTAC enthalpy, resulting in almost identical ΔG for complexes of both isoforms. The determined crystal structures showed that substitution in positions 64 and 118 did not influence the overall structure of LGB complexes. The chemical character of the ligand polar group did not affect the position of its aliphatic chain in protein β-barrel, indicating a major role of hydrophobic interactions in ligand binding that prevailed even with the repulsion between positively charged DTAC and lysine residues located at binding site entrance.

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

    Science.gov (United States)

    Mizutani, Kimihiko

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-03-17

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

  20. Single-crystal diamond refractive lens for focusing X-rays in two dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Antipov, S.; Baryshev, Sergey; Butler, J. E.; Antipova, O.; Liu, Zunping; Stoupin, S.

    2016-01-01

    The fabrication and performance evaluation of single-crystal diamond refractive X-ray lenses of which the surfaces are paraboloids of revolution for focusing X-rays in two dimensions simultaneously are reported. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses were stacked together to form a standard compound refractive lens (CRL). Owing to the superior physical properties of the material, diamond CRLs could become indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources for secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses.

  1. Single-crystal diamond refractive lens for focusing X-rays in two dimensions.

    Science.gov (United States)

    Antipov, S; Baryshev, S V; Butler, J E; Antipova, O; Liu, Z; Stoupin, S

    2016-01-01

    The fabrication and performance evaluation of single-crystal diamond refractive X-ray lenses of which the surfaces are paraboloids of revolution for focusing X-rays in two dimensions simultaneously are reported. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses were stacked together to form a standard compound refractive lens (CRL). Owing to the superior physical properties of the material, diamond CRLs could become indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources for secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses.

  2. Single Crystal Diamond Refractive Lens for Focusing X-rays in Two Dimensions

    CERN Document Server

    Antipov, S; Butler, J E; Antipova, O; Liu, Z; Stoupin, S

    2015-01-01

    We report the fabrication and performance evaluation of single crystal diamond refractive X-ray lenses with a paraboloid of rotation form factor for focusing X-rays in two dimensions simultaneously. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses can be stacked together to form a traditional compound refractive lens (CRL). Due to the superior physical properties of the material, diamond CRLs are enabling and indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources on secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses.

  3. 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.

  4. Testing LaMgAl11O19 crystal for X-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chen, H; Beiersdorfer, P; Baronova, E; Kalashnikova, I; Stepanenko, M

    2004-03-31

    We investigated the properties of the rare earth crystal LaMgAl{sub 11}O{sub 19} and its application to soft X-ray spectroscopy. Its relative reflectivity and half width rocking curve were measured to up to the reflection order of 28. In addition, a comparative measurement of the iron L-shell soft X-ray line emission was made on the EBIT-I Livermore electron beam ion trap by fielding the LaMgAl{sub 11}O{sub 19} crystal side by side with a rubidium hydrogen phthalate crystal in a flat crystal spectrometer. From these measurements, reflectivity and spectral resolving power were determined.

  5. Evaluation of sagittal focusing for a spherical quartz crystal x-ray analyzer with synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Nino R.; Macrander, Albert T.; Hill, Kenneth W.; Baronova, Elena O.; George, Kevin M.; Kotick, Jordan T.

    2015-10-01

    To attain optimum performance in applications such as x-ray imaging and spectroscopy, a spherically bent crystal must diffract well across its entire surface. X-ray topography of sample crystals shows isolated regions where diffraction is problematic, even for a crystal where inspection with visible light does not suggest problems. Covering problem spots may improve the crystal’s focus and decrease the background. We explore the special properties of synchrotron radiation to examine typical spherical crystals from alpha-quartz, in a perpendicular geometry that is especially convenient to examine sagittal focusing.

  6. Numerical modeling of thermal loading of diamond crystal in X-ray FEL oscillators

    Science.gov (United States)

    Song, Mei-Qi; Zhang, Qing-Min; Guo, Yu-Hang; Li, Kai; Deng, Hai-Xiao

    2016-04-01

    Due to high reflectivity and high resolution of X-ray pulses, diamond is one of the most popular Bragg crystals serving as the reflecting mirror and mono-chromator in the next generation of free electron lasers (FELs). The energy deposition of X-rays will result in thermal heating, and thus lattice expansion of the diamond crystal, which may degrade the performance of X-ray FELs. In this paper, the thermal loading effect of diamond crystal for X-ray FEL oscillators has been systematically studied by combined simulation with Geant4 and ANSYS, and its dependence on the environmental temperature, crystal size, X-ray pulse repetition rate and pulse energy are presented. Our results show that taking the thermal loading effects into account, X-ray FEL oscillators are still robust and promising with an optimized design. Supported by National Natural Science Foundation of China (11175240, 11205234, 11322550) and Program for Changjiang Scholars and Innovative Research Team in University (IRT1280)

  7. 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.

  8. Comparison of the structure of human recombinant short form stromelysin by multidimensional heteronuclear NMR and X-ray crystallography.

    Science.gov (United States)

    Gooley, P R; O'Connell, J F; Marcy, A I; Cuca, G C; Axel, M G; Caldwell, C G; Hagmann, W K; Becker, J W

    1996-01-01

    Stromelysin-1 is a matrix metalloprotease that has been implicated in a number of degenerative diseases. Here we present the refined NMR solution structure of the catalytic domain of stromelysin-1 complexed with a small inhibitor and compare it to the X-ray crystal structure of the same complex. The structures are similar in global fold and show an unusual bottomless S1' subsite. There are differences, however, in the least well defined regions, Phe83-Ile89, His224-Phe232 and Pro249- Pro250, reflecting the lack of NOE data and large B-factors. The region His224-Phe232 contains residues of the S1' subsite and, consequently, small differences are observed in this subsite. Hydrogen-bond data show that, in contrast to the crystal structure, the solution structure lacks a hydrogen bond between the amide of Tyr223 and the carbonyl of the P3' residue. Analysis of bound water shows two tightly bound water molecules both in the solution and the crystal structure; neither of these waters are in the inhibitor binding site.

  9. Perfectly Cold Crystals: What Happens When They Are X-rayed?

    Science.gov (United States)

    vanderWoerd, Mark; Ferree, Darren S.; Snell, Edward H.

    2003-01-01

    For many macromolecular crystals the cryo-preservation of these crystals during X-ray data collection is of crucial importance, particularly at synchrotron facilities where the crystals rapidly receive a high dose of radiation. A practical variable to ensure adequate preservation is the variation of the cryo-protectant present when the crystal is preserved. Our initial approach to study X-ray diffraction data quality as a function of cryo-protectant present when preserving a xylose isomerase crystal shows that the data quality can be tremendously improved by recipe adjustment. Guided by crystal mosaicity estimates, we optimized crystal growth conditions to obtain cryo-preserved xylose isomerase crystals that withstand a very high dose of X-rays, with only the smallest amount of radiation damage at ultra-high resolution (1.2Angstroms). The rate at which damage occurs allowed us to collect a series of complete data sets, which show how the data degradation proceeds over time. We are here presenting data for the xylose isomerase crystallization recipe improvement and our interpretation of the crystal degradation process during X-ray data collection.

  10. Coherent X-ray radiation excited by a diverging relativistic electron beam in a single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Blazhevich, S. V., E-mail: noskovbupk@mail.ru; Noskov, A. V. [Belgorod State National Research University (Russian Federation)

    2015-05-15

    We develop a dynamic theory of coherent X-rays generated in a single-crystal wafer by a diverging relativistic electron beam. The dependence of the spectral-angular density of coherent X-ray radiation on the angle of divergence is analyzed for the case when the angular spread can be described by the 2D Gaussian distribution. The theory constructed here makes it possible to analyze coherent radiation for an arbitrary angular distribution of electrons in the beam as well.

  11. Matching X-ray beam and detector properties to protein crystals of different perfection

    Energy Technology Data Exchange (ETDEWEB)

    Nave, Colin, E-mail: colin.nave@diamond.ac.uk [Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

    2014-03-18

    Expressions are given to match X-ray data collection facilities to the intrinsic diffraction properties of crystals with different degrees of perfection. An analysis is given of the effect of different beam and detector parameters on the sharpness of recorded diffraction features for macromolecular crystals of different quality. The crystal quality parameters include crystal strain, crystal or mosaic block size and mosaic block misorientation. Calculations are given for instrument parameters such as angular resolution of the detector, beam divergence and wavelength bandpass to be matched to the intrinsic diffraction properties from these crystals with the aim of obtaining the best possible data out of each crystal. Examples are given using typical crystal imperfections obtained from the literature for both room-temperature and cryo-cooled crystals. Possible implications for the choice of X-ray source, beamline design, detector specifications, instrument set-up and data processing are discussed, together with the limitations of the approach.

  12. The role for an invariant aspartic acid in hypoxanthine phosphoribosyltransferases is examined using saturation mutagenesis, functional analysis, and X-ray crystallography.

    Science.gov (United States)

    Canyuk, B; Focia, P J; Eakin, A E

    2001-03-01

    The role of an invariant aspartic acid (Asp137) in hypoxanthine phosphoribosyltransferases (HPRTs) was examined by site-directed and saturation mutagenesis, functional analysis, and X-ray crystallography using the HPRT from Trypanosoma cruzi. Alanine substitution (D137A) resulted in a 30-fold decrease of k(cat), suggesting that Asp137 participates in catalysis. Saturation mutagenesis was used to generate a library of mutant HPRTs with random substitutions at position 137, and active enzymes were identified by complementation of a bacterial purine auxotroph. Functional analyses of the mutants, including determination of steady-state kinetic parameters and pH-rate dependence, indicate that glutamic acid or glutamine can replace the wild-type aspartate. However, the catalytic efficiency and pH-rate profile for the structural isosteric mutant, D137N, were similar to the D137A mutant. Crystal structures of four of the mutant enzymes were determined in ternary complex with substrate ligands. Structures of the D137E and D137Q mutants reveal potential hydrogen bonds, utilizing several bound water molecules in addition to protein atoms, that position these side chains within hydrogen bond distance of the bound purine analogue, similar in position to the aspartate in the wild-type structure. The crystal structure of the D137N mutant demonstrates that the Asn137 side chain does not form interactions with the purine substrate but instead forms novel interactions that cause the side chain to adopt a nonfunctional rotamer. The results from these structural and functional analyses demonstrate that HPRTs do not require a general base at position 137 for catalysis. Instead, hydrogen bonding sufficiently stabilizes the developing partial positive charge at the N7-atom of the purine substrate in the transition-state to promote catalysis.

  13. A multi-cone x-ray imaging Bragg crystal spectrometer

    Science.gov (United States)

    Bitter, M.; Hill, K. W.; Gao, Lan; Efthimion, P. C.; Delgado-Apariccio, L.; Lazerson, S.; Pablant, N.

    2016-11-01

    This article describes a new x-ray imaging Bragg crystal spectrometer, which—in combination with a streak camera or a gated strip detector—can be used for time-resolved measurements of x-ray line spectra at the National Ignition Facility and other high power laser facilities. The main advantage of this instrument is that it produces perfect images of a point source for each wavelength in a selectable spectral range and that the detector plane can be perpendicular to the crystal surface or inclined by an arbitrary angle with respect to the crystal surface. These unique imaging properties are obtained by bending the x-ray diffracting crystal into a certain shape, which is generated by arranging multiple cones with different aperture angles on a common nodal line.

  14. Performance of the x-ray free-electron laser oscillator with crystal cavity

    Directory of Open Access Journals (Sweden)

    R. R. Lindberg

    2011-01-01

    Full Text Available Simulations of the x-ray free-electron laser (FEL oscillator are presented that include the frequency-dependent Bragg crystal reflectivity and the transverse diffraction and focusing using the two-dimensional FEL code GINGER. A review of the physics of Bragg crystal reflectors and the x-ray FEL oscillator is made, followed by a discussion of its numerical implementation in GINGER. The simulation results for a two-crystal cavity and realistic FEL parameters indicate ∼10^{9} photons in a nearly Fourier-limited, ps pulse. Compressing the electron beam to 100 A and 100 fs results in comparable x-ray characteristics for relaxed beam emittance, energy spread, and/or undulator parameters, albeit in a larger radiation bandwidth. Finally, preliminary simulation results indicate that the four-crystal FEL cavity can be tuned in energy over a range of a few percent.

  15. Crystallization and preliminary X-ray diffraction study of porcine carboxypeptidase B

    Energy Technology Data Exchange (ETDEWEB)

    Akparov, V. Kh., E-mail: valery@akparov.ru [Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms (Russian Federation); Timofeev, V. I., E-mail: inna@ns.crys.ras.ru; Kuranova, I. P., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2015-05-15

    Crystals of porcine pancreatic carboxypeptidase B have been grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction study showed that the crystals belong to sp. gr. P4{sub 1}2{sub 1}2 and have the following unit-cell parameters: a = b = 79.58 Å, c = 100.51 Å; α = β = γ = 90.00°. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one of the grown crystals at the SPring 8 synchrotron facility to 0.98 Å resolution.

  16. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Camattari, Riccardo; Guidi, Vincenzo; Bellucci, Valerio; Neri, Ilaria; Frontera, Filippo [Department of Physics and Earth Science, University of Ferrara, Via Saragat 1/c, 44122 Ferrara (Italy); CNR-IDASC SENSOR Lab. (Italy); Jentschel, Michael [Institut Laue Langevin, F-38042 Grenoble Cedex (France)

    2013-05-15

    A quasi mosaic bent crystal for high-resolution diffraction of X and {gamma} 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.

  18. Diffraction crystal for sagittally focusing x-rays

    Science.gov (United States)

    Ice, Gene E.; Sparks, Jr., Cullie J.

    1984-01-01

    The invention is a new type of diffraction crystal designed for sagittally focusing photons of various energies. The invention is based on the discovery that such focusing is not obtainable with conventional crystals because of distortion resulting from anticlastic curvature. The new crystal comprises a monocrystalline base having a front face contoured for sagittally focusing photons and a back face provided with rigid, upstanding, stiffening ribs restricting anticlastic curvature. When mounted in a suitable bending device, the reflecting face of the crystal can be adjusted to focus photons having any one of a range of energies.

  19. Diffraction crystals for sagittally focusing x-rays

    Science.gov (United States)

    Ice, G.E.; Sparks, C.J. Jr.

    1982-06-07

    The invention is a new type of diffraction crystal designed for sagittally focusing photons of various energies. The invention is based on the discovery that such focusing is not obtainable with conventional crystals because of distortion resulting from anticlastic curvature. The new crystal comprises a monocrystalline base having a front face contoured for sagittally focusing photons and a back face provided with rigid, upstanding, stiffening ribs restricting anticlastic curvature. When mounted in a suitable bending device, the reflecting face of the crystal can be adjusted to focus photons having any one of a range of energies.

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

    Science.gov (United States)

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

    2016-06-01

    Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α2β2 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 mm3) 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.

  1. 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.

  2. High Resolution Triple Axis X-Ray Diffraction Analysis of II-VI Semiconductor Crystals

    Science.gov (United States)

    Volz, H. M.; Matyi, R. J.

    1999-01-01

    The objective of this research program is to develop methods of structural analysis based on high resolution triple axis X-ray diffractometry (HRTXD) and to carry out detailed studies of defect distributions in crystals grown in both microgravity and ground-based environments. HRTXD represents a modification of the widely used double axis X-ray rocking curve method for the characterization of grown-in defects in nearly perfect crystals. In a double axis rocking curve experiment, the sample is illuminated by a monochromatic X-ray beam and the diffracted intensity is recorded by a fixed, wide-open detector. The intensity diffracted by the sample is then monitored as the sample is rotated through the Bragg reflection condition. The breadth of the peak, which is often reported as the full angular width at half the maximum intensity (FWHM), is used as an indicator of the amount of defects in the sample. This work has shown that high resolution triple axis X-ray diffraction is an effective tool for characterizing the defect structure in semiconductor crystals, particularly at high defect densities. Additionally, the technique is complimentary to X-ray topography for defect characterization in crystals.

  3. Double-slit dynamical diffraction of X-rays in ideal crystals (Laue case).

    Science.gov (United States)

    Balyan, Minas K

    2010-11-01

    The theoretical investigation of double-slit dynamical X-ray diffraction in ideal crystals shows that, on the exit surface of crystals, interference fringes similar to Young's fringes are formed. An expression for the period of the fringes was obtained. The visibility of the fringes depending on temporal and spatial coherent properties of the incident beam is studied. The polarization state of the incident beam also affects the visibility of the fringes, which in turn depends on the size of the slits. The deviation from Bragg's exact angle causes a shift of the fringes and can also affect the amplitude of the intensity. One of the parameters on which the visibility of the fringes depends is the source-crystal distance. The proposed scheme can be used as a Rayleigh X-ray interferometer. Use of the scheme as a Michelson X-ray stellar interferometer is also possible.

  4. Crystal optics for precision x-ray spectroscopy on highly charged ions—conception and proof

    Science.gov (United States)

    Beyer, H. F.; Gassner, T.; Trassinelli, M.; Heß, R.; Spillmann, U.; Banaś, D.; Blumenhagen, K.-H.; Bosch, F.; Brandau, C.; Chen, W.; Dimopoulou, Chr; Förster, E.; Grisenti, R. E.; Gumberidze, A.; Hagmann, S.; Hillenbrand, P.-M.; Indelicato, P.; Jagodzinski, P.; Kämpfer, T.; Kozhuharov, Chr; Lestinsky, M.; Liesen, D.; Litvinov, Yu A.; Loetzsch, R.; Manil, B.; Märtin, R.; Nolden, F.; Petridis, N.; Sanjari, M. S.; Schulze, K. S.; Schwemlein, M.; Simionovici, A.; Steck, M.; Stöhlker, Th; Szabo, C. I.; Trotsenko, S.; Uschmann, I.; Weber, G.; Wehrhan, O.; Winckler, N.; Winters, D. F. A.; Winters, N.; Ziegler, E.

    2015-07-01

    The experimental investigation of quantum-electrodydamic contributions to the binding energies of inner shells of highly charged heavy ions requires an accurate spectroscopy in the region of hard x-rays suitable at a limited source strength. For this purpose the focusing compensated asymmetric Laue crystal optics has been developed and a twin-spectrometer assembly has been built and commissioned at the experimental storage ring of the GSI Helmholtzzentrum Darmstadt. We characterize the crystal optics and demonstrate the usefulness of the instrumentation for accurate spectroscopy of both stationary and fast moving x-ray sources. The experimental procedures discussed here may also be applied for other spectroscopic studies where a transition from conventional germanium x-ray detectors to crystal spectrometers seems too demanding because of low source intensity.

  5. Insight Into the Radical Mechanism of Phycocyanobilin-Ferredoxin Oxidoreductase (Pcya) Revealed By X-Ray Crystallography And Biochemical Measurements

    Energy Technology Data Exchange (ETDEWEB)

    Tu, S.-L.; Rockwell, N.; Lagarias, J.C.; Fisher, A.J.; /Inst. Plant Microb. Biol., Taipei /UC, Davis

    2007-07-13

    The X-ray crystal structure of the substrate-free form of phycocyanobilin (PCB)-ferredoxin oxidoreductase (PcyA; EC 1.3.7.5) from the cyanobacterium Nostoc sp. PCC7120 has been solved at 2.5 angstrom resolution. A comparative analysis of this structure with those recently reported for substrate-bound and substrate-free forms of PcyA from the cyanobacterium Synechocystis sp. PCC6803 (Hagiwara et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 27-32; Hagiwara et al. (2006) FEBS Lett. 580, 3823-3828) provides a compelling picture of substrate-induced changes in the PcyA enzyme and the chemical basis of PcyA's catalytic activity. On the basis of these structures and the biochemical analysis of site-directed mutants of Nostoc PcyA, including mutants reported in recent studies (Tu et al. (2006) J. Biol. Chem. 281, 3127-3136) as well as mutants described in this study, a revised mechanism for the PcyA-mediated four-electron reduction of biliverdin IX{alpha} to 3E/3Z-phycocyanobilin via enzyme-bound bilin radical intermediates is proposed. The mechanistic insight of these studies, along with homology modeling, have provided new insight into the catalytic mechanisms of other members of the ferredoxin-dependent bilin reductase family that are widespread in oxygenic photosynthetic organisms.

  6. Content analyses in GaMnAs by double-crystal X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A model for analyzing point defects in compound crystals was improved. Based on this modified model,a method for measuring Mn content in GaMnAs was established. A technique for eliminating the zero-drift-error was also established in the experiments of X-ray diffraction. With these methods, the Mn content in GaMnAs single crystals fabricated by the ion-beam epitaxy system was analyzed.Kevwords: GaMnAs, diluted magnetic semiconductor, X-ray dff fraction, lattice parameter, content of Mn.

  7. Sensitive X-ray detectors made of methylammonium lead tribromide perovskite single crystals

    Science.gov (United States)

    Wei, Haotong; Fang, Yanjun; Mulligan, Padhraic; Chuirazzi, William; Fang, Hong-Hua; Wang, Congcong; Ecker, Benjamin R.; Gao, Yongli; Loi, Maria Antonietta; Cao, Lei; Huang, Jinsong

    2016-05-01

    The large mobilities and carrier lifetimes of hybrid perovskite single crystals and the high atomic numbers of Pb, I and Br make them ideal for X-ray and gamma-ray detection. Here, we report a sensitive X-ray detector made of methylammonium lead bromide perovskite single crystals. A record-high mobility-lifetime product of 1.2 × 10-2 cm2 V-1 and an extremely small surface charge recombination velocity of 64 cm s-1 are realized by reducing the bulk defects and passivating surface traps. Single-crystal devices with a thickness of 2-3 mm show 16.4% detection efficiency at near zero bias under irradiation with continuum X-ray energy up to 50 keV. The lowest detectable X-ray dose rate is 0.5 μGyair s-1 with a sensitivity of 80 μC Gy-1air cm-2, which is four times higher than the sensitivity achieved with α-Se X-ray detectors. This allows the radiation dose applied to a human body to be reduced for many medical and security check applications.

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

    Science.gov (United States)

    Edlund, Petra; Takala, Heikki; Claesson, Elin; Henry, Léocadie; Dods, Robert; Lehtivuori, Heli; Panman, Matthijs; Pande, Kanupriya; White, Thomas; Nakane, Takanori; Berntsson, Oskar; Gustavsson, Emil; Båth, Petra; Modi, Vaibhav; Roy-Chowdhury, Shatabdi; Zook, James; Berntsen, Peter; Pandey, Suraj; Poudyal, Ishwor; Tenboer, Jason; Kupitz, Christopher; Barty, Anton; Fromme, Petra; Koralek, Jake D.; Tanaka, Tomoyuki; Spence, John; Liang, Mengning; Hunter, Mark S.; Boutet, Sebastien; Nango, Eriko; Moffat, Keith; Groenhof, Gerrit; Ihalainen, Janne; Stojković, Emina A.; Schmidt, Marius; Westenhoff, Sebastian

    2016-01-01

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX. PMID:27756898

  9. Cloning, expression, purification and crystallization as well as X-ray fluorescence and preliminary X-ray diffraction analyses of human ADP-ribosylhydrolase 1.

    Science.gov (United States)

    Kernstock, Stefan; Koch-Nolte, Friedrich; Mueller-Dieckmann, Jochen; Weiss, Manfred S; Mueller-Dieckmann, Christoph

    2009-05-01

    Human ADP-ribosylhydrolase 1 (hARH1, ADPRH) cleaves the glycosidic bond of ADP-ribose attached to an Arg residue of a protein. hARH1 has been cloned, expressed heterologously in Escherichia coli, purified and crystallized in complex with K(+) and ADP. The orthorhombic crystals contained one monomer per asymmetric unit, exhibited a solvent content of 43% and diffracted X-rays to a resolution of 1.9 A. A prerequisite for obtaining well diffracting crystals was the performance of X-ray fluorescence analysis on poorly diffracting apo hARH1 crystals, which revealed the presence of trace amounts of K(+) in the crystal. Adding K-ADP to the crystallization cocktail then resulted in a crystal of different morphology and with dramatically improved diffraction properties.

  10. 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.

  11. Synchrotron X-Ray Reciprocal Space Mapping, Topography and Diffraction Resolution Studies of Macromolecular Crystal Quality

    Science.gov (United States)

    Boggon, T. J.; Helliwell, J. R.; Judge, Russell A.; Siddons, D. P.; Snell, Edward H.; Stojanoff, V.

    2000-01-01

    A comprehensive study of microgravity and ground grown chicken egg white lysozyme crystals is presented using synchrotron X-ray reciprocal space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed, on average, reduced intrinsic mosaicities but no differences in terms of stress over their earth grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the earth case at the diffraction peak only a small volume of the crystal contributed to the intensity. The techniques prove to be highly complementary with the reciprocal space mapping providing a quantitative measure of the crystal mosaicity and stress (or variation in lattice spacing) and topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out both at the synchrotron and in the laboratory.

  12. THE CRYSTAL STRUCTURE OF ANTIMONY (III) SULFOBROMIDE, SBSBR,

    Science.gov (United States)

    ANTIMONY COMPOUNDS, *SULFUR COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , BROMIDES, SYMMETRY(CRYSTALLOGRAPHY), FOURIER ANALYSIS, MOLECULAR STRUCTURE, CRYSTAL LATTICES, CHEMICAL BONDS, X RAY DIFFRACTION.

  13. Preparation and guest-uptake protocol for a porous complex useful for 'crystal-free' crystallography.

    Science.gov (United States)

    Inokuma, Yasuhide; Yoshioka, Shota; Ariyoshi, Junko; Arai, Tatsuhiko; Fujita, Makoto

    2014-02-01

    We recently reported a new method for single-crystal X-ray diffraction (SCD) analysis that does not require the crystallization of the target compound. In this 'crystal-free' crystallography, a tiny crystal of a porous complex is soaked in the solution of the target guest. The guest molecules are absorbed and oriented in the crystal pores and can be analyzed by X-ray diffraction. We describe here a detailed synthetic protocol for the preparation of uniform single crystals of the porous host complex and for the subsequent guest uptake. The protocol describes our most versatile porous complex, which is prepared from commercially available ZnI2 and 2,4,6-tri(4-pyridyl)-1,3,5-triazine. The host complex has large pores with a cross-section of 8 × 5 Å(2). Single crystals of the complex are grown from layered solutions of the two components. The pores of the as-synthesized complex are filled with nitrobenzene, which is replaced with the inert solvent cyclohexane. This solvent exchange is essential for the rapid and effective inclusion of target compounds. The most crucial and delicate step is the selection of high-quality single crystals from the mixture of crystals of various shapes and sizes. We suggest using the facial indices of the single crystals as a criterion for crystal selection. Single-crystal samples for X-ray analysis can be prepared by immersing the selected crystals in a cyclohexane/dichloromethane solution of target compound. After a very slow evaporation of the solvent, typically over 2 d, the final crystal can be picked and directly subjected to SCD analysis. The protocol can be completed within ∼16 d.

  14. Secondary Extinction in Cylindrical and Spherical Crystals for X-Ray and Neutron Diffraction

    Institute of Scientific and Technical Information of China (English)

    胡华琛; 李兆桓; 杨斌; 沈彩万; 乔英

    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.

  15. Focusing characteristics of diamond crystal x-ray monochromators. An experimental and theoretical comparison

    DEFF Research Database (Denmark)

    Rio, M.S. del; Grübel, G.; Als-Nielsen, J.

    1995-01-01

    Perfect crystals in transmission (Laue) geometry can be used effectively for x-ray monochromators, and moreover, perfect Laue crystals show an interesting focusing effect when the incident beam is white and divergent. This focusing is directly dependent on the incident beam divergence and on the ...... from a diamond crystal in Lane geometry, and we analyze and explain the results by comparison with ray-tracing simulations. (C) 1995 American Institute of Physics....

  16. Controllable reflection of X-rays on crystals of saccharose

    CERN Document Server

    Navasardyan, M A; Hayrapetyan, K T; Gabrielyan, R T

    2003-01-01

    Multiple (ten times and more) increase in intensities of separate reflections and of lauegram reflections from organic single crystals of saccharose (C sub 1 2H sub 2 2O sub 1 1) was observed under influence of certain temperature gradient. On the base of the present experiment and the data of our previous woks we show that the controllable reflection process has a common nature and the intensity of the diffracted beam under external influences does not depend on the total number of electrons per unit volume of the unit cell of the single crystal.

  17. Elliptically-bent crystal spectrograph for X-ray diagnosis of laser-produced plasmas

    Institute of Scientific and Technical Information of China (English)

    Xiancai Xiong(熊先才); Xianxin Zhong(钟先信); Shali Xiao(肖沙里); Guohong Yang(杨国洪); Jie Gao(高洁)

    2004-01-01

    In order to measure spatially and temporarily resolved laser-produced plasma X-ray spectra in 0.2 - 2nm region, a novel two-channel elliptically-bent crystal spectrograph has been developed. Dispersive elements are LiF, PET, Mica, and KAP crystals, which cover Bragg angles in the range of 30 - 67.5degrees. Eccentricity and focal distance of twin ellipses are 0.9586 and 1350 mm, respectively. Spatially resolved spectrum is photographically recorded with an X-ray film or X-CCD camera in one channel, and temporarily resolved one is photographically recorded with an X-ray streak camera in another channel,thus spatially and temporarily resolved spectra can be simultaneously obtained. Spectral images were acquired with X-CCD and PET in SHENGUANG-Ⅱ laser facility, and experimental results show that the spectral resolution of the spectrograph is about 0.002 nm.

  18. Crystallization and X-ray diffraction data of Thermus flavus 5S rRNA helices

    Science.gov (United States)

    Vallazza, Marco; Senge, Andrea; Lippmann, Corinna; Perbandt, Markus; Betzel, Christian; Bald, Rolf; Erdmann, Volker A.

    2001-11-01

    5S rRNA is an essential component of the large ribosomal subunit in prokaryotes and eukaryotes. Its unknown function in the ribosome will eventually be revealed in part by structural studies. To promote crystallization and enhance resolution in X-ray diffraction the molecule was subdivided into five domains A-E. Several RNA oligonucleotides were chemically produced by solid-phase phosphoramidite synthesis in order to construct the domains of the 5S rRNA. An improved RNA-MPD-screen was applied in crystallization which covers a complete 2D matrix for the components used. Crystallization analysis resulted in preferred combinations of pH, polyamine, monovalent and divalent cations for short RNA molecules. Six types of crystals corresponding to the domains B, C and E of Thermus flavus 5S rRNA could be obtained which were suitable for X-ray diffraction. Four RNA helices consist of seven base pairs and two of eight base pairs. As special features, they contain two adenines in a bulge position or G : U wobble base pairs assumed to be involved in RNA-protein recognition. With an increase in crystal size an increase in resolution by X-ray analysis was observed. X-ray diffraction data were collected to 1.5 Å resolution using synchrotron radiation and cryogenic cooling techniques.

  19. 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.

  20. Measuring the X-ray Resolving Power of Bent Potassium Acid Phthalate Diffraction Crystals

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-11-01

    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 (SNL) in Albuquerque, NM. 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 dual goniometer 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.

  1. A von Hamos x-ray spectrometer based on a segmented-type diffraction crystal for single-shot x-ray emission spectroscopy and time-resolved resonant inelastic x-ray scattering studies.

    Science.gov (United States)

    Szlachetko, J; Nachtegaal, M; de Boni, E; Willimann, M; Safonova, O; Sa, J; Smolentsev, G; Szlachetko, M; van Bokhoven, J A; Dousse, J-Cl; Hoszowska, J; Kayser, Y; Jagodzinski, P; Bergamaschi, A; Schmitt, B; David, C; Lücke, A

    2012-10-01

    We report on the design and performance of a wavelength-dispersive type spectrometer based on the von Hamos geometry. The spectrometer is equipped with a segmented-type crystal for x-ray diffraction and provides an energy resolution in the order of 0.25 eV and 1 eV over an energy range of 8000 eV-9600 eV. The use of a segmented crystal results in a simple and straightforward crystal preparation that allows to preserve the spectrometer resolution and spectrometer efficiency. Application of the spectrometer for time-resolved resonant inelastic x-ray scattering and single-shot x-ray emission spectroscopy is demonstrated.

  2. Diffraction imaging for in-situ characterization of double-crystal x-ray monochromators

    CERN Document Server

    Stoupin, Stanislav; Heald, Steve M; Brewe, Dale; Meron, Mati

    2015-01-01

    Imaging of the Bragg reflected x-ray beam is proposed and validated as an in-situ method for characterization of performance of double-crystal monochromators under the heat load of intense synchrotron radiation. A sequence of images is collected at different angular positions on the reflectivity curve of the second crystal and analyzed. The method provides rapid evaluation of the wavefront of the exit beam, which relates to local misorientation of the crystal planes along the beam footprint on the thermally distorted first crystal. The measured misorientation can be directly compared to results of finite element analysis. The imaging method offers an additional insight on the local intrinsic crystal quality over the footprint of the incident x-ray beam.

  3. Parametric X-ray radiation in crystals theory, experiments and applications

    CERN Document Server

    Baryshevsky, Vladimir G; Ulyanenkov, Alexander P

    2005-01-01

    This systematic and comprehensive monograph is devoted to parametric X-ray radiation (PXR). This radiation is generated by the motion of electrons inside a crystal, whereby the emitted photons are diffracted by the crystal and the radiation intensity critically depends on the parameters of the crystal structure. Nowadays PXR is the subject of numerous theoretical and experimental studies throughout the world. The first part of the book is a theoretical treatment of PXR, which includes a new approach to describe the radiation process in crystals. The second part is a survey of PXR experimental results and the possible applications of PXR as a tool for crystal structure analysis and a source of tunable X-ray radiation.

  4. Cryogenic cooling of x-ray crystals using porous matrix

    Energy Technology Data Exchange (ETDEWEB)

    Kuzay, T.M.

    1991-01-01

    It is well established that Si and SiC have very desirable thermophysical properties at cryogenic temperatures. This feature makes cryo-cooled optics potentially a good candidate for the first optical crystal of the presently built third generation synchrotron machines with very high heat flux levels. Currently, there is a great deal of interest in such cryo-cooled crystals pursued both experimentally and analytically. The analytical studies involve cut micro or capillary channel crystals. As opposed to the machined channels, porous matrices provide significant advantages. They operate very quietly. Such matrices are known to affect superior heat transfer enhancement. Data available in open literature suggest that surface heat flux levels up to {approximately}8 kW/cm{sup 2} are possible. For cryogens for which the boiling heat transfer heat flux is rather a low value in conventional geometries, the enhancement available with such matrices is a very significant characteristic. Cryogens are poor thermal conductors themselves. The fact that at the cryogenic temperatures the Si and/or SiC matrix itself becomes highly conductive, the matrix distributes the surface heat flux into the full volume effectively offsetting the poor conductivity of the coolant. In addition the tortuous path of the coolant through the matrix increases the dwell time for better heat transfer, however, at the expense of increased pressure drop. In this study, thermal conductivity of such composite matrices and the effective heat transfer coefficient obtainable using them are investigated. A first optics crystal model of Si with Si and/or Sic porous matrix as its heat exchanger and subject to prototype synchrotron level heat flux is analyzed and limits of the cooling possible with liquid nitrogen in single phase and subcooled boiling heat transfer modes are delineated.

  5. Characterization of x-ray imaging crystal spectrometer for high-resolution spatially-resolved x-ray Thomson scattering measurements in shock-compressed experiments

    Science.gov (United States)

    Lu, J.; Hill, K. W.; Bitter, M.; Pablant, N. A.; Delgado-Aparicio, L. F.; Efthimion, P. C.; Lee, H. J.; Zastrau, U.

    2017-01-01

    We have proposed, designed and built a dual-channel x-ray imaging crystal spectrometer (XICS) for spectrally- and spatially-resolved x-ray Thomson scattering (XRTS) measurements in the Matter in Extreme Conditions (MEC) end station at the Linac Coherent Light Source (LCLS). This spectrometer employs two spherically-bent germanium (Ge) 220 crystals, which are combined to form a large aperture dispersive element with a spectral bandwidth of 300 eV that enables both the elastic and inelastic x-ray scattering peaks to be simultaneously measured. The apparatus and its characterization are described. A resolving power of 1900 was demonstrated and a spatial resolution of 12 μm was achieved in calibration tests. For XRTS measurements, a narrow-bandwidth (ΔE/Ecarbon plasma produced in shock-compressed samples of different forms of carbon. Preliminary results of the scattering experiments from Pyrolytic Graphite samples that illustrate the utility of the instrument are presented.

  6. A pyrrolo-tetrathiafulvalene cage: Synthesis and X-ray crystal structure

    DEFF Research Database (Denmark)

    Nielsen, Kent A.; Jeppesen, Jan O.; Levillain, Eric

    2002-01-01

    A novel type of tetrathiafulvalene-cage 4 containing three monopyrrolo-tetrathiafulvalene units has been prepared employing a general and efficient synthetic approach. X-ray crystal structure analysis revealed that the cage is able to accommodate solvent molecules within a cavity in the solid state....

  7. Crystallization and preliminary X-ray diffraction of malate dehydrogenase from Plasmodium falciparum

    NARCIS (Netherlands)

    Wrenger, Carsten; Mueller, Ingrid B.; Butzloff, Sabine; Jordanova, Rositsa; Lunev, Sergey; Groves, Matthew R.

    2012-01-01

    The expression, purification, crystallization and preliminary X-ray diffraction characterization of malate dehydrogenase (MDH) from the malarial parasite Plasmodium falciparum (PfMDH) are reported. In order to gain a deeper understanding of the function and role of PfMDH, the protein was purified to

  8. X-RAY AND GAMMA-RAY LUMINESCENCE OF CE-3+ DOPED BAF2 CRYSTALS

    NARCIS (Netherlands)

    DORENBOS, P; VISSER, R; VANEIJK, CWE; HOLLANDER, RW; DENHARTOG, HW

    1991-01-01

    The scintillation properties of BaF2 doped with 0.002 to 10 mol% Ce3+ have been studied by means of X-ray and gamma ray excitation. The luminescence intensity increases with the Ce concentration until a maximum is reached for 0.2 mol% doped crystals. The light yield is then about 60% more intense th

  9. X-RAY AND GAMMA-RAY LUMINESCENCE OF CE-3+ DOPED BAF2 CRYSTALS

    NARCIS (Netherlands)

    DORENBOS, P; VISSER, R; VANEIJK, CWE; HOLLANDER, RW; DENHARTOG, HW

    1991-01-01

    The scintillation properties of BaF2 doped with 0.002 to 10 mol% Ce3+ have been studied by means of X-ray and gamma ray excitation. The luminescence intensity increases with the Ce concentration until a maximum is reached for 0.2 mol% doped crystals. The light yield is then about 60% more intense

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

    NARCIS (Netherlands)

    Abramova, V.V.; Sinitskii, A.S.; Grigoryeva, N.A.; Grigoriev, S.V.; Belov, D.V.; Petukhov, A.V.; Mistonov, A.A.; Vasilieva, A.V.; Tretyakov, Y.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 disti

  11. 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...

  12. 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.

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

    Science.gov (United States)

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

  14. High spatial resolution X-ray and gamma ray imaging system using diffraction crystals

    Science.gov (United States)

    Smither, Robert K.

    2011-05-17

    A method and a device for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation are provided. The device comprises a plurality of arrays, with each array comprising a plurality of elements comprising a first collimator, a diffracting crystal, a second collimator, and a detector.

  15. Integrated x-ray reflectivity measurements of elliptically curved pentaerythritol crystals

    Energy Technology Data Exchange (ETDEWEB)

    Haugh, M. J.; Jacoby, K. D.; Ross, P. W. [National Security Technologies, LLC, Livermore, California 94551 (United States); Regan, S. P.; Magoon, J.; Shoup, M. J. III [Laboratory for Laser Energetics, University of Rochester, Rochester, New York 14623 (United States); Barrios, M. A.; Emig, J. A.; Fournier, K. B. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)

    2012-10-15

    The elliptically curved pentaerythritol (PET) crystals used in the Supersnout 2 x-ray spectrometer on the National Ignition Facility at Lawrence Livermore National Laboratory have been calibrated photometrically in the range of 5.5-16 keV. The elliptical geometry provides broad spectral coverage and minimizes the degradation of spectral resolution due to the finite source size. The reflectivity curve of the crystals was measured using a x-ray line source. The integrated reflectivity (R{sub I}) and width of its curve ({Delta}{Theta}) were the measurements of major interest. The former gives the spectrometer throughput, and the latter gives the spectrometer resolving power. Both parameters are found to vary considerably with the radius of curvature of the crystal and with spectral energy. The results are attributed to an enhanced mosaic effect due to the increase in curvature. There are also contributions from the crystal cleaving and gluing processes.

  16. Linear parabolic single-crystal diamond refractive lenses for synchrotron X-ray sources.

    Science.gov (United States)

    Terentyev, Sergey; Polikarpov, Maxim; Snigireva, Irina; Di Michiel, Marco; Zholudev, Sergey; Yunkin, Vyacheslav; Kuznetsov, Sergey; Blank, Vladimir; Snigirev, Anatoly

    2017-01-01

    Linear parabolic diamond refractive lenses are presented, designed to withstand high thermal and radiation loads coming from upgraded accelerator X-ray sources. Lenses were manufactured by picosecond laser treatment of a high-quality single-crystal synthetic diamond. Twelve lenses with radius of curvature at parabola apex R = 200 µm, geometrical aperture A = 900 µm and length L = 1.5 mm were stacked as a compound refractive lens and tested at the ESRF ID06 beamline. A focal spot of size 2.2 µm and a gain of 20 were measured at 8 keV. The lens profile and surface quality were estimated by grating interferometry and X-ray radiography. In addition, the influence of X-ray glitches on the focusing properties of the compound refractive lens were studied.

  17. X-ray driven channeling acceleration in crystals and carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Young-Min; Still, Dean A.; Shiltsev, Vladimir

    2013-12-01

    Acceleration of particles channeling in a crystal by means of diffracted x-rays via Bormann anomalous transmission was conceived for heavy ions and muons by Tajima and Cavenago [Phys. Rev. Lett. 59, 1440 (1987)], which potentially offers an appreciably high field gradient on the order of GV/cm. The theoretical model of the high gradient acceleration has been studied in two kinds of atomic structure, crystals and carbon nanotubes (CNTs), with analytic calculations and electromagnetic eigenmode simulations. A range of acceleration gradients and cutoffs of the x-ray power (the lowest power limit to overcome the Bremsstrahlung radiation losses) are characterized in terms of the lattice constants, unit cell sizes, and photon energies. The parametric analysis indicates that the required x-ray power can be reduced to an order of megawatt by replacing crystals with CNTs. Eventually, the equivalent dielectric approximation of a multi-wall nanotube shows that 250–810 MeV muons can be synchronously coupled with x-rays of 0.65–1.32 keV in the accelerating structure.

  18. The structural chemistry of metallocorroles: combined X-ray crystallography and quantum chemistry studies afford unique insights.

    Science.gov (United States)

    Thomas, Kolle E; Alemayehu, Abraham B; Conradie, Jeanet; Beavers, Christine M; Ghosh, Abhik

    2012-08-21

    Although they share some superficial structural similarities with porphyrins, corroles, trianionic ligands with contracted cores, give rise to fundamentally different transition metal complexes in comparison with the dianionic porphyrins. Many metallocorroles are formally high-valent, although a good fraction of them are also noninnocent, with significant corrole radical character. These electronic-structural characteristics result in a variety of fascinating spectroscopic behavior, including highly characteristic, paramagnetically shifted NMR spectra and textbook cases of charge-transfer spectra. Although our early research on corroles focused on spectroscopy, we soon learned that the geometric structures of metallocorroles provide a fascinating window into their electronic-structural characteristics. Thus, we used X-ray structure determinations and quantum chemical studies, chiefly using DFT, to obtain a comprehensive understanding of metallocorrole geometric and electronic structures. This Account describes our studies of the structural chemistry of metallocorroles. At first blush, the planar or mildly domed structure of metallocorroles might appear somewhat uninteresting particularly when compared to metalloporphyrins. Metalloporphyrins, especially sterically hindered ones, are routinely ruffled or saddled, but the missing meso carbon apparently makes the corrole skeleton much more resistant to nonplanar distortions. Ruffling, where the pyrrole rings are alternately twisted about the M-N bonds, is energetically impossible for metallocorroles. Saddling is also uncommon; thus, a number of sterically hindered, fully substituted metallocorroles exhibit almost perfectly planar macrocycle cores. Against this backdrop, copper corroles stand out as an important exception. As a result of an energetically favorable Cu(d(x2-y2))-corrole(π) orbital interaction, copper corroles, even sterically unhindered ones, are inherently saddled. Sterically hindered substituents

  19. THE CRYSTAL STRUCTURE OF DIPHENYLTELLURIUM DIBROMIDE,

    Science.gov (United States)

    TELLURIUM COMPOUNDS, *ORGANOMETALLIC COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , BROMIDES, SYMMETRY(CRYSTALLOGRAPHY), X RAY DIFFRACTION, FOURIER ANALYSIS, LEAST SQUARES METHOD, MOLECULAR STRUCTURE, CHEMICAL BONDS.

  20. X-Ray Diffraction Analysis of NLO Crystals: Traditional Applications and More New Opportunities

    Science.gov (United States)

    Antipin, Mikhail Yu.; Clark, Ronald D.; Nesterov, Vladimir N.

    1998-01-01

    Single crystal X-ray diffraction analysis is one of the more important methods for the molecular and crystal structure determination of matter and therefore it has a great importance in material science including design and engineering of different compounds with non-linear optical (NLO) properties. It was shown in our previous publications that this method provides unique information about molecular structure of NLO compounds, their crystal symmetry and crystal packing arrays, molecular conformation and geometries and many other structural and electronic characteristics that are important for understanding the nature of NLO properties of solids. A very new application of the X-ray diffraction method is related to analysis of the electron density distribution p(r) in crystals and some of its characteristics (atomic and group charges, dipole and higher multipole moments, etc.), that may be obtained directly form the diffraction measurements. In the present work, we will discuss our preliminary low temperature high-resolution X-ray data for the m-nitroaniline (mNA) single crystal (VI). This is one of the "classical" organic NLO materials and electron density distribution analysis in this simple compound has a great scientific interest.

  1. Solving X-ray protein structures without a crystal: using X-ray Free Electron Laser, the fourth generation synchrotron light sources

    Institute of Scientific and Technical Information of China (English)

    Bo Huang

    2010-01-01

    @@ A synchrotron light source is a source of electromagnetic radiation artificially produced by specialized electron accelerators. Compared to the commonly used in-house X-ray sources, it is wavelength adjustable, much stronger and more focused. In the last two decades, synchrotron usage has become the mainstream for X-ray protein structure determination. Taking the advantage of micro-focus light beams of the third generation synchrotron, the size of a usable protein crystal for data collection decreases to micron level, which increases the rate of macromolecular structure determination to about 10 new protein data bank entries per day.

  2. 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.

  3. Crystal structure of Pigment Red 254 from X-ray powder diffraction data

    Directory of Open Access Journals (Sweden)

    Svetlana N. Ivashevskaya

    2017-04-01

    Full Text Available The crystal structure of Pigment Red 254 [P.R. 254, C18H10Cl2N2O2; systematic name: 3,6-bis(4-chlorophenyl-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione] was solved from laboratory X-ray powder diffraction data using the simulated annealing method followed by Rietveld refinement because the very low solubility of the pigment in all solvents impedes the growth of single crystals suitable for X-ray analysis. The molecule lies across an inversion center. The dihedral angle between the benzene ring and the pyrrole ring in the unique part of the molecule is 11.1 (2°. In the crystal, molecules are linked via N—H...O hydrogen bonds, forming chains along [110] incorporating R22(8 rings.

  4. 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)

  5. High resolution X-ray diffraction studies on unirradiated and irradiated strontium hexaferrite crystals

    Indian Academy of Sciences (India)

    Balwinder Kaur; Monita Bhat; F Licci; Ravi Kumar; K K Bamzai; P N Kotru

    2012-04-01

    High-resolution X-ray diffraction technique, employing a three-crystal monochromator–collimator combination is used to study the irradiation induced defects in flux grown Sr-hexaferrite crystals irradiated with 50 MeV Li3+ ion beams at room temperature with a fluence value of 1 × 1014 ions/cm2. The diffraction curves of the irradiated crystals suggest the possibility of creation of low angle grain boundaries and other point/clusters of defects causing amorphization in the irradiated crystals. The perfection of the irradiated and unirradiated (0001) cleaved surfaces of the crystals is studied using the bulk method of X-ray topography. The topographs supplement the findings suggestive of modifications in the crystalline quality of SrFe12O19 on irradiation with SHI of Li3+. Etching of the (0001) cleaved surfaces in H3PO4 at 120°C suggests that the dissolution characteristics of the surfaces get affected on irradiation with SHI of Li3+, besides supporting the findings of HRXRD and X-ray topography regarding modifications in the perfection of SrFe12O19 on irradiation.

  6. 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.

  7. A multi-cone x-ray imaging Bragg crystal spectrometer

    Science.gov (United States)

    Bitter, Manfred; Hill, K. W.; Gao, Lan; Efthimion, P. C.; Delgado-Aparicio, L.; Lazerson, S.; Pablant, N.

    2016-10-01

    In a recent article, see, we described a new x-ray imaging Bragg crystal spectrometer, which - in combination with a streak camera or a gated strip detector - can be used for time-resolved measurements of x-ray line spectra at the National Ignition Facility (NIF) and other high power laser facilities. The main advantage of this instrument is that it produces perfect images of a point source for each wavelength in a selectable spectral range and that the detector plane can be inclined by an arbitrary angle with respect to the crystal surface. These unique imaging properties are obtained by bending the x-ray diffracting crystal into a certain shape, which is generated by arranging multiple cones with different aperture angles on a common nodal line. In this paper, we present results from optical tests of these multi-cone structures and numerical results on the deteriorations of the spectral and spatial resolutions that may be caused by potential misalignments of the source, crystal, and detector. Princeton Plasma Physics Laboratory.

  8. Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus

    Energy Technology Data Exchange (ETDEWEB)

    Nakasako, Masayoshi, E-mail: nakasako@phys.keio.ac.jp [Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan); The RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Obata, Rika; Okubo, Ryosuke; Nakayama, Shyuichi [Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan); Miyamoto, Kenji; Ohta, Hiromichi [Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan); Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan)

    2008-07-01

    Crystals of arylmalonate decarboxylase from A. bronchisepticus were obtained which diffracted X-rays to a resolution of at least 3.0 Å. Arylmalonate decarboxylase catalyses the enantioselective decarboxylation of α-aryl-α-methylmalonates to produce optically pure α-arylpropionates. The enzyme was crystallized with ammonium sulfate under alkaline pH conditions with the aim of understanding the mechanism of the enantioselective reaction. X-ray diffraction data collected to a resolution of 3.0 Å at cryogenic temperature showed that the crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 83.13, b = 99.62, c = 139.64 Å. This suggested that the asymmetric unit would contain between four and six molecules. Small-angle X-ray scattering revealed that the enzyme exists as a monomer in solution. Thus, the assembly of molecules in the asymmetric unit was likely to have been induced during the crystallization process.

  9. Barbiturate bearing aroylhydrazine derivatives: Synthesis, NMR investigations, single crystal X-ray studies and biological activity

    Science.gov (United States)

    Giziroglu, Emrah; Sarikurkcu, Cengiz; Aygün, Muhittin; Basbulbul, Gamze; Soyleyici, H. Can; Firinci, Erkan; Kirkan, Bulent; Alkis, Ayse; Saylica, Tayfur; Biyik, Halil

    2016-03-01

    A series of barbituric acid aroylhydrazine derivatives have been prepared from their corresponding 1,3-dimethyl-5-acetyl barbituric acid and aroylhydrazines. All compounds have been fully characterized by using FT-IR, multinuclear NMR (1H, 13C) and Mass (MS) spectrometry. We also describe the X-ray crystal structure of 3a, which crystallizes in the monoclinic P21/n space group. The crystal structure is stabilized with infinite linear chains of dimeric units. Furthermore, all compounds were investigated for their tyrosinase inhibition, antioxidative and antimicrobial activies. The results from biological activity assays have shown that all of compounds have excellent antioxidant, significant tyrosinase inhibition and moderate antimicrobial activity.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Feifei [East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of (China); Gao, Feng [Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of (China); Li, Honglin [East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of (China); Gong, Weimin [Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of (China); Zhou, Lin, E-mail: gdtb-bg@vip.163.com [Center for Tuberculosis Control of Guangdong Province, Guangzhou, People’s Republic of (China); Bi, Lijun, E-mail: gdtb-bg@vip.163.com [East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of (China)

    2014-07-23

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-07-01

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

  12. Crystallization and X-ray diffraction of spray-dried and freeze-dried amorphous lactose.

    Science.gov (United States)

    Haque, Md Kamrul; Roos, Yrjö H

    2005-02-07

    Crystallization of spray-dried and freeze-dried amorphous lactose over different relative vapor pressures (RVP) and storage times was studied. Crystallization was observed from increasing peak intensities in X-ray diffraction patterns. Lactose was crystallized in the samples stored at RVP of 44.1% and above in both types of dehydrated powders. The rate of crystallization increased with increasing RVP and storage time. Similar crystallization behavior of both spray-dried and freeze-dried lactose was observed. Lactose crystallized as alpha-lactose monohydrate, anhydrous beta-lactose, and the anhydrous form of alpha- and beta-lactose in a molar ratio of 5:3 and 4:1 in both spray-dried and freeze-dried forms. Peak intensities of X-ray diffraction patterns for anhydrous beta-lactose were decreased, and for alpha-lactose monohydrate increased with increasing storage RVP and time. The crystallization data were successfully modeled using Avrami equation at RVP of 54.5% and above. The crystallization data obtained is helpful in understanding and predicting storage stability of lactose-containing food and pharmaceutical products.

  13. Instrument and method for X-ray diffraction, fluorescence, and crystal texture analysis without sample preparation

    Science.gov (United States)

    Gendreau, Keith (Inventor); Martins, Jose Vanderlei (Inventor); Arzoumanian, Zaven (Inventor)

    2010-01-01

    An X-ray diffraction and X-ray fluorescence instrument for analyzing samples having no sample preparation includes a X-ray source configured to output a collimated X-ray beam comprising a continuum spectrum of X-rays to a predetermined coordinate and a photon-counting X-ray imaging spectrometer disposed to receive X-rays output from an unprepared sample disposed at the predetermined coordinate upon exposure of the unprepared sample to the collimated X-ray beam. The X-ray source and the photon-counting X-ray imaging spectrometer are arranged in a reflection geometry relative to the predetermined coordinate.

  14. Performance characteristics needed for protein crystal diffraction x-ray detectors.

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, E. M.

    1999-09-21

    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.

  15. X-ray crystal structure of Staphylococcus aureus FemA.

    Science.gov (United States)

    Benson, Timothy E; Prince, D Bryan; Mutchler, Veronica T; Curry, Kimberly A; Ho, Andrea M; Sarver, Ronald W; Hagadorn, Jeanne C; Choi, Gil H; Garlick, Robert L

    2002-08-01

    The latter stages of peptidoglycan biosynthesis in Staphylococci involve the synthesis of a pentaglycine bridge on the epsilon amino group of the pentapeptide lysine side chain. Genetic and biochemical evidence suggest that sequential addition of these glycines is catalyzed by three homologous enzymes, FemX (FmhB), FemA, and FemB. The first protein structure from this family, Staphylococcus aureus FemA, has been solved at 2.1 A resolution by X-ray crystallography. The FemA structure reveals a unique organization of several known protein folds involved in peptide and tRNA binding. The surface of the protein also reveals an L-shaped channel suitable for a peptidoglycan substrate. Analysis of the structural features of this enzyme provides clues to the mechanism of action of S. aureus FemA.

  16. Heteroaryl Chalcones: Design, Synthesis, X-ray Crystal Structures and Biological Evaluation

    OpenAIRE

    2013-01-01

    Chalcone derivatives have attracted increasing attention due to their numerous pharmacological activities. Changes in their structures have displayed high degree of diversity that has proven to result in a broad spectrum of biological activities. The present study highlights the synthesis of some halogen substituted chalcones 3(a–i) containing the 5-chlorothiophene moiety, their X-ray crystal structures and the evaluation of possible biological activities such as antibacterial, antifungal and...

  17. Guiding synchrotron X-ray diffraction by multimodal video-rate protein crystal imaging

    OpenAIRE

    Newman, Justin A.; ZHANG, Shijie; Sullivan, Shane Z.; Dow, Ximeng Y.; Becker, Michael; Sheedlo, Michael J.; Stepanov, Sergey; Carlsen, Mark S.; Everly, R. Michael; Das, Chittaranjan; Fischetti, Robert F.; Simpson, Garth J.

    2016-01-01

    Synchronous digitization, in which an optical sensor is probed synchronously with the firing of an ultrafast laser, was integrated into an optical imaging station for macromolecular crystal positioning prior to synchrotron X-ray diffraction. Using the synchronous digitization instrument, second-harmonic generation, two-photon-excited fluorescence, one-photon-excited fluorescence, two-photon-excited ultraviolet fluorescence and bright field by laser transmittance were all acquired with perfect...

  18. Calculations and surface quality measurements of high-asymmetry angle x-ray crystal monochromators for advanced x-ray imaging and metrological applications

    Science.gov (United States)

    Zápražný, Zdenko; Korytár, Dušan; Jergel, Matej; Šiffalovič, Peter; Dobročka, Edmund; Vagovič, Patrik; Ferrari, Claudio; Mikulík, Petr; Demydenko, Maksym; Mikloška, Marek

    2015-03-01

    We present the numerical optimization and the technological development progress of x-ray optics based on asymmetric germanium crystals. We show the results of several basic calculations of diffraction properties of germanium x-ray crystal monochromators and of an analyzer-based imaging method for various asymmetry factors using an x-ray energy range from 8 to 20 keV. The important parameter of highly asymmetric monochromators as image magnifiers or compressors is the crystal surface quality. We have applied several crystal surface finishing methods, including advanced nanomachining using single-point diamond turning (SPDT), conventional mechanical lapping, chemical polishing, and chemomechanical polishing, and we have evaluated these methods by means of atomic force microscopy, diffractometry, reciprocal space mapping, and others. Our goal is to exclude the chemical etching methods as the final processing technique because it causes surface undulations. The aim is to implement very precise deterministic methods with a control of surface roughness down to 0.1 nm. The smallest roughness (˜0.3 nm), best planarity, and absence of the subsurface damage were observed for the sample which was machined using an SPDT with a feed rate of 1 mm/min and was consequently polished using a fine polishing 15-min process with a solution containing SiO2 nanoparticles (20 nm).

  19. High resolution X-ray spherically bent crystal spectrometer for laser-produced plasma diagnostics

    Institute of Scientific and Technical Information of China (English)

    Shali Xiao; Hongjian Wang; Jun Shi; Changhuan Tang; Shenye Liu

    2009-01-01

    A new high spectral resolution crystal spectrometer is designed to measure very low emissive X-ray spectra of laser-produced plasma in 0.5 - 0.9 nm range. A large open aperture (30 x 20 (mm)) mica (002) spherically bent crystal with curvature radius R = 380 mm is used as dispersive and focusing element. The imaging plate is employed to obtain high spectral resolution with effective area of 30 x 80 (mm). The long designed path of the X-ray spectrometer beam is 980 mm from the source to the detector via the crystal. Experiment is carried out at a 20-J laser facility. X-ray spectra in an absolute intensity scale is obtained from Al laser produced plasmas created by laser energy of 6.78 J. Samples of spectra obtained with spectral resolution of up to E/鈻矱 ~ 1500 are presented. The results clearly show that the device is good to diagnose laser high-density plasmas.

  20. Crystal-field and covalency effects in uranates: an X-ray spectroscopic study

    Energy Technology Data Exchange (ETDEWEB)

    Butorin, Sergei M. [Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); Kvashnina, Kristina O. [European Synchrotron Radiation Facility, CS40220, Grenoble (France); Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Resource Ecology, Dresden (Germany); Smith, Anna L. [Department of Radiation Science and Technology, TU Delft (Netherlands); Popa, Karin [European Commission, Joint Research Centre, Institute for Transuranium Elements, Karlsruhe (Germany); Martin, Philippe M. [CEA Marcoule, CEA, DEN, DTEC/SECA/LCC, Bagnols-sur-Ceze (France)

    2016-07-04

    The electronic structure of U{sup V}- and U{sup VI}-containing uranates NaUO{sub 3} and Pb{sub 3}UO{sub 6} was studied by using an advanced technique, namely X-ray absorption spectroscopy (XAS) in high-energy-resolution fluorescence-detection (HERFD) mode. Due to a significant reduction in core-hole lifetime broadening, the crystal-field splittings of the 5f shell were probed directly in HERFD-XAS spectra collected at the U 3d edge, which is not possible by using conventional XAS. In addition, the charge-transfer satellites that result from U 5f-O 2p hybridization were clearly resolved. The crystal-field parameters, 5f occupancy, and degree of covalency of the chemical bonding in these uranates were estimated by using the Anderson impurity model by calculating the U 3d HERFD-XAS, conventional XAS, core-to-core (U 4f-3d transitions) resonant inelastic X-ray scattering (RIXS), and U 4f X-ray photoelectron spectra. The crystal field was found to be strong in these systems and the 5f occupancy was determined to be 1.32 and 0.84 electrons in the ground state for NaUO{sub 3} and Pb{sub 3}UO{sub 6}, respectively, which indicates a significant covalent character for these compounds. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  1. Two-dimensional crystallization of integral membrane proteins for electron crystallography.

    Science.gov (United States)

    Stokes, David L; Rice, William J; Hu, Minghui; Kim, Changki; Ubarretxena-Belandia, Iban

    2010-01-01

    Although membrane proteins make up 30% of the proteome and are a common target for therapeutic drugs, determination of their atomic structure remains a technical challenge. Electron crystallography represents an alternative to the conventional methods of X-ray diffraction and NMR and relies on the formation of two-dimensional crystals. These crystals are produced by reconstituting purified, detergent-solubilized membrane proteins back into the native environment of a lipid bilayer. This chapter reviews methods for producing two-dimensional crystals and for screening them by negative stain electron microscopy. In addition, we show examples of the different morphologies that are commonly obtained and describe basic image analysis procedures that can be used to evaluate their promise for structure determination by cryoelectron microscopy.

  2. 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.

  3. Focused beam total reflection X-ray fluorescence with low power sources coupled to doubly curved crystal optics

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Z.W. [X-ray Optical Systems, Inc. East Greenbush, NY 12061 (United States)]. E-mail: zchen@xos.com; Mail, N. [Center For X-ray Optics, State University of New York, University at Albany (United States); Wei, F.Z. [X-ray Optical Systems, Inc. East Greenbush, NY 12061 (United States); MacDonald, C.A. [Center For X-ray Optics, State University of New York, University at Albany (United States); Gibson, W.M. [X-ray Optical Systems, Inc. East Greenbush, NY 12061 (United States)

    2005-04-30

    A focused beam total X-ray fluorescence technique was developed based on doubly curved crystal optics. This technique provides good detection sensitivity and spatial resolution for localized detection of surface deposits. Compact low power X-ray sources were used to demonstrate the benefit of the X-ray optics for focusing Cr K{alpha}, Cu K{alpha} and Mo K{alpha} radiation. The detection capability of the focused beam Total reflection X-ray fluorescence system was investigated with dried droplets of calibrated low concentration solutions. Detection limits at the femtogram level were demonstrated.

  4. THE CRYSTAL STRUCTURE OF ALPHA-DIMETHYLTELLURIUM DICHLORIDE,

    Science.gov (United States)

    TELLURIUM COMPOUNDS, *ORGANOMETALLIC COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , CHLORIDES, SYMMETRY(CRYSTALLOGRAPHY), MOLECULAR STRUCTURE, CHEMICAL BONDS, X RAY DIFFRACTION, ANISOTROPY, FOURIER ANALYSIS.

  5. Organic semiconducting single crystals as next generation of low-cost, room-temperature electrical X-ray detectors.

    Science.gov (United States)

    Fraboni, Beatrice; Ciavatti, Andrea; Merlo, Francesco; Pasquini, Luca; Cavallini, Anna; Quaranta, Alberto; Bonfiglio, Annalisa; Fraleoni-Morgera, Alessandro

    2012-05-02

    Direct, solid-state X-ray detectors based on organic single crystals are shown to operate at room temperature, in air, and at voltages as low as a few volts, delivering a stable and reproducible linear response to increasing X-ray dose rates, with notable radiation hardness and resistance to aging. All-organic and optically transparent devices are reported.

  6. Synthesis, X-ray crystallography, spectroscopic (FT-IR, 1H &13C NMR and UV), computational (DFT/B3LYP) and enzymes inhibitory studies of 7-hydroximinocholest-5-en-3-ol acetate

    Science.gov (United States)

    Ahmad, Faheem; Parveen, Mehtab; Alam, Mahboob; Azaz, Shaista; Malla, Ali Mohammed; Alam, Mohammad Jane; Lee, Dong-Ung; Ahmad, Shabbir

    2016-07-01

    The present study reports the synthesis of 7-Hydroximinocholest-5-en-3-ol acetate (syn. 3β-acetoxycholest-5-en-7-one oxime; in general, steroidal oxime). The identity of steroidal molecule was confirmed by NMR, FT-IR, MS, CHN microanalysis and X-ray crystallography. DFT calculations on the titled molecule have been performed. The molecular structure and spectra interpreted by Gaussian hybrid computational analysis theory (B3LYP) are found to be in good correlation with the experimental data obtained from the various spectrophotometric techniques. The vibrational bands appearing in the FTIR are assigned with great accuracy using harmonic frequencies along with intensities and animated modes. Molecular properties like HOMO-LUMO analysis, chemical reactivity descriptors, MEP mapping, dipole moment and natural atomic charges have been presented at the same level of theory. Moreover, the Hirshfeld analysis was carried out to ascertain the secondary interactions and associated 2D fingerprint plots. The percentages of various interactions are pictorialized by fingerprint plots of Hirshfeld surface. Steroidal oxime exhibited promising inhibitory activity against acetylcholinesterase (AChE) as compared to the reference drug, tacrine. Molecular docking was performed to introduce steroidal molecules into the X-ray crystal structures of acetylcholinesterase at the active site to find out the probable binding mode. The results of molecular docking admitted that steroidal oxime may exhibit enzyme inhibitor activity.

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

    Directory of Open Access Journals (Sweden)

    Roman Sommer

    2016-12-01

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

  8. Inhibition of d-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Kovalevsky, Andrey, E-mail: ayk@lanl.gov [Los Alamos National Laboratory, PO Box 1663, MS M888, Los Alamos, NM 87545 (United States); Hanson, B. Leif [University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606 (United States); Mason, Sax A. [Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble (France); Forsyth, V. Trevor [Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble (France); Keele University, Staffordshire (United Kingdom); Fisher, Zoe [Los Alamos National Laboratory, PO Box 1663, MS M888, Los Alamos, NM 87545 (United States); Mustyakimov, Marat [Los Alamos National Laboratory, PO Box 1663, MS M888, Los Alamos, NM 87545 (United States); Oak Ridge National Laboratory, PO Box 2008, MS 6475, Oak Ridge, TN 37831 (United States); Blakeley, Matthew P. [Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble (France); Keen, David A. [Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX (United Kingdom); Langan, Paul [Oak Ridge National Laboratory, PO Box 2008, MS 6475, Oak Ridge, TN 37831 (United States); Los Alamos National Laboratory, PO Box 1663, MS M888, Los Alamos, NM 87545 (United States)

    2012-09-01

    A joint X-ray/neutron structure of d-xylose isomerase in complex with the inhibitor sorbitol was determined at room temperature at an acidic pH of 5.9. Protonation of the O5 O atom of the sugar was directly observed in the nuclear density maps. Under acidic conditions sorbitol gains a water-mediated interaction with the enzyme active site, which may explain the increased potency of the inhibitor at low pH. d-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni{sup 2+} cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg{sup 2+} ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni{sup 2+} ions occupying the catalytic metal site (M2) were found at two locations, while Mg{sup 2+} in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.

  9. Curved crystal spectrometer for the measurement of X-ray lines from laser-produced plasmas

    Institute of Scientific and Technical Information of China (English)

    SHI Jun; XIAO Sha-li; WANG Hong-jian; TANG Chang-huan; LIU Shen-ye

    2008-01-01

    In order to diagnose the laser-produced plasmas, a focusing curved crystal spectrometer has been developed for measuring the X-ray lines radiated from a laser-produced plasmas. The design is based on the fact that the ray emitted from a source located at one focus of an ellipse will converge on the other focus by the reflection of the elliptical surface. The focal length and the eccentricity of the ellipse are 1350 mm and 0.9586, respectively. The spectrometer can be used to measure the X-ray lines in the wavelength range of 0.2-0.37 nm, and a LiF crystal (200) (2d = 0.4027 nm) is used as dispersive element covering Bragg angle from 30° to 67.5°. The spectrometer was tested on Shenguang-Ⅱ which can deliver laser energy of 60-80 J/pulse and the laser wavelength is 0.35 μm. Photographs of spectra including the 1s2p 1p1-1s2 1S0 resonance line(w),the 1s2p 3P2-1s2 1S0 magnetic quadrupole line(x), the 1s2p 3p1 1s2 1S0 intercombination lines(y), the 1s2p 3S1-1s2 1S0 forbidden line(z) in helium-like Ti X XI and the 1s2s2p 2P3/2-1s22s 2S1/2 line(q) in lithium-like Ti X X have been recorded with a X-ray CCD camera. The experimental result shows that the wavelength resolution(λ/△λ) is above 1000 and the elliptical crystal spectrometer is suitable for X-ray spectroscopy.

  10. Crystallization and X-ray diffraction studies of glutathione S-transferase from Escherichia coli

    Science.gov (United States)

    Nishida, Motohiko; Harada, Shigeharu; Satow, Yoshinori; Inoue, Hideshi; Takahashi, Kenji

    1996-10-01

    Crystals of glutathione S-transferase from Escherichia coli have been obtained by use of polyethylene glycol 6000 as a precipitant. The crystallization was performed in the presence of a glutathione sulfonate inhibitor under the acidic condition, with combination of the sitting-drop vapour-diffusion and the macro-seeding procedures. The crystals are of a thin-plate shape with typical sizes of 1.0 × 0.5 × 0.1 mm, and are stable against X-ray irradiation. They belong to the space group P2 12 12 1 with cell parameters of a = 90.47 Å, b = 93.87 Å and c = 51.10 Å, and diffract X-rays at least up to 2.3 Å resolution. The solvent content is 48% in volume, when a homodimeric molecule of the enzyme is assumed to occupy an asymmetric unit of the crystal. The crystals are suitable for three-dimensional structural studies. Diffraction data of the native crystal have been collected.

  11. 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.)

  12. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-11-12

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

  14. Disordered crystal structure of pentamethylcyclopentadienylsodium as seen by high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Tedesco, C; Dinnebier, R E; Olbrich, F; van Smaalen, S

    2001-10-01

    The crystal structure of pentamethylcyclopentadienylsodium, [NaC10H15] (NaCp*), has been determined from high-resolution X-ray powder diffraction. The compound crystallizes in space group Cmcm with lattice parameters a = 4.61030 (3), b = 16.4621 (3), c = 14.6751 (2) A, V = 1113.77 (4) A(3) (Z = 4). NaCp* forms polymeric multidecker chains along the a axis. The Rietveld refinement (R(p) = 0.050 and R(F) = 0.163) shows that the Cp* moieties occupy, with disorder, two different orientations rotated away from the eclipsed conformation by +/-13.8 degrees.

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

    Science.gov (United States)

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

    2005-01-01

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

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

    Science.gov (United States)

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

    2017-05-01

    ZnS-based materials have a long history of use as x-ray luminescent materials. ZnS was one of the first discovered scintillators and is reported to have one of the highest scintillator efficiencies. The use of ZnS for high energy luminescence has been thus far limited to thin powder screens, such as ZnS:Ag which is used for detecting alpha radiation, due to opacity to its scintillation light, primarily due to scattering. ZnS in bulk form (chemical vapor deposited, powder processed, and single crystal) has high transmission and low scattering compared to powder screens. In this paper, the performance of single crystalline ZnS is evaluated for low energy x-ray (decay time, and low levels of afterglow. We present a trade study which compares the calculated scintillation gain and absolute efficiency for low energy x-rays (<10 keV) comparing thin (<100 μm) ZnS to CsI:Tl, Bi4Ge3O12 (BGO), and Y3Al5O12:Ce (YAG:Ce). The study also gives insight into the spatial resolution of these scintillators. Further, photoluminescence (PL) and PL excitation (PLE) of several undoped ZnS single crystals is compared to their Radioluminescence (RL) spectra. It was found that the ZnS emission wavelength varies on the excitation source energy.

  17. Crystallization Dynamics of Organolead Halide Perovskite by Real-Time X-ray Diffraction.

    Science.gov (United States)

    Miyadera, Tetsuhiko; Shibata, Yosei; Koganezawa, Tomoyuki; Murakami, Takurou N; Sugita, Takeshi; Tanigaki, Nobutaka; Chikamatsu, Masayuki

    2015-08-12

    We analyzed the crystallization process of the CH3NH3PbI3 perovskite by observing real-time X-ray diffraction immediately after combining a PbI2 thin film with a CH3NH3I solution. A detailed analysis of the transformation kinetics demonstrated the fractal diffusion of the CH3NH3I solution into the PbI2 film. Moreover, the perovskite crystal was found to be initially oriented based on the PbI2 crystal orientation but to gradually transition to a random orientation. The fluctuating characteristics of the crystallization process of perovskites, such as fractal penetration and orientational transformation, should be controlled to allow the fabrication of high-quality perovskite crystals. The characteristic reaction dynamics observed in this study should assist in establishing reproducible fabrication processes for perovskite solar cells.

  18. Mass Spectrometry Guided In Situ Proteolysis to Obtain Crystals for X-ray Structure Determination

    Energy Technology Data Exchange (ETDEWEB)

    Gheyi, Tarun; Rodgers, Logan; Romero, Richard; Sauder, J. Michael; Burley, Stephen K. (Lilly)

    2012-04-30

    A strategy for increasing the efficiency of protein crystallization/structure determination with mass spectrometry has been developed. This approach combines insights from limited proteolysis/mass spectrometry and crystallization via in situ proteolysis. The procedure seeks to identify protease-resistant polypeptide chain segments from purified proteins on the time-scale of crystal formation, and subsequently crystallizing the target protein in the presence of the optimal protease at the right relative concentration. We report our experience with 10 proteins of unknown structure, two of which yielded high-resolution X-ray structures. The advantage of this approach comes from its ability to select only those structure determination candidates that are likely to benefit from application of in situ proteolysis, using conditions most likely to result in formation of a stable proteolytic digestion product suitable for crystallization.

  19. Redetermination of Dy3Ni from single-crystal X-ray data

    Science.gov (United States)

    Levytskyy, Volodymyr; Babizhetskyy, Volodymyr; Kotur, Bohdan; Smetana, Volodymyr

    2013-01-01

    The classification of the title compound, tridysprosium nickel, into the Fe3C (or Al3Ni) structure type has been deduced from powder X-ray diffraction data with lattice parameters reported in a previous study [Lemaire & Paccard (1967 ▶). Bull. Soc. Fr. Mineral. Cristallogr. 40, 311–315]. The current re-investigation of Dy3Ni based on single-crystal X-ray data revealed atomic positional parameters and anisotropic displacement parameters with high precision. The asymmetric unit consists of two Dy and one Ni atoms. One Dy atom has site symmetry .m. (Wyckoff position 4c) and is surrounded by twelve Dy and three Ni atoms. The other Dy atom (site symmetry 1, 8d) has eleven Dy and three Ni atoms as neighbours, forming a distorted Frank–Kasper polyhedron. The coordination polyhedron of the Ni atom (.m., 4c) is a tricapped trigonal prism formed by nine Dy atoms. PMID:24454015

  20. Redetermination of Dy3Ni from single-crystal X-ray data

    Directory of Open Access Journals (Sweden)

    Volodymyr Levytskyy

    2013-11-01

    Full Text Available The classification of the title compound, tridysprosium nickel, into the Fe3C (or Al3Ni structure type has been deduced from powder X-ray diffraction data with lattice parameters reported in a previous study [Lemaire & Paccard (1967. Bull. Soc. Fr. Mineral. Cristallogr. 40, 311–315]. The current re-investigation of Dy3Ni based on single-crystal X-ray data revealed atomic positional parameters and anisotropic displacement parameters with high precision. The asymmetric unit consists of two Dy and one Ni atoms. One Dy atom has site symmetry .m. (Wyckoff position 4c and is surrounded by twelve Dy and three Ni atoms. The other Dy atom (site symmetry 1, 8d has eleven Dy and three Ni atoms as neighbours, forming a distorted Frank–Kasper polyhedron. The coordination polyhedron of the Ni atom (.m., 4c is a tricapped trigonal prism formed by nine Dy atoms.

  1. Redetermination of Ba2CdTe3 from single-crystal X-ray data

    Directory of Open Access Journals (Sweden)

    Min Yang

    2012-10-01

    Full Text Available The previous structure determination of the title compound, dibarium tritelluridocadmate, was based on powder X-ray diffraction data [Wang & DiSalvo (1999. J. Solid State Chem. 148, 464–467]. In the current redetermination from single-crystal X-ray data, all atoms were refined with anisotropic displacement parameters. The previous structure report is generally confirmed, but with some differences in bond lengths. Ba2CdTe3 is isotypic with Ba2MX3 (M = Mn, Cd; X = S, Se and features 1∞[CdTe2/2Te2/1]4− chains of corner-sharing CdTe4 tetrahedra running parallel [010]. The two Ba2+ cations are located between the chains, both within distorted monocapped trigonal–prismatic coordination polyhedra. All atoms in the structure are located on a mirror plane.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-11-01

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

  3. Crystallization and preliminary X-ray studies of mouse centrin1

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jung Hee [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Krauss, Norbert [Institut für Biochemie, Charité - Universitätsmedizin Berlin, Monbijoustrasse 2, D-10117 Berlin (Germany); Pulvermüller, Alexander [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Scheerer, Patrick; Höhne, Wolfgang [Institut für Biochemie, Charité - Universitätsmedizin Berlin, Monbijoustrasse 2, D-10117 Berlin (Germany); Giessl, Andreas; Wolfrum, Uwe [Zell- und Matrixbiologie, Institut für Zoologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz (Germany); Hofmann, Klaus Peter, E-mail: kph@charite.de; Ernst, Oliver Peter [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Choe, Hui-Woog, E-mail: kph@charite.de [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Department of Chemistry, College of Natural Science, Chonbuk National University, 561-756 Chonju (Korea, Republic of)

    2005-05-01

    The expression, purification, crystallization and preliminary X-ray diffraction studies of mouse centrin1 are reported. Centrins belong to a family of Ca{sup 2+}-binding EF-hand proteins that play a fundamental role in centrosome duplication and the function of cilia. To shed light on the structure–function relationship of these proteins, mouse centrin1 has been crystallized. The mouse centrin1 has been expressed in Escherichia coli as a GST-centrin fusion protein containing a thrombin protease cleavage site between the fusion partners. Two constructs with different linking-sequence lengths were expressed and purified. Thrombin cleavage yielded functional centrin1 and N-terminally extended centrin1 containing 25 additional residues upstream of its N-terminus. Only N-terminally extended centrin1 (MW ≃ 22 240 Da) could be crystallized at room temperature, using 20–25%(w/v) PEG 1500, 5–10%(v/v) ethylene glycol and 1–2%(v/v) dioxane. Crystals were suitable for X-ray analysis, diffracting to 2.9 Å at 295 K using a rotating-anode X-ray source. They belong to space group C2, with unit-cell parameters a = 60.7, b = 59.6, c = 58.3 Å, β = 109.4°. Assuming the asymmetric cell to be occupied by one centrin1 molecule of 22.2 kDa, the unit cell contains 45% solvent with a crystal volume per protein weight, V{sub M}, of 2.2 Å{sup 3} Da{sup −1}.

  4. Synthesis of RNAs with up to 100 Nucleotides Containing Site-Specific 2-methylseleno Labels for use in X-ray Crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Hobartner,C.; Rieder, R.; Kreutz, C.; Puffer, B.; Lang, K.; Polonskaia, A.; Serganov, A.; Micura, R.

    2005-01-01

    The derivatization of nucleic acids with selenium is a new and highly promising approach to facilitate their three-dimensional structure determination by X-ray crystallography. Here, we report a comprehensive study on the chemical and enzymatic syntheses of RNAs containing 2'-methylseleno (2'-Se-methyl) nucleoside labels. Our approach includes the first synthesis of an appropriate purine nucleoside phosphoramidite building block. Most importantly, a substantially changed RNA solid-phase synthesis cycle, comprising treatment with threo-1, 4-dimercapto-2, 3-butanediol (DTT) after the oxidation step, is required for a reliable strand elongation. This novel operation allows for the chemical syntheses of multiple Se-labeled RNAs in sizes that can typically be achieved only for nonmodified RNAs. In combination with enzymatic ligation, biologically important RNA targets become accessible for crystallography. Exemplarily, this has been demonstrated for the Diels-Alder ribozyme and the add adenine riboswitch sequences. We point out that the approach documented here has been the chemical basis for the very recent structure determination of the Diels-Alder ribozyme which represents the first novel RNA fold that has been solved via its Se-derivatives.

  5. Evaluation of the Quality of Sapphire Using X-Ray Rocking Curves and Double-Crystal X-Ray Topography

    Science.gov (United States)

    1994-05-01

    hard, high-strength, chemically resistant optical windows; and sub- srates for the growth of epitaxial films. The quality of a sapphire crystal can... crystal diffractometer. Single- crystal sapphire may be grown by a variety of different methods, of which the more common are Verneuil (flame fusion...Linear features (L), which may represent slight variations in lattice parameter along the crystal growth front, or dislocation networks, ad small

  6. Single-crystal X-ray diffraction studies of photo-induced molecular species.

    Science.gov (United States)

    Cole, Jacqueline M

    2004-10-20

    This tutorial review gathers together the recent developments in single-crystal X-ray diffraction that are starting to enable one to quantify directly the nature of light-induced electronic perturbations in chemical structures. Such structural information is key to understanding many photo-activated chemical processes and physical properties, and a description of the scientific impetus behind this incipient area of structural science, from academic and industrial perspectives, is given. Photoisomerism processes, solid-state photochemical reactions and spin-cross-over magnetic transitions, that have long-lived or irreversible light-induced states, are best understood by unravelling their three-dimensional structures measured in situ in their photo-converted state. A review of steady-state laser-induced single-crystal X-ray diffraction studies conducted, to date, and the experimental methodologies used in order to realise such structures, is presented. The structural characterisation of more transient photo-induced species (down to picosecond lifetimes) is paramount to a better understanding of the materials that undergo high-speed electronic switching, which make operative much of the electronics and optics industry, since there exists an inherent relationship between the excited-state structure and the physical properties exhibited. Prime examples include excited-state structures of molecular conductors and luminescent materials with potential applications as molecular wires, light-emitting diodes, non-linear optics, triboluminescence and electroluminescence. Previously, only indirect and qualitative interpretations of the nature of these excited-states could be formulated via spectroscopic techniques, but the developments in ms-ps time-resolved laser pump, X-ray probe single-crystal diffraction techniques, described herein, are overcoming this barrier, affording results that are entirely quantitative via a three-dimensional structural representation. In this

  7. Tunable hard X-ray spectrometer utilizing asymmetric planes of a quartz transmission crystal.

    Science.gov (United States)

    Seely, John F; Henins, Albert; Feldman, Uri

    2016-05-01

    A Cauchois type hard x-ray spectrometer was developed that utilizes the (301) diffraction planes at an asymmetric angle of 23.51° to the normal to the surface of a cylindrically curved quartz transmission crystal. The energy coverage is tunable by rotating the crystal and the detector arm, and spectra were recorded in the 8 keV to 20 keV range with greater than 2000 resolving power. The high resolution results from low aberrations enabled by the nearly perpendicular angle of the diffracted rays with the back surface of the crystal. By using other asymmetric planes of the same crystal and rotating to selected angles, the spectrometer can operate with high resolution up to 50 keV.

  8. Synthesis and X-ray Crystal Structure of a New Molecular Clip

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The synthesis and X-ray crystal structure of a new molecular clip 2 was reported.It (C24H24N4O2, Mr = 400.47) crystallizes in the space group C2/c with a = 15.587(2), b =8.5805(12), c = 15.259(2)(A),β= 102.448(3)°, V = 1992.9 (5)(A)3, Z= 4, Dc = 1.335 g/cm3,μ= 0.087mm-1 and F(000) = 848.It remains monomeric in the crystal and a tape-like structure is formed in the crystal structure of molecular clip.The most unusual structural feature of 2 is the boat conformation of its cyclohexyl ring imposed by the ring fusion at C(9)-C(9a).

  9. Purification, crystallization, and preliminary X-ray diffraction study of purine nucleoside phosphorylase from E. coli

    Science.gov (United States)

    Abramchik, Yu. A.; Timofeev, V. I.; Zhukhlistova, N. E.; Muravieva, T. I.; Esipov, R. S.; Kuranova, I. P.

    2015-07-01

    Crystals of E. coli purine nucleoside phosphorylase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 0.99 Å resolution. The crystals belong to sp. gr. P21 and have the following unit-cell parameters: a = 74.1 Å, b = 110.2 Å, c = 88.2 Å, α = γ = 90°, β = 111.08°. The crystal contains six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is the biological active form of E. coli. purine nucleoside phosphorylase.

  10. Purification, crystallization, and preliminary X-ray diffraction study of purine nucleoside phosphorylase from E. coli

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

    Crystals of E. coli purine nucleoside phosphorylase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 0.99 Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unit-cell parameters: a = 74.1 Å, b = 110.2 Å, c = 88.2 Å, α = γ = 90°, β = 111.08°. The crystal contains six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is the biological active form of E. coli. purine nucleoside phosphorylase.

  11. Crystallization and preliminary X-ray analysis of CTP:phosphoethanolamine cytidylyltransferase (ECT) from Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Ohtsuka, Jun; Nagata, Koji; Lee, Woo Cheol [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan); Ono, Yusuke; Fukuda, Ryouichi; Ohta, Akinori [Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan); Tanokura, Masaru, E-mail: amtanok@mail.ecc.u-tokyo.ac.jp [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2006-10-01

    CTP:phosphoethanolamine cytidylyltransferase from S. cerevisiae has been expressed, purified and crystallized. CTP:phosphoethanolamine cytidylyltransferase (ECT) is the enzyme that catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine in the phosphatidylethanolamine-biosynthetic pathway (Kennedy pathway). ECT from Saccharomyces cerevisiae was crystallized by the sitting-drop vapour-diffusion method using PEG 4000 as precipitant. The crystals diffracted X-rays from a synchrotron-radiation source to 1.88 Å resolution. The space group was assigned as primitive tetragonal, P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 66.3, c = 150.8 Å. The crystals contain one ECT molecule in the asymmetric unit (V{sub M} = 2.2 Å{sup 3} Da{sup −1}), with a solvent content of 43%.

  12. X-ray perfection study of Verneuil-grown SrTiO 3 crystals

    Science.gov (United States)

    Yoshimura, J.; Sakamoto, T.; Usui, S.; Kimura, S.

    1998-07-01

    Dislocations, subgrain textures and other long-range strains in Verneuil-grown SrTiO 3 crystals, used widely as a substrate for growing high- Tc superconducting thin films, have been studied by reflection and transmission X-ray topography to characterize the crystal in regard to structural perfection. It was found that dislocations are nearly aligned along the directions and most of them are of pure edge type, presumably as a property of annealed crystals with simple cubic lattice. This entire dislocation alignment causes a strong long-range distortion about the [0 0 1] axis in anisotropic (1 1 0)-oriented crystal plates. Burgers vectors both of and types were observed. It was also found that the surfaces of some samples were finished highly strain-free as well as optically flat by the mechanochemical polishing.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Ji Yong; Lee, Hyung Ho; Yoon, Hye Jin; Kim, Hyoun Sook; 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)

    2006-11-01

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

  14. Characterisation of vapour grown CdZnTe crystals using synchrotron X-ray topography

    Science.gov (United States)

    Egan, Christopher K.; Choubey, Ashutosh; Moore, Moreton; Cernik, Robert J.

    2012-03-01

    Synchrotron white beam X-ray topography has been used to characterise bulk crystal defects of thick vapour grown CdZnTe crystals. Whole 50 mm diameter wafers with thicknesses in the range of 2-3 mm were sliced from boules grown by the multi-tube physical vapour transport method and analysed by diffraction topography in a transmission geometry. A variety of defects were observed including cracks, voids and grain boundaries. The largest quantity of defects observed were sub-grains appearing as localised increased intensity in the topographs. The periphery of the wafers showed the highest number of defects, whereas central regions where largely defect-free. We failed to observe any inclusions or precipitates within these crystals. Surface damage from wire-saw cutting was also observed on poorly processed wafers; these defects were otherwise invisible to standard characterisation methods. X-ray topography has proven to be a useful tool for non-destructively investigating bulk extended defects in CdZnTe crystals for radiation detector applications.

  15. Characterization of X-ray polycapillary optics by LiF crystal radiation detectors through confocal fluorescence microscopy

    Science.gov (United States)

    Bonfigli, Francesca; Hampai, Dariush; Dabagov, Sultan B.; Montereali, Rosa Maria

    2016-08-01

    Solid-state radiation imaging detectors based on photoluminescent colour centres in lithium fluoride (LiF) crystals have been successfully tested for both advanced 2D and 3D characterizations of X-ray polycapillary optics by a table-top laboratory system. Polycapillary optics can control X-ray beams propagation and allows obtaining quasi-parallel beam (half-lens) or focused beams (full-lens). The combination of a fine-focused micro X-ray tube and a polycapillary lens can provide the high intensity radiation fluxes that are necessary for high resolution X-ray imaging. In this paper we present novel results about advanced characterization of these complex optics by 2D as well as 3D confocal laser fluorescence microscopy of X-ray irradiated LiF crystal detectors. Two dimensional high spatial resolution images on a wide field of view of transmitted X-rays through a semi-lens and 3D direct inspection of the coloured volumes produced in LiF crystals by both focused and parallel X-ray beam transmitted by a full and a semi-lens, respectively, as well as their 3D reconstructions were obtained. The results show that the photoluminescent colour centres volume in LiF crystals combined with an optical sectioning reading system provide information about tomography of transmitted X-ray beams by policapillary optics in a single exposure process. For the first time, the use of LiF crystal plates as versatile radiation imaging luminescent detectors have been used to characterize the operation of polycapillary optics as X-ray lens, in focusing and parallel mode.

  16. Photonic Material Selection of Scintillation Crystals Using Monte Carlo Method for X-Ray Detection in Industrial Computed Tomography

    Directory of Open Access Journals (Sweden)

    Peng He

    2014-01-01

    Full Text Available Currently industrial X-CT system is designed according to characteristics of test objects, and test objects determine industrial X-CT system structure, X-ray detector/sensor property, scanning mode, and so forth. So there are no uniform standards for the geometry size of scintillation crystals of detector. Moreover, scintillation crystals are usually mixed with some highly toxic impurity elements, such as Tl and Cd. Thus, it is indispensable for establishing guidelines of engineering practice to simulate X-ray detection performances of different scintillation crystals. This paper focuses on how to achieve high efficient X-ray detection in industrial X-CT system which used Monte Carlo (MC method to study X-ray energy straggling characteristics, full energy peak efficiency, and conversion efficiency of some scintillation crystals (e.g., CsI(Tl, NaI(Tl, and CdWO4 after X-ray interacted with these scintillation crystals. Our experimental results demonstrate that CsI(Tl scintillation crystal has the advantages of conversion efficiency, spectral matching, manufacturing process, and full energy peak efficiency; it is an ideal choice for high efficient X-ray detection in industrial X-CT system.

  17. X-ray Imaging of MagLIF Experiments Using a Spherically-Bent Crystal Optic

    Science.gov (United States)

    Harding, E. C.; Gomez, M. R.; Jennings, C. A.; Knapp, P. F.; Slutz, S. A.; Sefkow, A. B.; Awe, T. J.; Hansen, S. B.; Peterson, K. J.; Hahn, K. D.; McBride, R. D.; Rochau, G. A.; Sinars, D. B.; Golovkin, I.

    2015-11-01

    The recent Magnetized Liner Inertial Fusion (MagLIF) experiments performed on Sandia's Z-machine produced significant thermonuclear DD fusion yields that were accompanied by observable x-ray emission [M.R. Gomez et. al., PRL (2014)]. The MagLIF experiments relied on a spherically-bent crystal optic to image portions of the x-ray continuum that were generated by the hot stagnation plasma. The images of stagnation show a long (6 to 8 mm) and narrow (~100 micron) column of x-ray emission with structure in both directions. This structure may be caused by variations in the electron temperature (Te) and density (ne) , as well as opacity variations in the surrounding Be pusher. Here we investigate the possible contributions from each of these effects. We will also discuss the development of a diagnostic technique in which Te and ne of the DD fuel are inferred from spectra emitted by Fe impurities that become ionized to a He-like charge state. Sandia National Labs is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DoE NNSA under contract DE-AC04-94AL85000.

  18. Determination of Fe charge-state distributions in PLT by Bragg crystal x-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    1978-08-01

    A curved-crystal Bragg x-ray spectrometer has been used to measure K..cap alpha.. or 1s-2p radiation from highly stripped Fe XVIII to Fe XXV impurity ions in the PLT tokamak. The spectrometer has sufficient energy resolution (approximately < 4 eV at 6400 eV) to distinguish between the different ionization states of iron by measuring the energy shift of the K..cap alpha.. x rays. The measured wavelengths agree well with theory and with spectra from solar flares and from laser-produced plasmas. The distribution of Fe charge states in the center of the discharge has been inferred from a comparison of the measured x-ray spectrum with theory. The shape of the spectrum depends strongly on electron temperature (T/sub e/) in the range T/sub e/ = 800 to 1500 eV. Within the factor of two uncertainty in L-shell ionization cross sections, measured intensities agree with theory, which is based on coronal equilibrium, indicating that the ion life-time in the center of the plasma is approximately equal to or greater than the equilibration time.

  19. Investigation of coloration of SrLaGaO sub 4 single crystals by X-ray photoelectron spectroscopy

    CERN Document Server

    Novosselov, A; Talik, E; Pajaczkowska, A

    2003-01-01

    An investigation of the X-ray photoelectron spectra of single crystals of SrLaGaO sub 4 grown by the Czochralski method at various oxygen pressures is reported. Light yellow, yellow and red colored crystals were grown at an oxygen pressure lower than about 5x10 sup - sup 4 atm while the green colored crystals were grown at an oxygen pressure higher than 5x10 sup - sup 3 atm. The presence of Ga sup 1 sup + ions for green colored crystals was demonstrated and the existence of interstitial oxygen atoms in the green and red colored crystals was proposed by using X-ray photoelectron spectroscopy.

  20. X-ray crystallographic studies of metalloproteins.

    Science.gov (United States)

    Volbeda, Anne

    2014-01-01

    Many proteins require metals for their physiological function. In combination with spectroscopic characterizations, X-ray crystallography is a very powerful method to correlate the function of protein-bound metal sites with their structure. Due to their special X-ray scattering properties, specific metals may be located in metalloprotein structures and eventually used for phasing the diffracted X-rays by the method of Multi-wavelength Anomalous Dispersion (MAD). How this is done is the principle subject of this chapter. Attention is also given to the crystallographic characterization of different oxidation states of redox active metals and to the complication of structural changes that may be induced by X-ray irradiation of protein crystals.

  1. Radiation of X-rays using polarized LiNbO3 single crystal in low-pressure ambient gas.

    Science.gov (United States)

    Fukao, Shinji; Nakanishi, Yoshikazu; Mizoguchi, Tadahiro; Ito, Yoshiaki; Yoshikado, Shinzo

    2009-09-01

    The dependence of X-ray intensity on the pressure and type of ambient gas was investigated for LiNbO(3) single crystals polarized in the c-axis direction at pressures of approximately 1 to 30 Pa. Ionization of surrounding gas molecules by the electric field generated by the crystal led to the production of both positive ions and free electrons. The electrons were accelerated toward a Cu target, radiating both white X-rays and X-rays specific to the crystal or target material by bremsstrahlung. The integrated X-ray intensity per cycle in the energy range 1 to 20 keV showed a local maximum value at a pressure P(max). The logarithm of P(max) was proportional to the Boltzmann factor using the first ionization energy of each ambient gas molecule. The value of P(max) was found to be independent of the electrical surface area of the crystal. The integrated X-ray intensity was approximated qualitatively by a quadratic function with pressure, which was upwardly convex. It was found that one of the causes of the reduction in X-ray intensity at pressures P > P(max) is the adsorption of positive ions generated by the ionization of gas molecules on the negative electric surface. It was also discovered that the lifetime of the X-ray radiation device could be improved when the X-ray radiation case was covered with another hermetically sealed decompression case. The gas with the smallest first ionization energy, with a partial pressure of P(max), was enclosed inside the X-ray radiation case (inner case) and the gas with the largest first ionization energy was enclosed at a suitable pressure between the inner and outer cases.

  2. High resolution x-ray and gamma ray imaging using diffraction lenses with mechanically bent crystals

    Science.gov (United States)

    Smither, Robert K.

    2008-12-23

    A method for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation is provided. High quality mechanically bent diffracting crystals of 0.1 mm radial width are used for focusing the radiation and directing the radiation to an array of detectors which is used for analyzing their addition to collect data as to the location of the source of radiation. A computer is used for converting the data to an image. The invention also provides for the use of a multi-component high resolution detector array and for narrow source and detector apertures.

  3. Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, V. I., E-mail: inna@ns.crys.ras.ru; Abramchik, Yu. A., E-mail: tostars@mail.ru; Zhukhlistova, N. E., E-mail: ugama@yandex.ru; Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2015-09-15

    Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-Å resolution. The crystals of PRPPS belong to sp. gr. P6{sub 3}22 and have the following unit-cell parameters: a = b = 104.44 Å, c = 124.98 Å, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-Å resolution.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Che-Yen [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Miyazaki, Naoyuki [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Yamashita, Tetsuo [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Institute for Microbial Diseases, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Higashiura, Akifumi; Nakagawa, Atsushi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Li, Tian-Cheng; Takeda, Naokazu [Department of Virology II, National Institute of Infectious Diseases, Tokyo (Japan); Xing, Li [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Hjalmarsson, Erik; Friberg, Claes [Crystal Research AB, 22370 Lund (Sweden); Liou, Der-Ming [Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Sung, Yen-Jen [Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Institute of Anatomy and Cell Biology, National Yang-Ming University, 112 Taipei,Taiwan (China); Tsukihara, Tomitake [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Matsuura, Yoshiharu [Institute for Microbial Diseases, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Miyamura, Tatsuo [Department of Virology II, National Institute of Infectious Diseases, Tokyo (Japan); Cheng, R. Holland, E-mail: rhch@ucdavis.edu [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden)

    2008-04-01

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

  5. Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli

    Science.gov (United States)

    Timofeev, V. I.; Abramchik, Yu. A.; Zhukhlistova, N. E.; Kuranova, I. P.

    2015-09-01

    Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-Å resolution. The crystals of PRPPS belong to sp. gr. P6322 and have the following unit-cell parameters: a = b = 104.44 Å, c = 124.98 Å, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-Å resolution.

  6. Revisit of alpha-chitin crystal structure using high resolution X-ray diffraction data.

    Science.gov (United States)

    Sikorski, Pawel; Hori, Ritsuko; Wada, Masahisa

    2009-05-11

    High resolution synchrotron X-ray fiber diffraction data recorded from crab tendon chitin have been used to describe the crystal structure of alpha-chitin. Crystal structures at 100 and 300 K have been solved using restrained crystallographic refinement against diffraction intensities measured from the fiber diffraction patterns. The unit cell contains two polymer chains in a 2(1) helix conformation and in the antiparallel orientation. The best agreement between predicated and observed X-ray diffraction intensities is obtained for a model that includes two distinctive conformations of C6-O6 hydroxymethl group. Those conformations are different from what is proposed in the generally accepted alpha-chitin crystal structure (J. Mol. Biol. 1978, 120, 167-181). Based on refined positions of the O6 atoms, a network of hydrogen bonds involving O6 is proposed. This network of hydrogen bonds can explain the main features of the polarized FTIR spectra of alpha-chitin and sheds some light on the origin of splitting of the amide I band observed on alpha-chitin IR spectra.

  7. Redetermination of LaZn5 based on single crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Igor Oshchapovsky

    2012-01-01

    Full Text Available The crystal structure of the already known binary title compound LaZn5 (lanthanum pentazinc (space group P6/mmm, Pearson symbol hP6, CaCu5 structure type has been redetermined from single-crystal X-ray diffraction data. In contrast to previous determinations based on X-ray powder data [Nowotny (1942. Z. Metallkd. 34, 247–253; de Negri et al. (2008. Intermetallics, 16, 168–178], where unit-cell parameters and assignment of the structure type were reported, the present study reveals anisotropic displacement parameters for all atoms. The crystal structure consists of three crytallographically distinct atoms. The La atom (Wyckoff site 1a, site symmetry 6/mmm is surrounded by 18 Zn atoms and two La atoms. The coordination polyhedron around one of the Zn atoms (Wyckoff site 2c, site symmetry -6m2 is an icosahedron made up from three La and nine Zn atoms. The other Zn atom (Wyckoff site 3g, site symmetry mmm is surrounded by four La and eight Zn atoms. Bonding between atoms is explored by means of the TB–LMTO–ASA (tight-binding linear muffin-tin orbital atomic spheres approximation program package. The positive charge density is localized around La atoms, and the negative charge density is around Zn atoms, with weak covalent bonding between the latter.

  8. 弯晶X射线光学%Bent crystal X-ray optics

    Institute of Scientific and Technical Information of China (English)

    E Forster

    2007-01-01

    Much effort has been exerted both in the development of modern dedicated synchrotrons and free electron lasers with unique properties.Femtosecond laser plasma sources provide ultra-short X-ray pulses of high peak brilliance and can thus be complementary X-ray sources to the undulator based sources.All these modern X-ray sources need dedicated X-ray optics for diagnostics and applications,respectively.X-ray spectroscopy is one of the most important diagnostics of plasmas in the context of laser fusion.Depending on the aims of these experiments,monochromatic X-ray images or high resolution spectra combined with either spatial or time resolution can be obtained.Sophisticated monochromatic imagers with up to 10 toroidally bent crystals have been developed to study the implosion processes in laser fusion experiments;time-resolved maps of plasma parameters are evaluated from the data.High-power femtosecond lasers provide a practical,relatively inexpensive,powerful X-ray pulse source.Information on production efficiency,the energy distribution and transport of hot electrons is needed to maximize X-ray output in desired K-shell emission lines or continuum ranges so that peak brilliances comparable to those of synchrotrons may be feasible.Combining these new sources with bent crystal optics enables diffraction experiments on sub-picosecond time scales.Laser-pump X-rayprobe experiments have shown evidence of structure changes in several crystals within 250 fs.These X-ray optics have been designed in our institute using ray tracing and Bragg reflection codes for the 1D or 2D bent crystals or combinations thereof.In the preparation process,extreme care has been taken over crystal perfection,selection of optimum reflections,precision bending,measurement of imaging and reflection properties.X-ray topographic cameras and diffractometers are used to check the relevant properties of the analyzer crystals.%近年来,人们付出很大精力研制新的具有独特性能的同步辐

  9. 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 developed and tested on micro-crystals of lysozyme and insulin. Different protein crystal forms were identified by comparing experimental powder diffraction patternswith patterns calculated from PDB coordinates. The key factor to bring the calculated patterns in agreement with the observed patterns...

  10. Purification, crystallization and preliminary X-ray analysis of uridine phosphorylase from Salmonella typhimurium.

    Science.gov (United States)

    Dontsova, Mariya V; Savochkina, Yulia A; Gabdoulkhakov, Azat G; Baidakov, Sergey N; Lyashenko, Andrey V; Zolotukhina, Maria; Errais Lopes, Liubov; Garber, Mariya B; Morgunova, Ekaterina Yu; Nikonov, Stanislav V; Mironov, Alexandr S; Ealick, Steven E; Mikhailov, Al 'Bert M

    2004-04-01

    The structural udp gene encoding uridine phosphorylase (UPh) was cloned from the Salmonella typhimurium chromosome and overexpressed in Escherichia coli cells. S. typhimurium UPh (StUPh) was purified to apparent homogeneity and crystallized. The primary structure of StUPh has high homology to the UPh from E. coli, but the enzymes differ substantially in substrate specificity and sensitivity to the polarity of the medium. Single crystals of StUPh were grown using hanging-drop vapor diffusion with PEG 8000 as the precipitant. X-ray diffraction data were collected to 2.9 A resolution. Preliminary analysis of the diffraction data indicated that the crystal belonged to space group P6(1(5)), with unit-cell parameters a = 92.3, c = 267.5 A. The solvent content is 37.7% assuming the presence of one StUPh hexamer per asymmetric unit.

  11. 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.

  12. Catalysis of GTP hydrolysis by small GTPases at atomic detail by integration of X-ray crystallography, experimental, and theoretical IR spectroscopy.

    Science.gov (United States)

    Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R; Gerwert, Klaus; Kötting, Carsten

    2015-10-02

    Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg(2+) coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg(2+) in GTPases. The Mg(2+) coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis.

  13. X-ray diffraction, X-ray photoelectron spectra, crystal structure, and optical properties of centrosymmetric strontium borate Sr2B16O26.

    Science.gov (United States)

    Reshak, Ali Hussain; Auluck, S; Kityk, I V; Chen, Xuean

    2009-07-09

    We report results of X-ray diffraction (XRD) and valence band X- ray photoelectron (VB-XPS) spectra for strontium borate Sr(2)B(16)O(26). The X-ray structural analysis shows that the single crystals of Sr(2)B(16)O(26) crystallize in the monoclinic space group P2(1)/c with a = 8.408(1) A, b = 16.672(1) A, c = 13.901(2) A, beta = 106.33(1) degrees , and Z = 4. The crystal structure consists of a 3D network of the complex borate anion [B(16)O(20)O(12/2)](4-), formed by 12 BO(3) triangles and four BO(4) tetrahedra, which can be viewed as three linked [B(3)O(3)O(4/2)](-) triborate groups bonded to one pentaborate [B(5)O(6)O(4/2)](-) group and two BO(3) triangles. Using this structure, we have performed theoretical calculations using the all-electron full potential linearized augmented plane wave (FP-LAPW) method for the band structure, density of states, electron charge density, and the frequency-dependent optical properties. Our experimental VB-XPS of Sr(2)B(16)O(26) is compared with results of our FP-LAPW calculations. Our calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Gamma of the Brillouin zone (BZ) resulting in a direct energy gap of about 5.31 eV. Our measured VB-XPS show reasonable agreement with our calculated total density of states for the valence band that is attributed to the use of the full potential method.

  14. Study of crystal structure at high temperature phase in KIO sub 3 crystal by synchrotron powder X-ray diffraction

    CERN Document Server

    Kasatani, H; Kuroiwa, Y; Yagi, K; Katayama, R; Terauchi, H

    2003-01-01

    The accurate crystal structure of the I-phase in KIO sub 3 crystal has been obtained at 530 K, for the first time, by the MEM/Rietveld analysis from high-energy X-ray powder-diffraction data. The crystal structure of the I-phase is the rhombohedral perovskite structure (space group R3m; Z=1). The MEM charge-density distributions reveal that the shorter I-O bond exhibits a covalent bonding character and others (I-K, K-O and longer I-O bonds) an ionic.

  15. Rotation of X-ray polarization in the glitches of a silicon crystal monochromator.

    Science.gov (United States)

    Sutter, John P; Boada, Roberto; Bowron, Daniel T; Stepanov, Sergey A; Díaz-Moreno, Sofía

    2016-08-01

    EXAFS studies on dilute samples are usually carried out by collecting the fluorescence yield using a large-area multi-element detector. This method is susceptible to the 'glitches' produced by all single-crystal monochromators. Glitches are sharp dips or spikes in the diffracted intensity at specific crystal orientations. If incorrectly compensated, they degrade the spectroscopic data. Normalization of the fluorescence signal by the incident flux alone is sometimes insufficient to compensate for the glitches. Measurements performed at the state-of-the-art wiggler beamline I20-scanning at Diamond Light Source have shown that the glitches alter the spatial distribution of the sample's quasi-elastic X-ray scattering. Because glitches result from additional Bragg reflections, multiple-beam dynamical diffraction theory is necessary to understand their effects. Here, the glitches of the Si(111) four-bounce monochromator of I20-scanning just above the Ni K edge are associated with their Bragg reflections. A fitting procedure that treats coherent and Compton scattering is developed and applied to a sample of an extremely dilute (100 micromolal) aqueous solution of Ni(NO3)2. The depolarization of the wiggler X-ray beam out of the electron orbit is modeled. The fits achieve good agreement with the sample's quasi-elastic scattering with just a few parameters. The X-ray polarization is rotated up to ±4.3° within the glitches, as predicted by dynamical diffraction. These results will help users normalize EXAFS data at glitches.

  16. Real-time, high-resolution x-ray diffraction measurements on shocked crystals at a synchrotron facility.

    Science.gov (United States)

    Gupta, Y M; Turneaure, Stefan J; Perkins, K; Zimmerman, K; Arganbright, N; Shen, G; Chow, P

    2012-12-01

    The Advanced Photon Source (APS) at Argonne National Laboratory was used to obtain real-time, high-resolution x-ray diffraction measurements to determine the microscopic response of shock-compressed single crystals. Disk shaped samples were subjected to plane shock wave compression by impacting them with half-inch diameter, flat-faced projectiles. The projectiles were accelerated to velocities ranging between 300 and 1200 m/s using a compact powder gun designed specifically for use at a synchrotron facility. The experiments were designed to keep the sample probed volume under uniaxial strain and constant stress for a duration longer than the 153.4 ns spacing between x-ray bunches. X-rays from a single pulse (crystals at the APS are presented. Analytic developments to determine the effects of crystal substructure and non-ideal geometry on the diffraction pattern position and shape are presented. Representative real-time x-ray diffraction data, indicating shock-induced microstructural changes, are presented for a shock-compressed Al(111) sample. The experimental developments presented here provided, in part, the impetus for the Dynamic Compression Sector (DCS) currently under development at the APS. Both the synchronization∕x-ray detection methods and the analysis equations for high-resolution single crystal x-ray diffraction can be used at the DCS.

  17. X-ray Luminescence Efficiency of GAGG:Ce Single Crystal Scintillators for use in Tomographic Medical Imaging Systems

    Science.gov (United States)

    David, S. L.; Valais, I. G.; Michail, C. M.; Kandarakis, I. S.

    2015-09-01

    The purpose of the present study was to evaluate different scintillator crystal samples, with a cross section of 3×3mm2 and various thicknesses ranging from 4mm up to 20mm, of the new mixed Gd3Al2Ga3O12:Ce (GAGG:Ce) scintillator material under X-ray irradiation, for potential applications in Tomographic Medical Imaging systems. Evaluation was performed by determining the X-ray luminescence efficiency (XLE) (emitted light energy flux over incident X-ray energy flux) in energies employed in general X-ray imaging. For the luminescence efficiency measurements, the scintillator samples were exposed to X-rays using a BMI General Medical Merate tube, with rotating Tungsten anode and inherent filtration equivalent to 2 mm Al. X-ray tube voltages between 50 to 130 kV were selected. An additional 20 mm filtration was introduced to the beam to simulate beam quality alternation equivalent to a human body. The emitted light energy flux measurements were performed using an experimental set up comprising a light integration sphere coupled to an EMI 9798B photomultiplier tube which was connected to a Cary 401 vibrating reed electrometer. The GAGG:Ce sample with dimensions 3×3×10 mm3 exhibited higher XLE values, in the whole X- ray energy range examined. XLE value equal to 0.013 was recorded for this crystal at 130 kVp - a setting frequently used in Computed Tomography applications.

  18. In situ X-ray diffraction based investigation of crystallization in solution deposited PZT thin films

    Science.gov (United States)

    Nittala, Krishna

    Solution deposited PZT based thin films have potential applications in embedded decoupling capacitors and pulse discharge capacitors. During solution deposition, precursor solution is deposited onto a substrate to obtain an amorphous film. The film is then crystallized by heating it at a high temperature (˜600 - 700°C). Conditions during the crystallization anneal such as precursor stoichiometry in solution, heating rate and adhesion layer in the substrate are known to influence phase and texture evolution in these films. However, a mechanistic understanding of the changes taking place in these thin films during crystallization is lacking. A better understanding of the crystallization processes in these thin films could enable tailoring the properties of thin films to suit specific applications. To explore the crystallization process in solution deposited PZT thin films, high temperature in situ laboratory and synchrotron X-ray diffraction based techniques were developed. Taking advantage of the high X-ray flux available at synchrotron facilities such as beamline 6-ID-B, Advanced Photon Source, Argonne National Laboratory, crystalline phases formed in the thin films during crystallization at the high heating rates (0.5 -- 60°C/s) typically used during film processing could be measured. Using a 2-D detector for these measurements allowed the simultaneous measurement of both phase and texture information during crystallization. Analytical treatment of the unconventional diffraction geometry used during the synchrotron based measurements was performed to develop methodologies for quantitative estimation of texture components. The nominal lead content in the starting solutions and the heating rate used during crystallization was observed to influence the sequence of phases formed during crystallization of the films. In films crystallized at fast heating rates, titanium segregation, probably due to diffusion of titanium from the adhesion layer, was observed. To

  19. Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

    Science.gov (United States)

    Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

    2014-12-11

    The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

  20. A triple axis double crystal multiple reflection camera for ultra small angle X-ray scattering

    Science.gov (United States)

    Lambard, Jacques; Lesieur, Pierre; Zemb, Thomas

    1992-06-01

    To extend the domain of small angle X-ray scattering requires multiple reflection crystals to collimate the beam. A double crystal, triple axis X-ray camera using multiple reflection channel cut crystals is described. Procedures for measuring the desmeared scattering cross-section on absolute scale are described as well as the measurement from several typical samples : fibrils of collagen, 0.3 μm diameter silica spheres, 0.16 μm diameter interacting latex spheres, porous lignite coal, liquid crystals in a surfactant-water system, colloidal crystal of 0.32 μm diameter silica spheres. L'extension du domaine de diffusion des rayons-X vers les petits angles demande l'emploi de cristaux à réflexions multiples pour collimater le faisceau. Nous décrivons une caméra à rayons-X à trois axes où les réflexions multiples sont réalisées dans deux cristaux à gorge. Nous donnons ensuite les procédures de déconvolution pour obtenir la section efficace de diffusion en échelle absolue, ainsi que les résultats des mesures effectuées avec plusieurs échantillons typiques : fibres de collagène, sphères de silice de 0,3 μm de diamètre, sphères de latex de 0,16 μm de diamètre en interaction, charbon lignite poreux, cristaux liquides formés dans un système eau-tensioactif, solution colloïdale de sphères de silice de 0,32 μm de diamètre.

  1. Crystallinity and crystallization mechanism of lithium aluminosilicate glass by X-ray diffractometry

    Institute of Scientific and Technical Information of China (English)

    GUO Xing-zhong; YANG hui; CAO Ming; HAN Chen; SONG Fang-fang

    2006-01-01

    The crystallinity of lithium aluminosilicate(LAS) glass after crystallization were studied at different temperatures by X-ray diffractometry and the crystallinity of the standard glass ceramic with known crystal and glass phases was examined. The crystallization mechanism of LAS glass was analyzed by the crystallinity, with a formula relating the crystallinity (Ⅹ) and temperature (7). The results show that the calculated crystallinity of LAS glass by XRD increases with the crystallization temperature,in the range of 40% -50%, which is close to the calculated ones of standard samples with spodumene quartz ratio of 40%-70%. The activation energy of LAS glass is different within different temperature ranges; nEc is 125.44 kJ/mol at 710-810 ℃ and nEc is 17.42 kJ/mol at 810-980 ℃, which indicates different crystallization mechanisms. It has been proved that the required energy for crystallization of glass in the lower temperature range includes the interfacial energy between glass and crystalline phase and the free energy difference of atoms in structures of glass and crystal, and in the higher temperature ranges only the interfacial energy between glass and crystalline phase is considered.

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

    Directory of Open Access Journals (Sweden)

    Klaus Mann

    2009-11-01

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

  3. Configuration Confirmation of Euphorbia Factor L1 by Single-crystal X-ray Diffraction

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A 6,(17)-epoxylathyrol diterpenoid ((2S*3S*4R*5R*6S*9S*11S*15R*)-5,15-diacetoxy-3- phenylacetoxy-14-oxolathyra-6(17),(12E)-diene-6(17)-epoxide) was isolated from the seeds of Euhporbia lathyris L. Its configuration was puzzled because of the incomplete X-ray results reported before. In this work, the atom connectivity and configuration were confirmed by single-crystal X-ray diffraction together with ESI-MS, 1H-, and 13C-NMR spectroscopy. The compound crystallizes in monoclinic, space group P21 with a = 11.386(1), b = 8.2839(7), c = 17.192(2)(A), β = 108.305(2)o, Z = 2, V = 1539.5(2)(A)3, C32H40O8, Mr = 552.64, Dc = 1.192 g/m3, F(000) = 592, μ(MoKα) = 0.085 mm-1, T = 293(2) K, the final R = 0.0398 and wR = 0.0950 for 2057 observed reflections with I > 2σ(I). The molecule shows a tricyclic terpenoid skeleton, consisting of fused five-, eleven- and three-membered rings. The configuration at C(5) is R* and that at C(6) S*.

  4. Triethylammonium salt of dimethyl diphenyldithiophosphates: Single crystal X-ray and DFT analysis

    Indian Academy of Sciences (India)

    SANDEEP KUMAR; RUCHI KHAJURIA; MANDEEP KOUR; RAKESH KUMAR; LOVE KARAN RANA; GEETA HUNDAL; VIVEK K GUPTA; RAJNI KANT; SUSHIL K PANDEY

    2016-06-01

    The present work demonstrates the single crystal X-ray and DFT analysis of $ [{(2,4-CH_{3})_{2}C_{6}H_{3}O}_{2}$PS_{2}HNEt_{3}]$ (1) and $ [{(3,4-CH_{3})_{2}$ $C_{6}H_{3}O}_{2}$ $PS_{2}HNEt_{3}]$ (2) along with computational analysis of $ [{(3,5-CH_{3})_{2}C_{6}H_{3}O}_{2} $PS_{2}HNEt_{3}]$ (3) by using density functional theory (DFT) in its hybrid form B3LYP method. Compounds1 and 2 crystallize in the orthorhombic space group Pbca and triclinic space groupP1,respectively andtheir X-ray analysis reveals that phosphorus atom is coordinated to the two S and two O atoms to form tetrahedralgeometry. The structure is stabilized by cation–anion N–H.... S hydrogen bonded interactions. The structuralparameters, vibrational bands and energy gaps of frontier orbitals (HOMO–LUMO) have been calculated.The calculated geometric and spectral results matched the experimental data with good agreement. Theoreticallycalculated frontier molecular orbitals (HOMO–LUMO) and their energies suggest that charge transferoccurs within the compounds.

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

    Science.gov (United States)

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

    2012-11-01

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

  6. Time-resolved soft X-ray diffraction reveals transient structural distortions of ternary liquid crystals.

    Science.gov (United States)

    Quevedo, Wilson; Peth, Christian; Busse, Gerhard; Scholz, Mirko; Mann, Klaus; Techert, Simone

    2009-11-04

    Home-based soft X-ray time-resolved scattering experiments with nanosecond time resolution (10 ns) and nanometer spatial resolution were carried out at a table top soft X-ray plasma source (2.2-5.2 nm). The investigated system was the lyotropic liquid crystal C(16)E(7)/paraffin/glycerol/formamide/IR 5. Usually, major changes in physical, chemical, and/or optical properties of the sample occur as a result of structural changes and shrinking morphology. Here, these effects occur as a consequence of the energy absorption in the sample upon optical laser excitation in the IR regime. The liquid crystal shows changes in the structural response within few hundred nanoseconds showing a time decay of 182 ns. A decrease of the Bragg peak diffracted intensity of 30% and a coherent macroscopic movement of the Bragg reflection are found as a response to the optical pump. The Bragg reflection movement is established to be isotropic and diffusion controlled (1 micros). Structural processes are analyzed in the Patterson analysis framework of the time-varying diffraction peaks revealing that the inter-lamellar distance increases by 2.7 A resulting in an elongation of the coherently expanding lamella crystallite. The present studies emphasize the possibility of applying TR-SXRD techniques for studying the mechanical dynamics of nanosystems.

  7. Chiral structure of thiolate-protected 28-gold-atom nanocluster determined by X-ray crystallography.

    Science.gov (United States)

    Zeng, Chenjie; Li, Tao; Das, Anindita; Rosi, Nathaniel L; Jin, Rongchao

    2013-07-10

    We report the crystal structure of a new nanocluster formulated as Au28(TBBT)20, where TBBT = 4-tert-butylbenzenethiolate. It exhibits a rod-like Au20 kernel consisting of two interpenetrating cuboctahedra. The kernel is protected by four dimeric "staples" (-SR-Au-SR-Au-SR-) and eight bridging thiolates (-SR-). The unit cell of Au28(TBBT)20 single crystals contains a pair of enantiomers. The origin of chirality is primarily rooted in the rotating arrangement of the four dimeric staples as well as the arrangement of the bridging thiolates (quasi-D2 symmetry). The enantiomers were separated by chiral HPLC and characterized by circular dichroism spectroscopy.

  8. Lanthanide complexes of macrocyclic polyoxovanadates by VO4 units: synthesis, characterization, and structure elucidation by X-ray crystallography and EXAFS spectroscopy.

    Science.gov (United States)

    Nishio, Masaki; Inami, Shinnosuke; Katayama, Misaki; Ozutsumi, Kazuhiko; Hayashi, Yoshihito

    2012-01-16

    Reactions of a tetravanadate anion, [V(4)O(12)](4-), with a series of lanthanide(III) salts yield three types of lanthanide complexes of macrocyclic polyoxovanadates: (Et(4)N)(6)[Ln(III)V(9)O(27)] [Ln = Nd (1), Sm (2), Eu (3), Gd (4), Tb (5), Dy (6)], (Et(4)N)(5)[(H(2)O)Ho(III)(V(4)O(12))(2)] (7), and (Et(4)N)(7)[Ln(III)V(10)O(30)] [Ln = Er (8), Tm (9), Yb (10), Lu (11)]. Lanthanide complexes 1-11 are isolated and characterized by IR, elemental analysis, single-crystal X-ray diffraction, and extended X-ray absorption fine structure spectroscopy (EXAFS). Lanthanide complexes 1-6 are composed of a square-antiprism eight-coordinated Ln(III) center with a macrocyclic polyoxovanadate that is constructed from nine VO(4) tetrahedra through vertex sharing. The structure of 7 is composed of a seven-coordinated Ho(III) center, which exhibits a capped trigonal-prism coordination environment by the sandwiching of two cyclic tetravanadates with a capping H(2)O ligand. Lanthanide complexes 8-11 have a six-coordinated Ln(III) center with a 10-membered vanadate ligand. The structural trend to adopt a larger coordination number for a larger lanthanide ion among the three types of structures is accompanied by a change in the vanadate ring sizes. These lanthanide complexes are examined by EXAFS spectroscopies on lanthanide L(III) absorption edges, and the EXAFS oscillations of each of the samples in the solid state and in acetonitrile are identical. The Ln-O and Ln···V bond lengths obtained from fits of the EXAFS data are consistent with the data from the single-crystal X-ray studies, reflecting retention of the structures in acetonitrile.

  9. Crystallization and preliminary X-ray analysis of alginate importer from Sphingomonas sp. A1.

    Science.gov (United States)

    Maruyama, Yukie; Itoh, Takafumi; Nishitani, Yu; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku

    2012-03-01

    Sphingomonas sp. A1 directly incorporates alginate polysaccharides through a 'superchannel' comprising a pit on the cell surface, alginate-binding proteins in the periplasm and an ABC transporter (alginate importer) in the inner membrane. Alginate importer, consisting of four subunits, AlgM1, AlgM2 and two molecules of AlgS, was crystallized in the presence of the binding protein AlgQ2. Preliminary X-ray analysis showed that the crystal diffracted to 3.3 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 72.5, b = 136.8, c = 273.3 Å, suggesting the presence of one complex in the asymmetric unit.

  10. Improving the energy resolution of bent crystal X-ray spectrometers with position-sensitive detectors.

    Science.gov (United States)

    Honkanen, Ari Pekka; Verbeni, Roberto; Simonelli, Laura; Moretti Sala, Marco; Al-Zein, Ali; Krisch, Michael; Monaco, Giulio; Huotari, Simo

    2014-07-01

    Wavelength-dispersive high-resolution X-ray spectrometers often employ elastically bent crystals for the wavelength analysis. In a preceding paper [Honkanen et al. (2014). J. Synchrotron Rad. 21, 104-110] a theory for quantifying the internal stress of a macroscopically large spherically curved analyser crystal was presented. Here the theory is applied to compensate for the corresponding decrease of the energy resolution. The technique is demonstrated with a Johann-type spectrometer using a spherically bent Si(660) analyser in near-backscattering geometry, where an improvement in the energy resolution from 1.0 eV down to 0.5 eV at 9.7 keV incident photon energy was observed.

  11. Overexpression, purification, crystallization and preliminary X-ray studies of Vibrio cholerae EpsG

    Energy Technology Data Exchange (ETDEWEB)

    Jens, Jason; Raghunathan, Kannan; Vago, Frank; Arvidson, Dennis; (MSU)

    2010-01-12

    EpsG is the major pseudopilin protein of the Vibrio cholerae type II secretion system. An expression plasmid that encodes an N-terminally truncated form of EpsG with a C-terminal noncleavable His tag was constructed. Recombinant EpsG was expressed in Escherichia coli; the truncated protein was purified and crystallized by hanging-drop vapor diffusion against a reservoir containing 6 mM zinc sulfate, 60 mM MES pH 6.5, 15% PEG MME 550. The crystals diffracted X-rays to a resolution of 2.26 {angstrom} and belonged to space group P2{sub 1}, with unit-cell parameters a = 88.61, b = 70.02, c = 131.54 {angstrom}.

  12. Crystallization and preliminary X-ray structure analysis of human ribosomal protein L30e.

    Science.gov (United States)

    Kawaguchi, Akiko; Ose, Toyoyuki; Yao, Min; Tanaka, Isao

    2011-12-01

    Many functions have been reported for the eukaryotic ribosomal protein L30e. L30e makes several inter-subunit and intra-subunit interactions with protein or RNA components of the 80S ribosome. Yeast L30e has been shown to bind to its own transcript to autoregulate expression at both the transcriptional and the translational levels. Furthermore, it has been reported that mammalian L30e is a component of the selenocysteine-incorporation machinery by binding to the selenocysteine-insertion sequence on mRNA. As high-resolution crystal structures of mammalian L30e are not available, the purification, crystallization and X-ray structure analysis of human L30e are presented here.

  13. Crystallization and preliminary X-ray analysis of glutathione transferases from cyanobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Feil, Susanne C.; Tang, Julian; Hansen, Guido; Gorman, Michael A.; Wiktelius, Eric; Stenberg, Gun; Parker, Michael W.; (SVIMR-A); (Uppsala)

    2009-05-08

    Glutathione S-transferases (GSTs) are a group of multifunctional enzymes that are found in animals, plants and microorganisms. Their primary function is to remove toxins derived from exogenous sources or the products of metabolism from the cell. Mammalian GSTs have been extensively studied, in contrast to bacterial GSTs which have received relatively scant attention. A new class of GSTs called Chi has recently been identified in cyanobacteria. Chi GSTs exhibit a high glutathionylation activity towards isothiocyanates, compounds that are normally found in plants. Here, the crystallization of two GSTs are presented: TeGST produced by Thermosynechococcus elongates BP-1 and SeGST from Synechococcus elongates PCC 6301. Both enzymes formed crystals that diffracted to high resolution and appeared to be suitable for further X-ray diffraction studies. The structures of these GSTs may shed further light on the evolution of GST catalytic activity and in particular why these enzymes possess catalytic activity towards plant antimicrobial compounds.

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

    Science.gov (United States)

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

    2010-12-01

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

  15. Performance of bent-crystal x-ray microscopes for high energy density physics research.

    Science.gov (United States)

    Schollmeier, Marius S; Geissel, Matthias; Shores, Jonathon E; Smith, Ian C; Porter, John L

    2015-06-01

    We present calculations for the field of view (FOV), image fluence, image monochromaticity, spectral acceptance, and image aberrations for spherical crystal microscopes, which are used as self-emission imaging or backlighter systems at large-scale high energy density physics facilities. Our analytic results are benchmarked with ray-tracing calculations as well as with experimental measurements from the 6.151 keV backlighter system at Sandia National Laboratories. The analytic expressions can be used for x-ray source positions anywhere between the Rowland circle and object plane. This enables quick optimization of the performance of proposed but untested, bent-crystal microscope systems to find the best compromise between FOV, image fluence, and spatial resolution for a particular application.

  16. Intramolecular hydrogen bonds in crystals of thiophosphorylbenzopyrane derivatives X-ray and FT-IR studies

    Science.gov (United States)

    Rybarczyk-Pirek, Agnieszka J.; Dubis, Alina T.; Grabowski, Sławomir J.; Nawrot-Modranka, Jolanta

    2006-01-01

    The crystal structures of two new benzopyrane derivatives are analyzed and compared with previous X-ray investigations on related compounds. A particular attention is focused on intramolecular interactions. For the chromone derivatives ( 1 and 3) only one kind of interaction is possible, i.e., N-H⋯O, whereas for the coumarine derivatives ( 2 and 4) two types of intramolecular hydrogen bonding are observed - N-H⋯O and O-H⋯N. Two types of H-bond for coumarine derivatives are the result of the existence of two tautomeric forms - enamine and iminoenol. Combined spectroscopic, NMR and IR measurements confirm such tautomeric equilibrium in solution. The influence of the additional intermolecular hydrogen bonds on the stabilization of tautomeric forms in crystals is also discussed here.

  17. Purification, crystallization and preliminary X-ray crystallographic studies of Drep2 CIDE domain.

    Science.gov (United States)

    Lee, Seung Mi; Park, Hyun Ho

    2014-10-01

    Drep2 is a novel nuclease from the fruit fly that might have a similar function in apoptosis to DFF40 and DFF45, which are primary players in apoptotic DNA fragmentation. Drep2 contains a conserved CIDE domain of ∼90 amino-acid residues that is involved in protein-protein interaction. In this study, the Drep2 CIDE domain was purified and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were then collected to a resolution of 2.3 Å. The crystals were found to belong to the orthorhombic space group P212121, with unit-cell parameters a = 50.28, b = 88.70, c = 113.37 Å.

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

    Science.gov (United States)

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

    2012-11-01

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

  19. Electron crystallography of three dimensional protein crystals

    NARCIS (Netherlands)

    Georgieva, Dilyana

    2008-01-01

    This thesis describes an investigation of the potential of electron diffraction for studying three dimensional sub-micro-crystals of proteins and pharmaceuticals. A prerequisite for using electron diffraction for structural studies is the predictable availability of tiny crystals. A method for grow

  20. Characterization of Pr:LuAG scintillating crystals for X-ray spectroscopy

    Science.gov (United States)

    Bertoni, R.; Bonesini, M.; Cervi, T.; Clemenza, M.; De Bari, A.; Falcone, A.; Mazza, R.; Menegolli, A.; Nastasi, M.; Rossella, M.

    2016-07-01

    The main features of the Pr doped Lu3Al5O12 (Pr:LuAG) scintillating crystals for X-ray spectroscopy applications have been studied using different radioactive sources and photo-detectors. Pr:LuAG is cheaper, compared to a Germanium detector, but with remarkable properties which make it useful for many applications, from fundamental physics measurements to the PET imaging for medical purposes: high density, elevate light yield, fast response, high energy resolution, no hygroscopicity. A sample of Pr:LuAG crystals with 14 mm×14 mm surface area and 13 mm thickness and a NaI crystal of the same surface and 26 mm thickness used as a reference have been characterized with several radioactive sources, emitting photons in the range 100-1000keV. Different light detectors were adopted for the Pr:LuAG studies, sensitive to its UV emission (peak at 310 nm): a 3 in. PMT (Hamamatsu R11065) and new arrays of Hamamatsu SiPM S13361, with siliconic resin as a window. Preliminary results are presented on the performance of the Pr:LuAG crystals, to be mounted in a 2 × 2 array to be tested in the 2015 run of the FAMU experiment at RIKEN-RAL muon facility. The goal is the detection of the X-rays (around 130 keV) emitted during the de-excitation processes of the muonic hydrogen after the excitation with an IR laser with wavelength set at the resonance of the hyperfine splitting, to measure the muonic atom proton radius with unprecedented precision.

  1. Double-crystal monochromator for a PF 60-period soft x-ray undulator (abstract)

    Science.gov (United States)

    Ishikawa, T.; Maezawa, H.; Nomura, M.; Ando, M.

    1989-07-01

    Since undulator light is sharply collimated itself, it can be effectively monochromatized by a perfect crystal. An x-ray double-crystal monochromator with a fixed exit has been designed and built for the use of undulator light from a 60-period undulator at Photon Factory (beamline 2A). Available Bragg angle ranges from 7° to 80°. Angle scan is made by means of a goniometer outside the vacuum chamber, with the finest step of 0.1 arcsec. Magnetic fluid is used as the vacuum seal of the feedthrough. The fixed exit beam position is kept by translating the second crystal along the two mechanical guides: one for normal and the other for parallel to the crystal surface. Adjustment of the parallelity of two crystals is made manually with flexible wires. Since a total power in the central coherent portion which is limited by a 1×1-mm2 slit is not so much, a stable operation is possible without cooling the crystal. Currently, InSb (111) reflection is used. The diffracting planes of the first cyrstal is 1° off from the surface and the second is the symmetric reflection. At its fifth harmonics, brilliant undulator light of approximately 1012 photons/s mm2 with 1-eV energy resolution is available (E=2 keV).

  2. Crystallization and X-ray diffraction analysis of human CLEC-2

    Energy Technology Data Exchange (ETDEWEB)

    Watson, Aleksandra A.; O’Callaghan, Christopher A., E-mail: chrisoc@ccmp.ox.ac.uk [Henry Wellcome Building of Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

    2005-12-01

    Recombinant human CLEC-2 was crystallized in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} and X-ray diffraction data were collected to 2.0 Å. The human C-type lectin-like protein CLEC-2 has recently been shown to be expressed on the surface of platelets and to function as a receptor for the snake-venom protein rhodocytin. The C-type lectin-like domain (CTLD) of CLEC-2 was expressed in Escherichia coli, refolded and purified. Crystals of this recombinant CLEC-2 were grown by sitting-drop vapour diffusion using polyethylene glycol (PEG) 6000 as a precipitant. After optimization, crystals were grown which diffracted to 2.0 Å using in-house radiation (λ = 1.5418 Å). These crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 35.407, b = 55.143, c = 56.078 Å. The presence of one molecule per asymmetric unit is consistent with a crystal volume per unit weight (V{sub M}) of 1.82 Å{sup 3} Da{sup −1} and a solvent content of 32.6%. These results suggest that crystals producing diffraction of this quality will be suitable for the structural determination of human CLEC-2.

  3. Crystallization and preliminary X-ray diffraction analysis of restriction endonuclease EcoRII

    Science.gov (United States)

    Karpova, E. A.; Meehan, E.; Pusey, M. L.; Chen, L.

    1999-01-01

    Crystals of the restriction endonuclease EcoRII have been obtained by the vapor-diffusion technique in the presence of ammonium sulfate or polyethylene glycol. The best crystals were grown with ammonium sulfate as a precipitant. Crystals with dimensions of up to 0.6 x 0. 6 x 0.6 mm have been observed. The crystals diffract to about 4.0 A resolution at a cryo-temperature of 100 K using a rotating-anode X-ray source and a Rigaku R-AXIS IV imaging-plate detector. The space group has been determined to be either I23 or I2(1)3, with unit-cell parameters a = b = c = 160.3 A, alpha = beta = gamma = 90 degrees. The crystal asymmetric unit contains two protein molecules, and self-rotation function analysis shows a pseudo-twofold symmetry relating the two monomers. Attempts to improve the resolution of crystal diffraction and to search for heavy-atom derivatives are under way.

  4. Determination By X-Ray Crystallography of the Three Dimensional- Structure of Acetylcholinesterase from Torpedo Electric Organ

    Science.gov (United States)

    1993-04-17

    organ tissue of Electrophorus electricus (27). Although preliminary characterization of these crystals was reported over 25 years ago by Chothia...The different oligomeric forms of AChE in the electric organ of the electric fish, Electrophorus and Torpedo, are structurally homologous to those in...attached phosphatidylinositol (PI) (10). This dirmer has a simpler quaternary structure than Electrophorus AChE, and its sequence and the arrangement of

  5. Flat Crystal x-ray Spectrometer for Quantitative Spectral Measurement in the 2-5 keV Region

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yang; ZHANG Ji-Yan; YANG Jia-Min; WEI Min-Xi; DENG Bo; ZHU Tuo; HU Zhi-Min; XIONG Gang; SHANG Wan-Li; KUANG Long-Yu; YANG Guo-Hong

    2011-01-01

    @@ A technique of fiat crystal x-ray spectrometer for quantitative spectral measurement is described.For the flat crystal spectrograph geometry, the quantitative reduction of relating the CCD counts back to the photon flux from the x-ray source is established.The absolute calibrations of the integral diffraction coefficients of the crystal and the CCD sensitivity make it possible to measure absolute photons flux within the energy range of 2000-5000 eV.The uncertainty analysis of the calibrations is carried out to obtain the energy resolved uncertainties of crystal and CCD.Thus, the experimentai spectra with spectral resolved intensity uncertainties are available.Then, a performing experiment of laser-produced Ti plasma is carried out and the absolute x-ray spectra with intensity uncertainty less than 8.5% are obtained.The technique is promising for absolute spectral measurement of high temperature plasmas in a kilo-electron-volt region.

  6. High-resolution X-ray focusing concave (elliptical) curved crystal spectrograph for laser-produced plasma

    Institute of Scientific and Technical Information of China (English)

    Shali xiao(肖沙里); Yingjun Pan(潘英俊); Xianxin Zhong(钟先信); Xiancai Xiong(熊先才); Guohong Yang(杨国洪); Zongli Liu(刘宗礼); Yongkun Ding(丁永坤)

    2004-01-01

    The X-ray spectrum emitted from laser-produced plasma contains plentiful information.X-ray spectrometer is a powerful tool for plasma diagnosis and studying the information and evolution of the plasma.X-ray concave(elliptical)curved crystals analyzer was designed and manufactured to investigate the properties of laser-produced plasma.The experiment was carried out on Mianyang Xingguang-ⅡFacility and aimed at investigating the characteristics of a high density iron plasma.Experimental results using KAP,LIF,PET,and MICA curved crystal analyzers are described,and the spectra of Au,Ti laser-produced plasma are shown.The focusing crystal analyzer clearly gave an increase in sensitivity over a flat crystal.

  7. Crystallization and preliminary X-ray analysis of ocr, the product of gene 0.3 of bacteriophage T7.

    Science.gov (United States)

    Sturrock, S S; Dryden, D T; Atanasiu, C; Dornan, J; Bruce, S; Cronshaw, A; Taylor, P; Walkinshaw, M D

    2001-11-01

    Ocr, the product of gene 0.3 of bacteriophage T7, prevents the action of restriction endonucleases of the host bacteria. The amino-acid sequence of ocr has less than 20% similarity to any protein of known three-dimensional structure. Ocr has been crystallized in a number of different crystal forms and X-ray data for the seleno-L-methionine-substituted form has been collected to a resolution of 1.8 A. The presence of caesium was found to be required for good crystal growth. Anomalous X-ray data was used to identify possible positions for Se and Cs atoms in the unit cell.

  8. Solvent-dependent assembly of discrete and continuous CoCl₂ adamantane-based ligand complexes: observations by CSI-mass spectrometry and X-ray crystallography.

    Science.gov (United States)

    Ohara, Kazuaki; Tominaga, Masahide; Azumaya, Isao; Yamaguchi, Kentaro

    2013-01-01

    Discrete and continuous coordination structures were obtained in single crystals of CoCl₂ and an adamantane-based bidentate ligand bearing imidazolyl groups, depending on the methanol concentration in a methanol-chloroform mixture. Single-crystal X-ray structure analysis revealed that the metal centers exhibited a tetrahedral geometry in the discrete complex and an octahedral geometry in the continuous metal complex. Conventional analytical methods, including UV-vis and NMR spectroscopy, could not identify those two complexes in solution. In contrast, cold-spray ionization mass spectrometry could detect differences between the discrete complex and the continuous metal complex, and ion peaks due to continuous ligand adducts were found only in the spectrum of the continuous metal complex.

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

    Energy Technology Data Exchange (ETDEWEB)

    Dobson, Renwick C. J., E-mail: rdobson@unimelb.edu.au; Atkinson, Sarah C. [Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010 (Australia); Gorman, Michael A. [St Vincents Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Newman, Janet M. [CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Parker, Michael W. [Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010 (Australia); St Vincents Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Perugini, Matthew A. [Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010 (Australia)

    2008-03-01

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

  10. Crystallization and preliminary X-ray crystallographic analysis of yeast NAD{sup +}-specific isocitrate dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Gang [Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); Taylor, Alexander B. [Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); McAlister-Henn, Lee [Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); Hart, P. John, E-mail: pjhart@biochem.uthscsa.edu [Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States)

    2005-05-01

    Yeast NAD{sup +}-isocitrate dehydrogenase has been purified and crystallized using sodium citrate, a competitive inhibitor of the enzyme, as a precipitant. Preliminary X-ray analyses indicate the molecular boundaries of the molecule and large continuous solvent channels in the crystal. NAD{sup +}-specific isocitrate dehydrogenase (IDH; EC 1.1.1.41) is a complex allosterically regulated enzyme in the tricarboxylic acid cycle. Yeast IDH is believed to be an octamer containing four catalytic IDH2 and four regulatory IDH1 subunits. Crystals of yeast IDH have been obtained and optimized using sodium citrate, a competitive inhibitor of the enzyme, as the precipitating agent. The crystals belong to space group R3, with unit-cell parameters a = 302.0, c = 112.1 Å. Diffraction data were collected to 2.9 Å from a native crystal and to 4.0 Å using multiwavelength anomalous diffraction (MAD) methods from an osmium derivative. Initial electron-density maps reveal large solvent channels and the molecular boundaries of the allosteric IDH multimer.

  11. Structural analysis of flexible proteins in solution by SmallAngle X-ray Scattering combined with crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Tsutakawa, Susan E.; Hura, Greg L.; Frankel, Ken A.; Cooper,Priscilla K.; Tainer, John A.

    2006-05-25

    In the last few years, SAXS of biological materials has been rapidly evolving and promises to move structural analysis to a new level. Recent innovations in SAXS data analysis allow ab initio shape predictions of proteins in solution. Furthermore, experimental scattering data can be compared to calculated scattering curves from the growing data base of solved structures and also identify aggregation and unfolded proteins. Combining SAXS results with atomic resolution structures enables detailed characterizations in solution of mass, radius, conformations, assembly, and shape changes associated with protein folding and functions. SAXS can efficiently reveal the spatial organization of protein domains, including domains missing from or disordered in known crystal structures, and establish cofactor or substrate-induced conformational changes. For flexible domains or unstructured regions that are not amenable for study by many other structural techniques, SAXS provides a unique technology. Here, we present SAXS shape predictions for PCNA that accurately predict a trimeric ring assembly and for a full-length DNA repair glycosylase with a large unstructured region. These new results in combination with illustrative published data show how SAXS combined with high resolution crystal structures efficiently establishes architectures, assemblies, conformations, and unstructured regions for proteins and protein complexes in solution.

  12. Soft x-ray backlighting of cryogenic implosions using a narrowband crystal imaging system (invited).

    Science.gov (United States)

    Stoeckl, C; Bedzyk, M; Brent, G; Epstein, R; Fiksel, G; Guy, D; Goncharov, V N; Hu, S X; Ingraham, S; Jacobs-Perkins, D W; Jungquist, R K; Marshall, F J; Mileham, C; Nilson, P M; Sangster, T C; Shoup, M J; Theobald, W

    2014-11-01

    A high-performance cryogenic DT inertial confinement fusion implosion experiment is an especially challenging backlighting configuration because of the high self-emission of the core at stagnation and the low opacity of the DT shell. High-energy petawatt lasers such as OMEGA EP promise significantly improved backlighting capabilities by generating high x-ray intensities and short emission times. A narrowband x-ray imager with an astigmatism-corrected bent quartz crystal for the Si Heα line at ∼1.86 keV was developed to record backlit images of cryogenic direct-drive implosions. A time-gated recording system minimized the self-emission of the imploding target. A fast target-insertion system capable of moving the backlighter target ∼7 cm in ∼100 ms was developed to avoid interference with the cryogenic shroud system. With backlighter laser energies of ∼1.25 kJ at a 10-ps pulse duration, the radiographic images show a high signal-to-background ratio of >100:1 and a spatial resolution of the order of 10 μm. The backlit images can be used to assess the symmetry of the implosions close to stagnation and the mix of ablator material into the dense shell.

  13. X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors.

    Science.gov (United States)

    Catalano, Alessia; Luciani, Rosaria; Carocci, Alessia; Cortesi, Debora; Pozzi, Cecilia; Borsari, Chiara; Ferrari, Stefania; Mangani, Stefano

    2016-11-10

    Infections caused by Enterococcus faecalis (Ef) represent nowadays a relevant health problem. We selected Thymidylate synthase (TS) from this organism as a potential specific target for antibacterial therapy. We have previously demonstrated that species-specific inhibition of the protein can be achieved despite the relatively high structural similarity among bacterial TSs and human TS. We had previously obtained the EfTS crystal structure of the protein in complex with the metabolite 5-formyl-tetrahydrofolate (5-FTHF) suggesting the protein role as metabolite reservoir; however, protein-inhibitors complexes were still missing. In the present work we identified some inhibitors bearing the phthalimidic core from our in-house library and we performed crystallographic screening towards EfTS. We obtained two X-ray crystallographic structures: the first with a weak phthalimidic inhibitor bound in one subunit and 5-hydroxymethylene-6-hydrofolic acid (5-HMHF) in the other subunit; a second X-ray structure complex with methotrexate. The structural information achieved confirm the role of EfTS as an enzyme involved in the folate pool system and provide a structural basis for structure-based drug design.

  14. Parabolic single-crystal diamond compound refractive lenses for coherent x-ray imaging (Conference Presentation)

    Science.gov (United States)

    Terentyev, Sergey; Blank, Vladimir D.; Polyakov, Sergey; Zholudev, Sergey; Snigirev, Anatoly A.; Polikarpov, Maxim; Kolodziej, Tomasz; Qian, Jun; Zhou, Hua; Shvyd'ko, Yuri V.

    2016-09-01

    We demonstrate parabolic single-crystal diamond compound refractive lenses [1] designed for coherent x-ray imaging resilient to extreme thermal and radiation loading expected from next generation light sources. To ensure the preservation of coherence and resilience, the lenses are manufactured from the highest-quality single-crystalline synthetic diamond material grown by a high-pressure high-temperature technique. Picosecond laser milling is applied to machine lenses to parabolic shapes with a 1-micron precision and surface roughness. A compound refractive lens comprised of six lenses with a radius of curvature R=200 microns at the vertex of the parabola and a geometrical aperture A=900 microns focuses 10 keV x-ray photons from an undulator source at the Advanced Photon Source facility to a focal spot size of 10x40 microns^2 with a gain factor of 100. [1] S. Terentyev, V. Blank, S. Polyakov, S. Zholudev, A. Snigirev, M. Polikarpov, T. Kolodziej, J. Qian, H. Zhou, and Yu. Shvyd'ko Applied Physics Letters 107, 111108 (2015); doi: 10.1063/1.4931357

  15. On the possibility of using X-ray Compton scattering to study magnetoelectrical properties of crystals

    Energy Technology Data Exchange (ETDEWEB)

    Collins, S. P., E-mail: steve.collins@diamond.ac.uk; Laundy, D.; Connolley, T.; Laan, G. van der; Fabrizi, F. [Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE (United Kingdom); Janssen, O. [Department of Physics, New York University, New York, NY 10003 (United States); Cooper, M. J. [Department of Physics, University of Warwick, CV4 7AL (United Kingdom); Ebert, H.; Mankovsky, S. [Universität München, Department Chemie, Haus E2.033, Butenandtstrasse 5-13, D-81377 München (Germany)

    2016-02-16

    The possibility of using X-ray Compton scattering to reveal antisymmetric components of the electron momentum density, as a fingerprint of magnetoelectric sample properties, is investigated experimentally and theoretically by studying the polar ferromagnet GaFeO{sub 3}. This paper discusses the possibility of using Compton scattering – an inelastic X-ray scattering process that yields a projection of the electron momentum density – to probe magnetoelectrical properties. It is shown that an antisymmetric component of the momentum density is a unique fingerprint of such time- and parity-odd physics. It is argued that polar ferromagnets are ideal candidates to demonstrate this phenomenon and the first experimental results are shown, on a single-domain crystal of GaFeO{sub 3}. The measured antisymmetric Compton profile is very small (≃ 10{sup −5} of the symmetric part) and of the same order of magnitude as the statistical errors. Relativistic first-principles simulations of the antisymmetric Compton profile are presented and it is shown that, while the effect is indeed predicted by theory, and scales with the size of the valence spin–orbit interaction, its magnitude is significantly overestimated. The paper outlines some important constraints on the properties of the antisymmetric Compton profile arising from the underlying crystallographic symmetry of the sample.

  16. A synchrotron small-angle X-ray scattering study of order/disorder in colloidal crystals

    NARCIS (Netherlands)

    Dolbnya, Igor Petrovich

    2004-01-01

    The present work reports results of a detailed x-ray diffraction study of the structure and long-range order of colloidal crystals, self-grown in suspensions of quartz spheres with diameter of about a quarter of a micron. The crystals are found to consist of a randomly-stacked sequence of hexagonal

  17. Crystallization and Preliminary X-ray Diffraction Analysis of the Glucuronoyl Esterase Catalytic Domain from Hypocrea jecorina

    Science.gov (United States)

    The catalytic domain of the glucuronoyl esterase from Hypocrea jecorina (anamorph Trichoderma reesei) was over-expressed, purified, and crystallized by sitting-drop vapor-diffusion method using 1.4 M sodium/potassium phosphate pH 6.9. Crystals had space group P212121 and X-ray diffraction data were...

  18. Statistical dynamical theory of X-ray diffraction in the Bragg case: application to triple-crystal diffractometry

    Science.gov (United States)

    Pavlov; Punegov

    2000-05-01

    The statistical dynamical theory of X-ray diffraction is developed for a crystal containing statistically distributed microdefects. Fourier-component equations for coherent and diffuse (incoherent) scattered waves have been obtained in the case of so-called triple-crystal diffractometry. New correlation lengths and areas are introduced for characterization of the scattered volume.

  19. AG, TL, and IRSL dosimetric properties in X-ray irradiated HPHT diamond crystals

    Energy Technology Data Exchange (ETDEWEB)

    Gil-Tolano, M.I. [Programa de Posgrado, Departamento de Investigacion en Fisica, Universidad de Sonora, A. P. 5-088, Hermosillo, Sonora, 83190, Mexico (Mexico); Melendrez, R.; Lancheros-Olmos, J.C.; Soto-Puebla, D.; Chernov, V.; Pedroza-Montero, M.; Barboza-Flores, M. [Departamento de Investigacion en Fisica, Universidad de Sonora, A. P. 5-088, Hermosillo, Sonora, 83190, Mexico (Mexico); Castaneda, B. [Departamento de Fisica, Universidad de Sonora, Blvd. Luis Encinas y Rosales S/N, Hermosillo, Sonora, 83000, Mexico (Mexico)

    2014-10-15

    HPHT diamonds have been studied for several years for their potential in different applications. In previous studies it has been found that the thermoluminescence (TL) glow curves of ''as-grown'' HPHT diamonds are non-reproducible. In this work, we study the afterglow (AG), thermoluminescent (TL), and optically stimulated luminescence (OSL) response of commercial samples of synthetic HPHT type-Ib diamond crystals exposed to X-ray irradiation (0.75 mA, 35 kV) at a dose rate of 0.624 Gy/s, after a high gamma ({sup 60}Co) dose irradiation of 500 kGy followed by a thermal treatment at 1073 K for 1 h in nitrogen atmosphere. Deconvolution of the TL glow curves shows four peaks, located around 379, 509, 561, and 609 K. The crystals exhibit evident AG recorded for 300 s immediately after X-ray irradiation, due to the thermal emptying of the traps responsible for the low-temperature TL peaks (below 400 K). The stimulation of irradiated crystals with 870-nm light, creates pronounced OSL and destroys all TL peaks with the exception of the high-temperature peak at 609 K. The dose responses of the integrated AG, TL, and OSL are linear in the range of 0.6-5 Gy and saturated at higher doses. The reproducibility of AG, TL, and OSL measurements is about 5%. The fading in the first hour of storage in dark conditions at RT of TL signal of HPHT diamond is mainly associated to the emptying of the traps responsible for the 379-K TL peaks. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. Quaternary association in -prism I fold plant lectins: Insights from X-ray crystallography, modelling and molecular dynamics

    Indian Academy of Sciences (India)

    Alok Sharma; Mamannamana Vijayan

    2011-12-01

    Dimeric banana lectin and calsepa, tetrameric artocarpin and octameric heltuba are mannose-specific -prism I fold lectins of nearly the same tertiary structure. MD simulations on individual subunits and the oligomers provide insights into the changes in the structure brought about in the protomers on oligomerization, including swapping of the N-terminal stretch in one instance. The regions that undergo changes also tend to exhibit dynamic flexibility during MD simulations. The internal symmetries of individual oligomers are substantially retained during the calculations. Energy minimization and simulations were also carried out on models using all possible oligomers by employing the four different protomers. The unique dimerization pattern observed in calsepa could be traced to unique substitutions in a peptide stretch involved in dimerization. The impossibility of a specific mode of oligomerization involving a particular protomer is often expressed in terms of unacceptable steric contacts or dissociation of the oligomer during simulations. The calculations also led to a rationale for the observation of a heltuba tetramer in solution although the lectin exists as an octamer in the crystal, in addition to providing insights into relations among evolution, oligomerization and ligand binding.

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

    Science.gov (United States)

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

    2012-09-01

    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.

  2. Cloning, expression, crystallization and preliminary X-ray data analysis of norcoclaurine synthase from Thalictrum flavum

    Energy Technology Data Exchange (ETDEWEB)

    Pasquo, Alessandra [ENEA Casaccia Research Centre, Dipartimento BIOTEC, Sezione Genetica e Genomica Vegetale, PO Box 2400, I-00100 Rome (Italy); Bonamore, Alessandra; Franceschini, Stefano; Macone, Alberto; Boffi, Alberto; Ilari, Andrea, E-mail: andrea.ilari@uniroma1.it [Istituto di Biologia e Patologia Molecolari, CNR (IBPM) and Department Of Biochemical Sciences, University of Roma ‘La Sapienza’, Piazza Aldo Moro 5, 00179 Roma (Italy); ENEA Casaccia Research Centre, Dipartimento BIOTEC, Sezione Genetica e Genomica Vegetale, PO Box 2400, I-00100 Rome (Italy)

    2008-04-01

    The cloning, expression, crystallization and preliminary X-ray data analysis of norcoclaurine synthase from T. flavum, a protein which catalyzes the first committed step in the biosynthesis of benzylisoquinoline alkaloids, are reported. Norcoclaurine synthase (NCS) catalyzes the condensation of 3,4-dihydroxyphenylethylamine (dopamine) and 4-hydroxyphenylacetaldehyde (4-HPAA) as the first committed step in the biosynthesis of benzylisoquinoline alkaloids in plants. The protein was cloned, expressed and purified. Crystals were obtained at 294 K by the hanging-drop vapour-diffusion method using ammonium sulfate and sodium chloride as precipitant agents and diffract to better than 3.0 Å resolution using a synchrotron-radiation source. The crystals belong to the trigonal space group P3{sub 1}21, with unit-cell parameters a = b = 86.31, c = 118.36 Å. A selenomethionine derivative was overexpressed, purified and crystallized in the same space group. A complete MAD data set was collected at 2.7 Å resolution. The model is under construction.

  3. Expression, crystallization and preliminary X-ray diffraction studies of recombinant Clostridium perfringens β2-toxin

    Energy Technology Data Exchange (ETDEWEB)

    Gurjar, Abhijit A. [Department of Veterinary and Biomedical Science, The Pennsylvania State University (United States); Yennawar, Neela H.; Yennawar, Hemant P. [Macromolecular X-ray Crystallography Facility, The Pennsylvania State University (United States); Rajashankar, Kanagalaghatta R. [Argonne National Laboratory (United States); Hegde, Narasimha V.; Jayarao, Bhushan M., E-mail: bmj3@psu.edu [Department of Veterinary and Biomedical Science, The Pennsylvania State University (United States)

    2007-06-01

    The cloning, expression, purification and crystallization of recombinant Clostridium perfringens β2-toxin is described. The crystals diffracted to 2.9 Å resolution. Clostridium perfringens is a Gram-positive sporulating anaerobic bacterium that is responsible for a wide spectrum of diseases in animals, birds and humans. The virulence of C. perfringens is associated with the production of several enterotoxins and exotoxins. β2-toxin is a 28 kDa exotoxin produced by C. perfringens. It is implicated in necrotic enteritis in animals and humans, a disease characterized by a sudden acute onset with lethal hemorrhagic mucosal ulceration. The recombinant expression, purification and crystallization of β2-toxin using the batch-under-oil technique are reported here. Native X-ray diffraction data were obtained to 2.9 Å resolution on a synchrotron beamline at the F2 station at Cornell High Energy Synchrotron Source (CHESS) using an ADSC Quantum-210 CCD detector. The crystals belong to space group R3, with a dimer in the asymmetric unit; the unit-cell parameters are a = b = 103.71, c = 193.48 Å, α = β = 90, γ = 120° using the hexagonal axis setting. A self-rotation function shows that the two molecules are related by a noncrystallographic twofold axis with polar angles ω = 90.0, ϕ = 210.3°.

  4. Crystallization and X-ray diffraction analysis of recombinant Coprinus cinereus peroxidase.

    Science.gov (United States)

    Petersen, J F; Tams, J W; Vind, J; Svensson, A; Dalbøge, H; Welinder, K G; Larsen, S

    1993-08-01

    Crystals suitable for an X-ray diffraction investigation have been obtained of recombinant Coprinus cinereus peroxidase expressed in Aspergillus oryzae. The crystals were grown by the hanging drop method with polyethylene glycol 6000 as the precipitant. A pH range from 6.2 to 8.0 and CaCl2 or MgCl2 present at a concentration of 0.35 M were essential for the crystal growth. A metastable monoclinic modification can be obtained under certain conditions, and with variations in temperature they are transformed into a stable orthorhombic modification. With CaCl2 as the additive, the unit cell dimensions were a = 74.9 A, b = 76.8 A and c = 128.2 A. With two peroxidase molecules per asymmetric unit, the solvent content is 49% (v/v). In the diffraction pattern, the reflections Okl are systematically very weak for k = 2n + 1. Combined with an analysis of the Patterson function, this showed that the two independent molecules are related by the pseudotranslational symmetry 0.29a + 0.5b. The possible space groups are P2(1)2(1)2(1) or P2(1)22(1) because of this pseudosymmetry. The crystals diffract to a resolution of 2.9 A.

  5. Perfection of Apoferritin Crystals: An Advanced X-Ray Imaging and Diffraction Study

    Science.gov (United States)

    Hu, Z. W.; Thomas, B. R.; Chernov, A. A.; Chu, Y. S.

    2003-01-01

    Ferritin is a well-known iron-storage protein, and is a spherical shell that consists of 24 identical subunits packed in a 432 symmetry. The typically large protein size and its distinction from lysozyme as to chemical and physical characteristics make ferritin an attractive model protein for crystal growth and perfection investigation-as an alternative to the most widely studied lysozyme. In this contribution, the latest results obtained from coherence-based x-ray diffraction imaging and diffraction experiments will be presented on octahedral apoferritin (a demetalized form of ferritin) crystals grown from various growth conditions. Crystal specimens, which have the measured rocking-curve widths varying from a few arcseconds to several tens arcseconds (or more), are comparatively examined by intrinsically highly sensitive mapping of lattice perfection and defects. The richness of the observed defects and growth features offers insight into perfection and growth of protein crystals. Beautiful interference fringe patterns formed in diffraction images and fine oscillation structure of rocking curves observed will be discussed for understanding of physical origins and the underlying impact.

  6. Crystallization and preliminary X-ray diffraction analysis of human adenovirus

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, V.S.; Natchiar, S.K.; Gritton, L.; Mullen, T.-M.; Stewart, P.L.; Nemerow, G.R. (Scripps); (Vanderbilt)

    2010-07-22

    Replication-defective and conditionally replicating adenovirus (AdV) vectors are currently being utilized in {approx}25% of human gene transfer clinical trials. Unfortunately, progress in vector development has been hindered by a lack of accurate structural information. Here we describe the crystallization and preliminary X-ray diffraction analysis of a HAdV5 vector that displays a short flexible fiber derived from HAdV35. Crystals of Ad35F were grown in 100 mM HEPES pH 7.0, 200 mM Ca(OAc){sub 2}, 14% PEG 550 MME, 15% glycerol in 100 mM Tris-HCl 8.5. Freshly grown crystals diffracted well to 4.5 {angstrom} resolution and weakly to 3.5 {angstrom} at synchrotron sources. HAdV crystals belong to space group P1 with unit cell parameters a = 854.03 {angstrom}, b = 855.17 {angstrom}, c = 865.24 {angstrom}, {alpha} = 119.57{sup o}, {beta} = 91.71{sup o}, {gamma} = 118.08{sup o} with a single particle in the unit cell. Self-rotation and locked-rotation function analysis allowed the determination of the particle orientation. Molecular replacement, density modification and phase-extension procedures are being employed for structure determination.

  7. A focussing iron line crystal spectrometer for Spacelab. [cosmic X-ray detection

    Science.gov (United States)

    Catura, R. C.; Culhane, J. L.; Rapley, C. G.; Gabriel, A. H.; Walker, A. B. C., Jr.; Woodgate, B. E.

    1977-01-01

    A crystal spectrometer system is described which employs conical focusing of 12 curved LiF crystal panels to minimize the detector size and reduce the background counting rate. The wavelength range from 1.70 to 1.98 A is covered, including the resonance lines of Fe XXV and Fe XXVI as well as the Fe I K-alpha line and absorption edge. Operation of the spectrometer is discussed, noting that diffracted X-rays are registered in one-dimensional position-sensitive detectors and that the arrival position of a photon in a detector is related to its wavelength due to the fixed curvature of the crystal panels in the dispersion plane. Some characteristics of the multianode position-sensitive detectors are reviewed along with the crystal arrangement and mounting. The instrument sensitivity is evaluated in relation to the strengths of 6.7-keV emission features detected by the Ariel 5 and OSO 8 proportional-counter spectrometers.

  8. X-ray Crystal Structures Elucidate the Nucleotidyl Transfer Reaction of Transcript Initiation Using Two Nucleotides

    Energy Technology Data Exchange (ETDEWEB)

    M Gleghorn; E Davydova; R Basu; L Rothman-Denes; K Murakami

    2011-12-31

    We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groups of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.

  9. Diffuse X-ray scattering from partially transformed 3C-SiC single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Dompoint, D., E-mail: deborah.dompoint@etu.unilim.fr [Science des Procedes Ceramiques et de Traitements de Surface (SPCTS), CNRS UMR 6638, Centre Europeen de la Ceramique, 12 rue atlantis, 87068 Limoges (France); Boulle, A. [Science des Procedes Ceramiques et de Traitements de Surface (SPCTS), CNRS UMR 6638, Centre Europeen de la Ceramique, 12 rue atlantis, 87068 Limoges (France); Galben-Sandulache, I.G.; Chaussende, D. [Laboratoire des Materiaux et du Genie Physique (LMGP), CNRS UMR 5628, Grenoble INP, Minatec, 3 parvis Louis Neel, BP 257, 38016 Grenoble Cedex 01 (France)

    2012-08-01

    The 3C-6H polytypic transition in 3C-SiC single crystals is studied by means of diffuse X-ray scattering (DXS) coupled with numerical simulations. It is shown that the presence of spatially correlated stacking faults (characteristic of this type of re-stacking transition) gives rise to extended diffuse scattering in the reciprocal space perpendicularly to the fault plane. The simulation of the diffuse intensity allows to determine both the volume fraction of transformed material and the transformation level within these regions. It is further shown that the evolution with time and temperature of the transition implies the multiplication and glide of partial dislocations, the kinetics of which are quantified by means of DXS.

  10. Crystal structure of trirubidium citrate from laboratory X-ray powder diffraction data and DFT comparison.

    Science.gov (United States)

    Rammohan, Alagappa; Kaduk, James A

    2017-02-01

    The crystal structure of trirubidium citrate, 3Rb(+)·C6H5O7(3-), has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The two independent Rb(+) cations are seven- and eight-coordinate, with bond-valence sums of 0.99 and 0.92 valence units. The coordination polyhedra share edges and corners to form a three-dimensional framework. The only hydrogen bond is an intra-molecular one between the hy-droxy group and the central carboxyl-ate, with graph set S(5). The hydro-phobic methyl-ene groups lie in pockets in the framework.

  11. Crystal structure of trirubidium citrate from laboratory X-ray powder diffraction data and DFT comparison

    Science.gov (United States)

    Kaduk, James A.

    2017-01-01

    The crystal structure of trirubidium citrate, 3Rb+·C6H5O7 3−, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The two independent Rb+ cations are seven- and eight-coordinate, with bond-valence sums of 0.99 and 0.92 valence units. The coordination polyhedra share edges and corners to form a three-dimensional framework. The only hydrogen bond is an intra­molecular one between the hy­droxy group and the central carboxyl­ate, with graph set S(5). The hydro­phobic methyl­ene groups lie in pockets in the framework. PMID:28217353

  12. Synthesis, X-ray crystal structure and theoretical calculations of antileishmanial neolignan analogues

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Josenaide P. do; Santos, Lourivaldo S.; Carmo, Maria Carolina L. do; Brasil, Davi S.B.; Alves, Claudio N., E-mail: nahum@ufpa.b [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Inst. de Ciencias Exatas e Naturais; Santos, Regina Helena A.; Tozzo, Erica; Ferreira, Janaina G. [Universidade de Sao Paulo (IQSC/USP), Sao Carlos, SP (Brazil). Inst. de Quimica

    2010-07-01

    The synthesis and X-ray crystal diffraction structure of two analogues of neolignans, 2-(4-chlorophenyl)-1-phenylethanone (20) and 2-[(4-chlorophenyl)thio]-1-(3,4-dimethoxyphenyl) propan-1-one (12) is described. The compound 12 presents activity against intracellular Leishmania donovani and Leishmania amazonensis amastigotes that cause cutaneous and visceral leishmaniasis. In addition, the density functional theory (DFT) with the B3LYP hybrid functional was employed to calculate a set of molecular descriptors for nineteen synthetic analogues of neolignans with antileishmanial activities. Afterwards, the stepwise discriminant analysis was performed to investigate possible relationship between the molecular descriptors and biological activities. Through this analysis the compounds were classified into two groups active and inactive according to their degree of biological activities, and the more important properties were charges on some key atoms, electronic affinity and ClogP. (author)

  13. Crystal structure of defect-containing semiconductor nanocrystals. An X-ray diffraction study

    Energy Technology Data Exchange (ETDEWEB)

    Buljan, Maja [Karlova Univ., Prague (Czech Republic). Fakulta Matematicko-Fyzikalni; Institut Rudjer Boskovic, Zagreb (Croatia); Desnica, Uros V.; Radic, Nikola [Institut Rudjer Boskovic, Zagreb (Croatia); Drazic, Goran [Institut Jozef Stefan, Ljubljana (Slovenia); Matej, Zdenek; Vales, Vaclav; Holy, Vaclav [Karlova Univ., Prague (Czech Republic). Fakulta Matematicko-Fyzikalni

    2009-08-15

    Defects of crystal structure in semiconductor nanocrystals embedded in an amorphous matrix are studied by X-ray diffraction and a full-profile analysis of the diffraction curves based on the Debye formula. A new theoretical model is proposed, describing the diffraction from randomly distributed intrinsic and extrinsic stacking faults and twin blocks in the nanocrystals. The application of the model to full-profile analysis of experimental diffraction curves enables the determination of the concentrations of individual defect types in the nanocrystals. The method has been applied for the investigation of selforganized Ge nanocrystals in an SiO{sub 2} matrix, and the dependence of the structure quality of the nanocrystals on their deposition and annealing parameters was obtained. (orig.)

  14. Heteroaryl Chalcones: Design, Synthesis, X-ray Crystal Structures and Biological Evaluation

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2013-10-01

    Full Text Available Chalcone derivatives have attracted increasing attention due to their numerous pharmacological activities. Changes in their structures have displayed high degree of diversity that has proven to result in a broad spectrum of biological activities. The present study highlights the synthesis of some halogen substituted chalcones 3(a–i containing the 5-chlorothiophene moiety, their X-ray crystal structures and the evaluation of possible biological activities such as antibacterial, antifungal and reducing power abilities. The results indicate the tested compounds show a varied range of inhibition values against all the tested microbial strains. Compound 3c with a p-fluoro substituent on the phenyl ring exhibits elevated antimicrobial activity, whereas the compounds 3e and 3f displayed the least antimicrobial activities. The compounds 3d, 3e, 3f and 3i showed good ferric and cupric reducing abilities, and the compounds 3b and 3c showed the weakest reducing power in the series.

  15. Heteroaryl chalcones: design, synthesis, X-ray crystal structures and biological evaluation.

    Science.gov (United States)

    Kumar, C S Chidan; Loh, Wan-Sin; Ooi, Chin Wei; Quah, Ching Kheng; Fun, Hoong-Kun

    2013-10-15

    Chalcone derivatives have attracted increasing attention due to their numerous pharmacological activities. Changes in their structures have displayed high degree of diversity that has proven to result in a broad spectrum of biological activities. The present study highlights the synthesis of some halogen substituted chalcones 3(a-i) containing the 5-chlorothiophene moiety, their X-ray crystal structures and the evaluation of possible biological activities such as antibacterial, antifungal and reducing power abilities. The results indicate the tested compounds show a varied range of inhibition values against all the tested microbial strains. Compound 3c with a p-fluoro substituent on the phenyl ring exhibits elevated antimicrobial activity, whereas the compounds 3e and 3f displayed the least antimicrobial activities. The compounds 3d, 3e, 3f and 3i showed good ferric and cupric reducing abilities, and the compounds 3b and 3c showed the weakest reducing power in the series.

  16. Processing of X-ray snapshots from crystals in random orientations

    Energy Technology Data Exchange (ETDEWEB)

    Kabsch, Wolfgang, E-mail: kabsch@mpimf-heidelberg.mpg.de [Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg (Germany)

    2014-08-01

    A new method for the treatment of partial reflections from X-ray snapshots is implemented in the program package nXDS, which yields intensity data of almost the same quality as those obtained by the classical rotation method. A functional expression is introduced that relates scattered X-ray intensities from a still or a rotation snapshot to the corresponding structure-factor amplitudes. The new approach was implemented in the program nXDS for processing monochromatic diffraction images recorded by a multi-segment detector where each exposure could come from a different crystal. For images containing indexable spots, the intensities of the expected reflections and their variances are obtained by profile fitting after mapping the contributing pixel contents to the Ewald sphere. The varying intensity decline owing to the angular distance of the reflection from the surface of the Ewald sphere is estimated using a Gaussian rocking curve. This decline is dubbed ‘Ewald offset correction’, which is well defined even for still images. Together with an image-scaling factor and other corrections, an explicit expression is defined that predicts each recorded intensity from its corresponding structure-factor amplitude. All diffraction parameters, scaling and correction factors are improved by post-refinement. The ambiguous case of a lower point group than the lattice symmetry is resolved by a method reminiscent of the technique of ‘selective breeding’. It selects the indexing alternative for each image that yields, on average, the highest correlation with intensities from all other images. Processing a test set of rotation images by XDS and treating the same images by nXDS as snapshots of crystals in random orientations yields data of comparable quality, clearly indicating an anomalous signal from Se atoms.

  17. Demonstration of Single-Crystal Self-Seeded Two-Color X-Ray Free-Electron Lasers

    Energy Technology Data Exchange (ETDEWEB)

    Lutman, A. A.; Decker, F. -J; Arthur, J.; Chollet, M.; Feng, Y.; Hastings, J.; Huang, Z.; Lemke, H.; Nuhn, H. -D.; Marinelli, A.; Turner, J. L.; Wakatsuki, S.; Welch, J.; Zhu, D.

    2014-12-18

    A scheme for generating two simultaneous hard-x-ray free-electron laser pulses with a controllable difference in photon energy is described and then demonstrated using the self-seeding setup at the Linac Coherent Light Source (LCLS). The scheme takes advantage of the existing LCLS equipment, which allows two independent rotations of the self-seeding diamond crystal. The two degrees of freedom are used to select two nearby crystal reflections, causing two wavelengths to be present in the forward transmitted seeding x-ray pulse. The free-electron laser system must support amplification at both desired wavelengths.

  18. On the size of the secondary electron cloud in crystals irradiated by hard X-ray photons

    Science.gov (United States)

    Grum-Grzhimailo, Alexei N.; Pikuz, Tatiana; Faenov, Anatoly; Matsuoka, Takeshi; Ozaki, Norimasa; Albertazzi, Bruno; Pikuz, Sergei; Inubushi, Yuichi; Yabashi, Makina; Tono, Kensuke; Yumoto, Hirokatsu; Ohashi, Haruhiko; Ishikawa, Tetsuya; Kodama, Ryosuke

    2017-03-01

    A simple theoretical recipe is proposed to estimate the size of the secondary electron cloud, generated in matter by incoming hard X-ray photons. An exclusive response of the LiF crystal to deposited X-ray doses by proportional generation of secondary electrons, which cause creation of color centers density inside the crystal, provides a unique possibility to validate the theoretical predictions for the size of the electron cloud with submicron resolution. The radius of the electron cloud measured for 10.1 keV photons is in agreement with the theoretical predictions.

  19. Third-order nonlinear and linear time-dependent dynamical diffraction of X-rays in crystals.

    Science.gov (United States)

    Balyan, Minas K

    2016-07-01

    For the first time the third-order nonlinear time-dependent Takagi's equations of X-rays in crystals are obtained and investigated. The third-order nonlinear and linear time-dependent dynamical diffraction of X-rays spatially restricted in the diffraction plane pulses in crystals is investigated theoretically. A method of solving the linear and the third-order nonlinear time-dependent Takagi's equations is proposed. Based on this method, results of analytical and numerical calculations for both linear and nonlinear diffraction cases are presented and compared.

  20. X-ray investigation of gene-engineered human insulin crystallized from a solution containing polysialic acid

    Science.gov (United States)

    Timofeev, V. I.; Chuprov-Netochin, R. N.; Samigina, V. R.; Bezuglov, V. V.; Miroshnikov, K. A.; Kuranova, I. P.

    2010-01-01

    Attempts to crystallize the noncovalent complex of recombinant human insulin with polysialic acid were carried out under normal and microgravity conditions. Both crystal types belonged to the same space group, I213, with unit-cell parameters a = b = c = 77.365 Å, α = β = γ = 90.00°. The reported space group and unit-cell parameters are almost identical to those of cubic insulin reported in the PDB. The results of X-ray studies confirmed that the crystals obtained were cubic insulin crystals and that they contained no polysialic acid or its fragments. Electron-density maps were calculated using X-ray diffraction sets from earth-grown and microgravity-grown crystals and the three-dimensional structure of the insulin molecule was determined and refined. The conformation and secondary-structural elements of the insulin molecule in different crystal forms were compared. PMID:20208155

  1. Purification, crystallization and preliminary X-ray analysis of the membrane-bound [NiFe] hydrogenase from Allochromatium vinosum

    Energy Technology Data Exchange (ETDEWEB)

    Kellers, Petra; Ogata, Hideaki; Lubitz, Wolfgang, E-mail: lubitz@mpi-muelheim.mpg.de [Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr (Germany)

    2008-08-01

    This article describes the first successful crystallization of a membrane-bound [NiFe] hydrogenase isolated from a photosynthetic organism (A. vinosum). The crystals obtained produced diffraction patterns up to 2.5 Å resolution. The membrane-bound [NiFe] hydrogenase is a unique metalloprotein that is able to catalyze the reversible oxidation of hydrogen to protons and electrons during a complex reaction cycle. The [NiFe] hydrogenase was isolated from the photosynthetic purple sulfur bacterium Allochromatium vinosum and its crystallization and preliminary X-ray analysis are reported. It was crystallized by the hanging-drop vapour-diffusion method using sodium citrate and imidazole as crystallization agents. The crystals belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 205.00, b = 217.42, c = 120.44 Å. X-ray diffraction data have been collected to 2.5 Å resolution.

  2. Combining flat crystals, bent crystals and compound refractive lenses for high-energy X-ray optics.

    Science.gov (United States)

    Shastri, S D

    2004-03-01

    Compound refractive lenses (CRLs) are effective for collimating or focusing high-energy X-ray beams (50-100 keV) and can be used in conjunction with crystal optics in a variety of configurations, as demonstrated at the 1-ID undulator beamline of the Advanced Photon Source. As a primary example, this article describes the quadrupling of the output flux when a collimating CRL, composed of cylindrical holes in aluminium, is inserted between two successive monochromators, i.e. a modest-energy-resolution premonochromator followed by a high-resolution monochromator. The premonochromator is a cryogenically cooled divergence-preserving bent double-Laue Si(111) crystal device delivering an energy width DeltaE/E approximately 10(-3), which is sufficient for most experiments. The high-resolution monochromator is a four-reflection flat Si(111) crystal system resembling two channel-cuts in a dispersive arrangement, reducing the bandwidth to less than 10(-4), as required for some applications. Tests with 67 and 81 keV photon energies show that the high-resolution monochromator, having a narrow angular acceptance of a few microradians, exhibits a fourfold throughput enhancement due to the insertion of a CRL that reduces the premonochromatized beam's vertical divergence from 29 micro rad to a few microradians. The ability to focus high-energy X-rays with CRLs having long focal lengths (tens of meters) is also shown by creating a line focus of 70-90 micro m beam height in the beamline end-station with both the modest-energy-resolution and the high-energy-resolution monochromatic X-rays.

  3. Polarizable atomic multipole X-ray refinement: application to peptide crystals

    Energy Technology Data Exchange (ETDEWEB)

    Schnieders, Michael J. [Department of Chemistry, Stanford, CA 94305 (United States); Fenn, Timothy D. [Department of Molecular and Cellular Physiology, Stanford, CA 94305 (United States); Howard Hughes Medical Institute (United States); Pande, Vijay S., E-mail: pande@stanford.edu [Department of Chemistry, Stanford, CA 94305 (United States); Brunger, Axel T., E-mail: pande@stanford.edu [Department of Molecular and Cellular Physiology, Stanford, CA 94305 (United States); Howard Hughes Medical Institute (United States); Department of Chemistry, Stanford, CA 94305 (United States)

    2009-09-01

    A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.

  4. Single crystal X-ray diffraction studies of DNA and DNA-drug complexes

    CERN Document Server

    Todd, A K

    1999-01-01

    The structure of the brominated oligonucleotide d(ACGTACG(5-BrU)) sub 2 was solved using the multiwavelength anomalous diffraction (MAD) technique. The space group was P4 sub 3 2 sub 1 2, with unit cell a=b=43.60A, c=26.27A. This structure was an A-DNA, isomorphous with many other previously solved octomers. Single crystal X-ray diffraction data were collected from crystals of the intercalation complexes N-[2-(dimethylamino)ethyl] acridine-4-carboxamide (DACA), d(CGTACG) sub 2 and N-[2-(dimethylamino)ethyl] 9-aminoacridine-4-carboxamide (9- aminoDACA) and some of their derivatives. An attempt was made to solve the structure of the DACA derivative N-[2-(dimethylamino)butyl]-acridine-4-carboxamide (DACA4) by molecular replacement, using the crystal structure of the daunomycin d(CGTACG) sub 2 complex as a search model. Attempts were made to position the molecule in the unit cell based on an SIR map, knowledge of the symmetry and unit cell dimensions. The structure of the 9-amino-5-bromo DACA - d(CGT(5-BrU)CG) su...

  5. Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase

    Science.gov (United States)

    Milton, Morgan E.; Choe, Jun-yong; Honzatko, Richard B.; Nelson, Scott W.

    2015-01-01

    Infection by the parasite Plasmodium falciparum is the leading cause of malaria in humans. The parasite has a unique and essential plastid-like organelle called the apicoplast. The apicoplast contains a genome that undergoes replication and repair through the action of a replicative polymerase (apPOL). apPOL has no direct orthologs in mammalian polymerases and is therefore an attractive antimalarial drug target. No structural information exists for apPOL, and the Klenow fragment of Escherichia coli DNA polymerase I, which is its closest structural homolog, shares only 28% sequence identity. Here, conditions for the crystallization of and preliminary X-ray diffraction data from crystals of P. falciparum apPOL are reported. Data complete to 3.5 Å resolution were collected from a single crystal (2 × 2 × 5 µm) using a 5 µm beam. The space group P6522 (unit-cell parameters a = b = 141.8, c = 149.7 Å, α = β = 90, γ = 120°) was confirmed by molecular replacement. Refinement is in progress. PMID:25760711

  6. Crystal structure of nitarsone determined from synchrotron X-ray powder diffraction data

    Science.gov (United States)

    van der Lee, A.; Richez, P.; Tapiero, C.

    2005-05-01

    The crystal structure of nitarsone, 4-nitrophenylarsonic acid, a substitute for nifursol and dimetridazole in the prevention and treatment of turkey histomoniasis desease, has been determined from synchrotron X-ray powder diffraction data. Nitarsone crystallizes in the monoclinic space group P2 1/ n with unit cell parameters a=7.46413(5), b=25.68543(17), c=4.657388(32) Å, β=105.4670(5)°. The structure was solved using simulated annealing techniques by treating the molecule as a rigid body for which the configuration resulting from an energy minimization was used in slightly adapted form. Structure refinement treated the NO 2 and the AsO(OH) 2 groups as free groups, leading to final confidence factors Rp=0.059 and Rwp=0.071. The crystal structure contains 4 molecules per unit cell that are hydrogen bonded to form infinite chains of dimers running along the c-axis. Nitarsone's low toxicity when compared with inorganic sources of arsenic is explained by the existence of a partial double C-As bond (1.866(5) Å) which confers greater stability so that under physiological conditions nitarsone is not converted to mineral-like As V or III.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-11-19

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

  8. X-ray diffraction of protein crystal grown in a nano-liter scale droplet in a microchannel and evaluation of its applicability.

    Science.gov (United States)

    Maeki, Masatoshi; Yoshizuka, Saori; Yamaguchi, Hiroshi; Kawamoto, Masahide; Yamashita, Kenichi; Nakamura, Hiroyuki; Miyazaki, Masaya; Maeda, Hideaki

    2012-01-01

    We describe the technical aspects of the in-situ X-ray diffraction of a protein crystal prepared by a nanodroplet-based crystallization method. We were able to obtain diffraction patterns from a crystal grown in a capillary without any manipulation. Especially in our experimental approach, the crystals that moved to the nanodroplet interface were fixed strongly enough to carry out X-ray diffraction measurements that could be attributed to the high surface tension of the nanodroplet. The crystal was damaged by an indirect action of the X-rays because our in-situ X-ray diffraction measurement was carried out in the liquid phase without freezing the crystal; however, the obtained several diffraction patterns were of sufficiently fine quality for the crystal structure factors to be generated. We consider the technical examination presented in this paper to represent a seamless coupling of crystallization to X-ray analysis.

  9. Contrasting coordination behavior of Group 12 perchlorate salts with an acyclic N3O2 donor ligand by X-ray crystallography and (1)H NMR.

    Science.gov (United States)

    Tice, Daniel B; Pike, Robert D; Bebout, Deborah C

    2016-08-09

    An unbranched N3O2 ligand 2,6-bis[((2-pyridinylmethyl)oxy)methyl]pyridine (L1) was used to prepare new mononuclear heteroleptic Group 12 perchlorate complexes characterized by IR, (1)H NMR and X-ray crystallography. Racemic complexes with pentadentate L1 and one to four oxygens from either water or perchlorate bound to a metal ion were structurally characterized. Octahedral [Zn(L1)(OH2)](ClO4)2 (1) and pentagonal bipyramidal [Cd(L1)(OH2)(OClO3)]ClO4 (2) structures were found with lighter congeners. The polymorphic forms of [Hg(L1)(ClO4)2] characterized (3 in P1[combining macron] and 4 in P21/c) had a mix of monodentate, anisobidentate and bidentate perchlorates, providing the first examples of a tricapped trigonal prismatic Hg(ii) coordination geometry, as well as additional examples of a rare square antiprismatic Hg(ii) coordination geometry. Solution state (1)H NMR characterization of the Group 12 complexes in CD3CN indicated intramolecular reorganization remained rapid under conditions where intermolecular M-L1 exchange was slow on the chemical shift time scale for Zn(ii) and on the J(M(1)H) time scale for Cd(ii) and Hg(ii). Solution studies with more than one equivalent of ligand also suggested that a complex with a 1 : 2 ratio of M : L1 contributed significantly to solution equilibria with Hg(ii) but not the other metal ions. The behavior of related linear pentadentate ligands with Group 12 perchlorate salts is discussed.

  10. Isolation, purification, crystallization, and preliminary X-ray diffraction study of the crystals of HU protein from M. gallisepticum

    Science.gov (United States)

    Nikolaeva, A. Yu.; Timofeev, V. I.; Boiko, K. M.; Korzhenevskii, D. A.; Rakitina, T. V.; Dorovatovskii, P. V.; Lipkin, A. V.

    2015-11-01

    HU proteins are involved in bacterial DNA and RNA repair. Since these proteins are absent in cells of higher organisms, inhibitors of HU proteins can be used as effective and safe antibiotics. The crystallization conditions for the M. gallisepticum HU protein were found and optimized by the vapor-diffusion method. The X-ray diffraction data set was collected to 2.91 Å resolution from the crystals grown by the vapor-diffusion method on a synchrotron source. The crystals of the HU protein belong to sp. gr. P41212 and have the following unit-cell parameters: a = b = 97.94 Å, c = 77.92 Å, α = β = γ = 90°.

  11. Crystallization and preliminary X-ray diffraction study of phosphopantetheine adenylyltransferase from M. tuberculosis crystallizing in space group P32

    Science.gov (United States)

    Timofeev, V. I.; Chupova, L. A.; Esipov, R. S.; Kuranova, I. P.

    2015-09-01

    Crystals of M. tuberculosis phosphopantetheine adenylyltransferase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 2.00-Å resolution. The crystals belong to sp. gr. P32 and have the following unit-cell parameters: a = b = 106.47 Å, c = 71.32 Å, α = γ = 90°, β = 120°. The structure was solved by the molecular-replacement method. There are six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is a biologically active form of phosphopantetheine adenylyltransferase from M. tuberculosis.

  12. Neutron Nucleic Acid Crystallography.

    Science.gov (United States)

    Chatake, Toshiyuki

    2016-01-01

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

  13. CheShift-2 resolves a local inconsistency between two X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Sue, Shih-Che [Scripps Research Institute, Department of Molecular Biology (United States); Fraser, James S. [University of California, California Institute of Quantitative Biosciences (QB3) and Department of Cellular and Molecular Pharmacology (United States); Scheraga, Harold A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Dyson, H. Jane, E-mail: dyson@scripps.edu [Scripps Research Institute, Department of Molecular Biology (United States)

    2012-10-15

    Since chemical shifts provide important and relatively accessible information about protein structure in solution, a Web server, CheShift-2, was developed for structure interrogation, based on a quantum mechanics database of {sup 13}C{sup {alpha}} chemical shifts. We report the application of CheShift-2 to a local inconsistency between two X-ray crystal structures (PDB IDs 1IKN and 1NFI) of the complex between the p65/p50 heterodimer of NF{kappa}B and its inhibitor I{kappa}B{alpha}. The availability of NMR resonance assignments that included the region of the inconsistency provided an opportunity for independent validation of the CheShift-2 server. Application of the server showed that the {sup 13}C{sup {alpha}} chemical shifts measured for the Gly270-Pro281 sequence close to the C-terminus of I{kappa}B{alpha} were unequivocally consistent with the backbone structure modeled in the 1IKN structure, and were inconsistent with the 1NFI structure. Previous NOE measurements had demonstrated that the position of a tryptophan ring in the region immediately N-terminal in this region was not consistent with either structure. Subsequent recalculation of the local structure in this region, based on the electron density of the deposited structure factors for 1IKN, confirmed that the local backbone structure was best modeled by 1IKN, but that the rotamer of Trp258 is consistent with the 1NFI structure, including the presence of a hydrogen bond between the ring N{epsilon}H of Trp258 and the backbone carbonyl group of Gln278. The consensus between all of these measures suggests that the CheShift-2 server operates well under circumstances in which backbone chemical shifts are available but where local plasticity may render X-ray structural data ambiguous.

  14. X-ray Multiple Diffraction Topographic Imaging Technique For Growth History Study of Habit Modifying Impurity Doped Crystals

    Institute of Scientific and Technical Information of China (English)

    LAI X.; MA C.; K. J. Robert; M. C. Miller

    2004-01-01

    A novel crystal characterization instrument has been built up in which a combination of X-ray multiple diffraction and X-ray topography is applied to enabling the cross-correlation between micro-crystallographic symmetry and its spatial dependence in relation to lattice defects. This facility is used to examine, in a selfconsistent manner, growth sector-dependant changes to both the crystallographic structure and the lattice defects associated with the action of habit-modifying additives in a number of representative crystal growth systems. In addition, the new instrument can be used to probe micro-crystallographic aspects (such as distortion to crystal symmetry) and relate these in a spatially resolved manner to the crystal defect structure in crystals doped with known habit modifiers.

  15. Recombinant formate dehydrogenase from Arabidopsis thaliana: Preparation, crystal growth in microgravity, and preliminary X-ray diffraction study

    Energy Technology Data Exchange (ETDEWEB)

    Shabalin, I. G., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Serov, A. E.; Skirgello, O. E. [Moscow State University, Faculty of Chemistry (Russian Federation); Timofeev, V. I.; Samygina, V. R. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Popov, V. O. [Russian Academy of Sciences, Bach Institute of Biochemistry (Russian Federation); Tishkov, V. I. [Moscow State University, Faculty of Chemistry (Russian Federation); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-09-15

    Crystals of high-purity recombinant NAD{sup +}-dependent formate dehydrogenase from the higher plant Arabidopsis thaliana (AraFDH) were grown in microgravity in the Modul'-1 protein crystallization apparatus on the International Space Station. The space-grown crystals have larger sizes than those grown on Earth. X-ray diffraction data suitable for determining the three-dimensional structure were collected from the space-grown crystals to a resolution of 1.22 A using an X-ray synchrotron source. The crystals belong to sp. gr. P4{sub 3}2{sub 1}2; the unit-cell parameters are a = b = 107.865 A, c = 71.180 A, {alpha} = {beta} = {gamma} = 90 deg.

  16. Single-Crystal X-Ray Diffraction of Pyrope Garnet to 84 GPa

    Science.gov (United States)

    Finkelstein, G. J.; Dera, P. K.; Duffy, T. S.

    2012-12-01

    Garnets are characteristic minerals of many metamorphic and igneous rocks, and are also important upper-mantle constituents. Mg-rich (pyrope) garnets occur in both peridotite and eclogite compositions in the upper mantle. At high temperatures and pressures above 25 GPa, garnets transform to the perovskite structure. The post-garnet transition kinetics are sluggish, and in cold subducting slabs garnets could persist metastably at temperatures as high as 1700 K on geological timescales. These phases could add positive buoyancy to a subducting slab, inhibiting subduction. There has been minimal previous work on the 300 K compression behavior of aluminosilicate garnets at pressures higher than 10 GPa. In this work, we have collected single-crystal X-ray diffraction data on near end-member natural pyrope (Dora Maira pyrope) to 84 GPa. By extending the compression of pyrope to much higher pressures, we can better constrain the equation of state while also characterizing the structural response to such extreme pressures for the first time. Crystals were polished to ~5-10 μm in thickness, and loaded in a diamond anvil cell with gold foil and ruby balls as pressure calibrants. Helium was used as a pressure-transmitting medium. High-pressure single-crystal X-ray diffraction experiments were performed at the GSECARS 13-ID-D beamline of the Advanced Photon Source and the 12.2.2 beamline of the Advanced Light Source. Structure refinements were carried out successfully to the highest pressure using Shelx-97, extending the range over which the compression behavior of this material has been characterized by a factor of nearly three. Pyrope exhibits smooth compression behavior and no phase transitions over the investigated pressure range. A preliminary 3rd order Birch-Murnaghan equation of state was successfully fit to data up to 52 GPa. If the bulk modulus is fixed to 170 GPa, a value consistent with previous Brillouin and Ultrasonic studies, our data yields a pressure derivative

  17. Synthesis, X-ray crystal structures, thermal and electrochemical properties of thiosemicarbazidatodioxouranium(VI) complexes.

    Science.gov (United States)

    Sahin, Musa; Koca, Atıf; Ozdemir, Namık; Dinçer, Muharrem; Büyükgüngör, Orhan; Bal-Demirci, Tülay; Ulküseven, Bahri

    2010-11-14

    The stable uranyl complexes, [UO(2)(L)C(9)H(19)OH], were obtained from 3,5-dichlorosalicyl-(L(I)) and salicyl-aldehyde-S-propyl-thiosemicarbazones (L(II)) with substituted-salicylaldehyde in nonyl alcohol. The structures of the complexes have been characterized by elemental analysis, IR, (1)H NMR, conductivity, magnetic moment measurements, cyclic voltammetry, thermal gravimetric analysis and single crystal X-ray diffraction technique. The U(VI) centre is seven-coordinated in a distorted pentagonal bipyramidal geometry. The relative orientations of the nonyl alcohol and S-propyl group in the title complexes are completely different due to different crystal packing. Electrochemical behaviors of the thiosemicarbazone ligands and the uranyl complexes were studied using cyclic voltammetry and square wave voltammetry. Redox processes of the compounds are significantly influenced by the central metal ions and the nature of substituents on the thiosemicarbazones, which are important factors in controlling the redox properties. In situ spectroelectrochemical studies were employed to determine the colors and spectra of electro-generated species of the complexes.

  18. Crystallization of medium length 1-alcohols in mesoporous silicon: An X-ray diffraction study

    CERN Document Server

    Henschel, Anke; Knorr, Klaus

    2008-01-01

    The linear 1-alcohols n-C16H33OH, n-C17H35OH, n-C19H37OH have been imbibed and solidified in lined up, tubular mesopores of silicon with 10 nm and 15 nm mean diameters, respectively. X-ray diffraction measurements reveal a set of six discrete orientation states (''domains'') characterized by a perpendicular alignment of the molecules with respect to the long axis of the pores and by a four-fold symmetry about this direction, which coincides with the crystalline symmetry of the Si host. A Bragg peak series characteristic of the formation of bilayers indicates a lamellar structure of the spatially confined alcohol crystals in 15 nm pores. By contrast, no layering reflections could be detected for 10 nm pores. The growth mechanism responsible for the peculiar orientation states is attributed to a nano-scale version of the Bridgman technique of single-crystal growth, where the dominant growth direction is aligned parallelly to the long pore axes. Our observations are analogous to the growth phenomenology encounte...

  19. Pyrazolato metal complexes: synthesis, characterization and X-ray crystal structures of rhenium(I) derivaties

    Energy Technology Data Exchange (ETDEWEB)

    Ardizzoia, G.A; LaMonica, G.; Maspero, A. [Milan Univ. (Italy). Dipt. di Chimica Inorganica, Metallorganica e Analitica; Moret, M.; Masciocchi, N. [Milan Univ. (Italy). Dipt. di Chimica Strutturale e Stereochimica Inorganica

    1998-10-01

    The mononuclear complexes [Re(CO){sub 3}(Hpz){sub 2}Br] (1) and [Re(CO){sub 3}(Hdmpz){sub 2}Br] (2) were obtained by treating [Re(CO){sub 5}Br] with pyrazole (Hpz) or 3,5-dimethylpyrazole (Hdmpz). Complex 1 reacted with triethylamine affording a mixture of the ionic dinuclear derivative (Et{sub 3}NH)[Re{sub 2}(CO){sub 6}(pz){sub 2}Br] (3) and of the mononuclear species [Re(CO){sub 3}(Hpz){sub 2}(pz)] (4). Complex 4 was obtained in a pure form by carrying out the reaction in the presence of excess free pyrazole. Treatment of 4 with pyridine afforded the [Re(CO){sub 3}(py)(Hpz)(pz)] species (6). The analogues of 4 and 6 with Hdmpz, i.e. [Re(CO){sub 3}(Hdmpz){sub 2}(dmpz)] (7) and [Re(CO){sub 3}(py)(Hdmpz)(dmpz)] (8) were also synthesized. All species were characterized in solution by {sup 1}H-NMR spectroscopy, while the crystal structures of complexes 1, 3, 4 and 6 were determined by single-crystal X-ray diffraction analysis. The [(CO){sub 3}Re({mu}-pz){sub 2}({mu}-Br)Re(CO){sub 3}]{sup -} anion represents the first structurally characterized species containing rhenium(I) atoms bridged by mu-pyrazolate ligands. (orig.)

  20. A United Effort for Crystal Growth, Neutron Scattering, and X-ray Scattering Studies of Novel Correlated Electron Materials

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young S. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2015-02-12

    The research accomplishments during the award involved experimental studies of correlated electron systems and quantum magnetism. The techniques of crystal growth, neutron scattering, x-ray scattering, and thermodynamic & transport measurements were employed, and graduate students and postdoctoral research associates were trained in these techniques.

  1. Extreme UV and X-ray scattering measurements from a rough LiF crystal surface characterized by electron micrography

    DEFF Research Database (Denmark)

    Alehyane; Arbaoui; Barchewitz

    1989-01-01

    XUV and X-ray scattering by a LiF crystal is measured. The angular distribution of the scattered radiation (ADSR) reveals characteristic features, side peaks or asymmetry. The surface of the sample is statistically characterized by a microdensitometer analysis of electron micrographs resolving th...

  2. Collimating Montel mirror as part of a multi-crystal analyzer system for resonant inelastic x-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jungho; Shi, Xianbo; Casa, Diego; Qian, Jun; Huang, XianRong; Gog, Thomas

    2016-07-01

    Advances in resonant inelastic x-ray scattering (RIXS) have come in lockstep with improvements in energy resolution. Currently, the best energy resolution at the Ir-L3 edge stands at ~25 meV, which is achieved using a diced Si spherical analyzer. An angular dispersion analyzer system using multiple flat crystals provides a promising way to achieve higher energy resolution, namely 10 meV or better, thereby overcoming the intrinsic energy resolution limit of diced spherical crystal analyzers. One essential component for a practical use of such multi-crystal systems is the xray collimation optics. In this work, a laterally graded, parabolic collimation Montel mirror was designed with larger than 10 mrad acceptance, collimating the x-ray beam to smaller than 100 μrad divergence at the Ir-L3 absorption energy. The x-ray collimation performance was investigated at beamline 27-ID of the Advanced Photon Source, using incident photons from a Diamond (111) monochromator illuminating a controlled 40 mrad divergence scattering source of 5 μm diameter. A flat Si (111) crystal served as the analyzer. It is found from experimental data and ray-tracing simulations, combined with metrology results, that the manufactured Montel mirror satisfies the required specifications of angular acceptance and collimated x-ray divergence for a high resolution RIXS spectrometer at the Ir-L3 edge.

  3. An optimal strategy for X-ray data collection on macromolecular crystals with position-sensitive detectors

    NARCIS (Netherlands)

    Vicković, Ivan; Kalk, Kor H.; Drenth, Jan; Dijkstra, Bauke W.

    1994-01-01

    X-ray data collection on macromolecular crystals is preferably done with minimum exposure time and high completeness. A Fortran procedure - DCS - has been written in the environment of the MADNES program to predict the completeness of data before the start of actual data collection. In addition, the

  4. Time-dependent Takagi-Taupin eikonal theory of X-ray diffraction in rapidly changing crystal structures.

    Science.gov (United States)

    Adams, Bernhard W

    2004-03-01

    The Takagi-Taupin theory is extended by synthesizing it with the eikonal theory in a unified space-time approach based upon microscopic electromagnetism. The principal goal is the description of X-ray diffraction in a crystal undergoing subpicosecond and few-femtosecond changes.

  5. SCALING OF X-RAY-DIFFRACTION INTENSITIES FOR CRYSTALS WITH A ONE-DIMENSIONAL, INCOMMENSURATE, DISPLACIVE MODULATION

    NARCIS (Netherlands)

    LAM, EJW; BEURSKENS, PT; VANSMAALEN, S

    1992-01-01

    A statistical method is presented for the determination of the scale factor, an overall isotropic temperature factor and an overall modulation amplitude from the X-ray diffraction intensities of crystals with a one-dimensional, incommensurate, displacive modulation. Application to several compounds

  6. The first X-ray crystal structure of the glucocorticoid receptor bound to a non-steroidal agonist

    Energy Technology Data Exchange (ETDEWEB)

    Madauss, Kevin P.; Bledsoe, Randy K.; Mclay, Iain; Stewart, Eugene L.; Uings, Iain J.; Weingarten, Gordon; Williams, Shawn P. (GSKNC); (GSK)

    2009-07-23

    The amino-pyrazole 2,6-dichloro-N-ethyl benzamide 1 is a selective GR agonist with dexamethasone-like in vitro potency. Its X-ray crystal structure in the GR LBD (Glucocorticoid ligand-binding domain) is described and compared to other reported structures of steroidal GR agonists in the GR LBD (3E7C).

  7. Crystal engineering on industrial diaryl pigments using lattice energy minimizations and X-ray powder diffraction.

    Science.gov (United States)

    Schmidt, Martin U; Dinnebier, Robert E; Kalkhof, Holger

    2007-08-23

    Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was

  8. Crystal Engineering on Industrial Diaryl Pigments Using Lattice Energy Minimizations and X-ray Powder Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt,M.; Dinnebier, R.; Kalkhof, H.

    2007-01-01

    Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was

  9. Single-crystal X-ray diffraction study of synthetic sodium-hydronium jarosite

    Science.gov (United States)

    Najorka, Jens; Lewis, James M. T.; Spratt, John; Sephton, Mark A.

    2016-05-01

    Na-H3O jarosite was synthesized hydrothermally at 413 K for 8 days and investigated using single-crystal X-ray diffraction (XRD) and electron microprobe analysis (EMPA). The chemical composition of the studied crystal is [Na0.57(3) (H3O)0.36 (H2O)0.07]A Fe2.93(3) (SO4)2 (OH)5.70 (H2O)0.30, and Fe deficiency was confirmed by both EMPA and XRD analysis. The single-crystal XRD data were collected at 298 and 102 K, and crystal structures were refined in space group Roverline{3}m. The room-temperature data match structural trends of the jarosite group, which vary linearly with the c axis. The low-temperature structure at 102 K shows an anisotropic decrease in the unit cell parameters, with c and a decreasing by 0.45 and 0.03 %, respectively. Structural changes are mainly confined to the A site environment. Only minor changes occur in FeO6 and SO4 polyhedra. The structure responds upon cooling by increasing bond length distortion and by decreasing quadratic elongation of the large AO12 polyhedra. The structural parameters at low temperature follow very similar patterns to structural changes that correspond to compositional variation in the jarosite group, which is characterised by the flexibility of AO12 polyhedra and rigidity of Fe(OH)4O2-SO4 layers. The most flexible areas in the jarosite structure are localized at AO12 edges that are not shared with neighbouring FeO6 octahedra. Importantly, for the application of XRD in planetary settings, the temperature-related changes in jarosite can mimic compositional change.

  10. Liquid crystal thermography as compared to X-ray diagnostics, clinical findings and capillary microscopy in sclerodermia progressiva

    Energy Technology Data Exchange (ETDEWEB)

    Loreck, D.; Buehler, G.; Brenke, A.; Schmidt, P.; Heerdegen, I.; Huege, H.

    1985-01-01

    The hands of 55 patients suffering from progressive sclerodermia were examined by liquid crystal thermography. The findings were compared with those of X-ray diagnosis and with clinical results. In 20 patients also capillary microscopy was applied. All patients revealed hypothermias in the fingers, independent from X-ray results, duration of the disease and Raynaud's phenomenon. Hypothermia could involve all fingers and was localized proximally or distally. In most of the patients also hyperthermias, not to be cooled, were found. They were diarthrodial and vasal, respectively.

  11. Crystal Structure and X-ray Powder Diffraction Data for Rare Earth Compound PrNiSn

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The compound PrNiSn was studied by X-ray powder diffraction technique. The crystal structure and the X-ray diffraction data for this compound at room temperature were reported. The compound PrNiSn is orthorhombic with lattice parameters a=0.74569(3) nm, b=0.76851(5) nm, c=0.45676(8) nm, V=0.26176 nm3, Z=4 and Dx=8.076 g·cm-3, space group Pna21(33). The figure of merit FN for the compound is F30=54 (0.0093, 60).

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

    Science.gov (United States)

    Abramchik, Yu. A.; Timofeev, V. I.; Muravieva, T. I.; Esipov, R. S.; Kuranova, I. P.

    2016-11-01

    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. P1211 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.

  13. Studies on Crystal Orientation of ZnO Film on Sapphire Using High-throughout X-ray Diffraction

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The orientation of the nano-columnar ZnO films grown on sapphire using the technique of metal-organic chemical vapor deposition (MOCVD) exhibits deviation because of the mismatch between the crystal lattices of the films and the sapphire substrate. A high-throughout X-ray diffraction method was employed to determine the crystal orientation of the ZnO films at a time scale of the order of minutes based on the general area detection diffraction system (GADDS). This rapid, effective, and ready method, adapted for characterizing the orientation of the nano-columnar crystals is used to directly explain the results of observation of the X-ray diffraction images, by the measurements of the orientations of the crystal columns of the ZnO films along c-axis and in parallel to ab plane.

  14. Redetermination of the crystal structure of β-zinc molybdate from single-crystal X-ray diffraction data.

    Science.gov (United States)

    Mtioui-Sghaier, Olfa; Mendoza-Meroño, Rafael; Ktari, Lilia; Dammak, Mohamed; García-Granda, Santiago

    2015-07-01

    The crystal structure of the β-polymorph of ZnMoO4 was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005 ▸). Eur. J. Inorg. Chem. pp. 3080-3087; Cavalcante et al. (2013 ▸). Polyhedron, 54, 13-25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4 adopts the wolframite structure type and is composed of distorted ZnO6 and MoO6 octa-hedra, both with point group symmetry 2. The distortion of the octa-hedra is reflected by variation of bond lengths and angles from 2.002 (3)-2.274 (4) Å, 80.63 (11)-108.8 (2)° for equatorial and 158.4 (2)- 162.81 (14)° for axial angles (ZnO6), and of 1.769 (3)-2.171 (3) Å, 73.39 (16)-104.7 (2), 150.8 (2)-164.89 (15)° (MoO6), respectively. In the crystal structure, the same type of MO6 octa-hedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexa-gonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octa-hedral voids.

  15. Redetermination of the crystal structure of β-zinc molybdate from single-crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Olfa Mtioui-Sghaier

    2015-07-01

    Full Text Available The crystal structure of the β-polymorph of ZnMoO4 was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005. Eur. J. Inorg. Chem. pp. 3080–3087; Cavalcante et al. (2013. Polyhedron, 54, 13–25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4 adopts the wolframite structure type and is composed of distorted ZnO6 and MoO6 octahedra, both with point group symmetry 2. The distortion of the octahedra is reflected by variation of bond lengths and angles from 2.002 (3–2.274 (4 Å, 80.63 (11–108.8 (2° for equatorial and 158.4 (2– 162.81 (14° for axial angles (ZnO6, and of 1.769 (3–2.171 (3 Å, 73.39 (16–104.7 (2, 150.8 (2–164.89 (15° (MoO6, respectively. In the crystal structure, the same type of MO6 octahedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexagonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octahedral voids.

  16. Diagnosis of a two wire X-pinch by X-ray absorption spectroscopy utilizing a doubly curved ellipsoidal crystal

    Energy Technology Data Exchange (ETDEWEB)

    Cahill, A. D., E-mail: adc87@cornell.edu; Hoyt, C. L., E-mail: adc87@cornell.edu; Shelkovenko, T. A., E-mail: adc87@cornell.edu; Pikuz, S. A., E-mail: adc87@cornell.edu; Hammer, D. A., E-mail: adc87@cornell.edu [Cornell University, 439 Rhodes Hall, Ithaca, NY 14853 (United States)

    2014-12-15

    X-ray absorption spectroscopy is a powerful tool for the diagnosis of plasmas over a wide range of both temperature and density. However, such a measurement is often limited to probing plasmas with temperatures well below that of the x-ray source in order to avoid object plasma emission lines from obscuring important features of the absorption spectrum. This has excluded many plasmas from being investigated by this technique. We have developed an x-ray spectrometer that provides the ability to record absorption spectra from higher temperature plasmas than the usual approach allows without the risk of data contamination by line radiation emitted by the plasma under study. This is accomplished using a doubly curved mica crystal which is bent both elliptically and cylindrically. We present here initial absorption spectra obtained from an aluminum x-pinch plasma.

  17. A seven-crystal Johann-type hard x-ray spectrometer at the Stanford Synchrotron Radiation Lightsource

    Energy Technology Data Exchange (ETDEWEB)

    Sokaras, D.; Weng, T.-C.; Nordlund, D.; Velikov, P.; Wenger, D.; Garachtchenko, A.; George, M.; Borzenets, V.; Johnson, B.; Rabedeau, T. [Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Alonso-Mori, R.; Bergmann, U. [Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)

    2013-05-15

    We present a multicrystal Johann-type hard x-ray spectrometer ({approx}5-18 keV) recently developed, installed, and operated at the Stanford Synchrotron Radiation Lightsource. The instrument is set at the wiggler beamline 6-2 equipped with two liquid nitrogen cooled monochromators - Si(111) and Si(311) - as well as collimating and focusing optics. The spectrometer consists of seven spherically bent crystal analyzers placed on intersecting vertical Rowland circles of 1 m of diameter. The spectrometer is scanned vertically capturing an extended backscattering Bragg angular range (88 Degree-Sign -74 Degree-Sign ) while maintaining all crystals on the Rowland circle trace. The instrument operates in atmospheric pressure by means of a helium bag and when all the seven crystals are used (100 mm of projected diameter each), has a solid angle of about 0.45% of 4{pi} sr. The typical resolving power is in the order of (E/{Delta}E){approx}10 000. The spectrometer's high detection efficiency combined with the beamline 6-2 characteristics permits routine studies of x-ray emission, high energy resolution fluorescence detected x-ray absorption and resonant inelastic x-ray scattering of very diluted samples as well as implementation of demanding in situ environments.

  18. High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

    Science.gov (United States)

    Chiu, Thang K.; Kubelka, Jan; Herbst-Irmer, Regine; Eaton, William A.; Hofrichter, James; Davies, David R.

    2005-01-01

    The 35-residue subdomain of the villin headpiece (HP35) is a small ultrafast folding protein that is being intensely studied by experiments, theory, and simulations. We have solved the x-ray structures of HP35 and its fastest folding mutant [K24 norleucine (nL)] to atomic resolution and compared their experimentally measured folding kinetics by using laser temperature jump. The structures, which are in different space groups, are almost identical to each other but differ significantly from previously solved NMR structures. Hence, the differences between the x-ray and NMR structures are probably not caused by lattice contacts or crystal/solution differences, but reflect the higher accuracy of the x-ray structures. The x-ray structures reveal important details of packing of the hydrophobic core and some additional features, such as cross-helical H bonds. Comparison of the x-ray structures indicates that the nL substitution produces only local perturbations. Consequently, the finding that the small stabilization by the mutation is completely reflected in an increased folding rate suggests that this region of the protein is as structured in the transition state as in the folded structure. It is therefore a target for engineering to increase the folding rate of the subdomain from ≈0.5 μs–1 for the nL mutant to the estimated theoretical speed limit of ≈3 μs–1. PMID:15894611

  19. Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy

    Science.gov (United States)

    Nho, Hyun Woo; Kalegowda, Yogesh; Shin, Hyun-Joon; Yoon, Tae Hyun

    2016-01-01

    For the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties. PMID:27087141

  20. Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy

    Science.gov (United States)

    Nho, Hyun Woo; Kalegowda, Yogesh; Shin, Hyun-Joon; Yoon, Tae Hyun

    2016-04-01

    For the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties.

  1. Powder X-ray diffraction can differentiate between enantiomeric variants of calcium lactate pentahydrate crystal in cheese.

    Science.gov (United States)

    Tansman, G F; Kindstedt, P S; Hughes, J M

    2014-12-01

    Powder X-ray diffraction has been used for decades to identify crystals of calcium lactate pentahydrate in Cheddar cheese. According to this method, diffraction patterns are generated from a powdered sample of the crystals and compared with reference cards within a database that contains the diffraction patterns of known crystals. During a preliminary study of crystals harvested from various Cheddar cheese samples, we observed 2 slightly different but distinct diffraction patterns that suggested that calcium lactate pentahydrate may be present in 2 different crystalline forms. We hypothesized that the 2 diffraction patterns corresponded to 2 enantiomeric forms of calcium lactate pentahydrate (L- and DL-) that are believed to occur in Cheddar cheese, based on previous studies involving enzymatic analyses of the lactate enantiomers in crystals obtained from Cheddar cheeses. However, the powder X-ray diffraction database currently contains only one reference diffraction card under the title “calcium lactate pentahydrate.” To resolve this apparent gap in the powder X-ray diffraction database, we generated diffraction patterns from reagent-grade calcium l-lactate pentahydrate and laboratory-synthesized calcium dl-lactate pentahydrate. From the resulting diffraction patterns we determined that the existing reference diffraction card corresponds to calcium dl-lactate pentahydrate and that the other form of calcium lactate pentahydrate observed in cheese crystals corresponds to calcium l-lactate pentahydrate. Therefore, this report presents detailed data from the 2 diffraction patterns, which may be used to prepare 2 reference diffraction cards that differentiate calcium l-lactate pentahydrate from calcium dl-lactate pentahydrate. Furthermore, we collected crystals from the exteriors and interiors of Cheddar cheeses to demonstrate the ability of powder X-ray diffraction to differentiate between the 2 forms of calcium lactate pentahydrate crystals in Cheddar cheeses

  2. Note: application of a pixel-array area detector to simultaneous single crystal X-ray diffraction and X-ray absorption spectroscopy measurements.

    Science.gov (United States)

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

    2014-04-01

    X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) are two main x-ray techniques in synchrotron radiation facilities. In this Note, we present an experimental setup capable of performing simultaneous XRD and XAS measurements by the application of a pixel-array area detector. For XRD, the momentum transfer in specular diffraction was measured by scanning the X-ray energy with fixed incoming and outgoing x-ray angles. By selecting a small fixed region of the detector to collect the XRD signal, the rest of the area was available for collecting the x-ray fluorescence for XAS measurements. The simultaneous measurement of XRD and X-ray absorption near edge structure for Pr0.67Sr0.33MnO3 film was demonstrated as a proof of principle for future time-resolved pump-probe measurements. A static sample makes it easy to maintain an accurate overlap of the X-ray spot and laser pump beam.

  3. Monoalkylated barbiturate derivatives: X-ray crystal structure, theoretical studies, and biological activities

    Science.gov (United States)

    Barakat, Assem; Al-Majid, Abdullah Mohammed; Soliman, Saied M.; Islam, Mohammad Shahidul; Ghawas, Hussain Mansur; Yousuf, Sammer; Choudhary, M. Iqbal; Wadood, Abdul

    2017-08-01

    Barbiturate derivatives are privileged structures with a broad range of pharmaceutical applications. We prepared a series of 5-monoalkylated barbiturate derivatives (3a-l) and evaluated, in vitro, their antioxidant (DPPH assay), and α-glucosidase inhibitory activities. Compounds 3a-l were synthesized via Michael addition. The structure of compound 3k was determined using X-ray single-crystal diffraction, and geometric parameters were calculated using density functional theory at the B3LYP/6-311G(d,p) level of theory. Further, the structural analysis of 3k were also investigated. Biological studies revealed that compounds 3b (IC50 = 133.1 ± 3.2 μM), 3d (IC50 = 305 ± 7.7 μM), and 3e (IC50 = 184 ± 2.3 μM) have potent α-glucosidase enzyme inhibitors and showed greater activity than the standard drug acarbose (IC50 = 841 ± 1.73 μM). Compounds 3a-3i were found to show weak antioxidant activity against 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radicals (IC50 = 91 ± 0.75 to 122 ± 1.0 μM) when tested against a standard antioxidant, gallic acid (IC50 = 23 ± 0.43 μM).

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

    Science.gov (United States)

    Kohn, V G; Khikhlukha, D R

    2016-05-01

    This paper reports computer simulations of the transmitted-beam intensity distribution for the case of six-beam (000, 220, 242, 044, -224, -202) diffraction of X-rays in a perfect silicon crystal of thickness 1 mm. Both the plane-wave angular dependence and the six-beam section topographs, which are usually obtained in experiments with a restricted beam (two-dimensional slit), are calculated. The angular dependence is calculated in accordance with Ewald's theory. The section topographs are calculated from the angular dependence by means of the fast Fourier transformation procedure. This approach allows one to consider, for the first time, the transformation of the topograph's structure due to the two-dimensional slit sizes and the distance between the slit and the detector. The results are in good agreement with the results of other works and with the experimental data. This method of calculation does not require a supercomputer and it was performed on a standard laptop. A detailed explanation of the main features of the diffraction patterns at different distances between the slit and the detector is presented.

  5. Binding of the influenza A virus to cell-surface receptors: structures of five hemagglutinin-sialyloligosaccharide complexes determined by X-ray crystallography.

    Science.gov (United States)

    Eisen, M B; Sabesan, S; Skehel, J J; Wiley, D C

    1997-05-26

    The structures of five complexes of the X-31 influenza A (H3N2) virus hemagglutinin with sialyloligosaccharide receptor analogs have been determined from 2.5 to 2.8 A resolution by X-ray crystallography. There is well-defined electron density for three to five saccharides in all five complexes and a striking conformational difference between two linear pentasaccharides with the same composition but different linkage [alpha(2-->6) or alpha(2-->3)] at the terminal sialic acid. The bound position of the terminal sialic acid (NeuAc) is the same in all five complexes and is identical to that reported previously from the study of mono- and trisaccharides. The two oligosaccharides with NeuAc alpha(2-->6)Gal linkages and GlcNAc at the third position have a folded conformation with the GlcNAc doubled back to contact the sialic acid. The pentasaccharide with a terminal NeuAc alpha(2-->3)Gal linkage and GlcNAc at the third position has an extended (not folded) conformation and exits from the opposite side of the binding site than the alpha(2-->6)-linked molecule of the same composition. The difference between the conformation of the pentasaccharide with a 2,6 linkage and the trisaccharide 2,6-sialyllactose suggests that 2,6-sialyllactose is not, as previously believed, an appropriate analog of natural influenza A virus receptors. The oligosaccharides studied are NeuAc alpha(2-->3)Gal beta(1-->4)Glc, NeuAc alpha(2-->6)Gal beta(1-->4)Glc, NeuAc alpha(2-->3)Gal beta(1-->3)GlcNAc beta(1-->3)Gal beta(1-->4)Glc, NeuAc alpha(2-->6)Gal beta(1-->4)GlcNAc beta(1-->3)Gal beta(1-->4)Glc, and [NeuAc alpha(2-->6)Gal beta(1-->4)GlcNAc]2 beta(1-->3/6)Gal-beta-O-(CH2)5-COOCH3.

  6. X-Ray Sources and High-Throughput Data Collection Methods

    Energy Technology Data Exchange (ETDEWEB)

    Snell, Gyorgy

    2012-03-15

    X-ray diffraction experiments on protein crystals are at the core of the structure determination process. An overview of X-ray sources and data collection methods to support structure-based drug design (SBDD) efforts is presented in this chapter. First, methods of generating and manipulating X-rays for the purpose of protein crystallography, as well as the components of the diffraction experiment setup are discussed. SBDD requires the determination of numerous protein-ligand complex structures in a timely manner, and the second part of this chapter describes how to perform diffraction experiments efficiently on a large number of crystals, including crystal screening and data collection.

  7. Pressure dependence of X-rays produced by an LiTaO{sub 3} single crystal at low pressures

    Energy Technology Data Exchange (ETDEWEB)

    Hanamoto, Katsumi, E-mail: hana@md.okayama-u.ac.jp [Graduate School of Health Sciences, Okayama University, 5-1 Shikata-cho, 2-chome, Kita-ku, Okayama 700-8558 (Japan); Kawabe, Atsushi; Sakoda, Akihiro; Kataoka, Takahiro; Okada, Mari; Yamaoka, Kiyonori [Graduate School of Health Sciences, Okayama University, 5-1 Shikata-cho, 2-chome, Kita-ku, Okayama 700-8558 (Japan)

    2012-03-21

    The energy spectra of X-rays produced by an LiTaO{sub 3} single crystal have been measured at pressures of 5-50 Pa. The energy spectra showed that the amount of X-rays increased exponentially and the endpoint energy of the spectra increased linearly with the decrease of pressure at pressures of 10-25 Pa. A maximum endpoint energy of about 22 keV was obtained using an LiTaO{sub 3} single crystal with 0.5 mm thickness at the pressure of 10 Pa. The maximum energy produced by the present experimental setup was estimated assuming that the LiTaO{sub 3} single crystal forms a parallel-plate capacitor. The estimated energy reasonably agreed with the energy obtained. The pressure dependence of the endpoint energy was discussed in relation to the breakdown potential at low pressures.

  8. Purification, crystallization and preliminary X-ray analysis of CMS1MS2: a cysteine proteinase from Carica candamarcensis latex

    Science.gov (United States)

    Gomes, Marco Túlio Ribeiro; Teixeira, Raphael Dias; Ribeiro, Henrique de Assis Lopes; Turchetti, Andréia Pereira; Junqueira, Caroline Furtado; Lopes, Míriam Tereza Paz; Salas, Carlos Edmundo; Nagem, Ronaldo Alves Pinto

    2008-01-01

    Cysteine proteinases from the latex of plants of the family Caricaceae are widely used industrially as well as in pharmaceutical preparations. In the present work, a 23 kDa cysteine proteinase from Carica candamarcensis latex (designated CMS1MS2) was purified for crystallization using three chromatography steps. The enzyme shows about fourfold higher activity than papain with BAPNA as substrate. Crystals suitable for X-ray diffraction experiments were obtained by the hanging-drop method in the presence of PEG and ammonium sulfate as precipitants. The crystals are monoclinic (space group P21), with unit-cell parameters a = 53.26, b = 75.71, c = 53.23 Å, β = 96.81°, and diffract X-rays to 1.8 Å resolution. PMID:18540057

  9. Crystal Tilts in Epitaxially Laterally Overgrown GaN Films Determined by Four-Circle X-Ray Diffraction

    Institute of Scientific and Technical Information of China (English)

    汪峰; 张荣; 陈志忠; 吴小山; 顾书林; 沈波; 郑有堃; 蒋树声

    2001-01-01

    Crystal tilts in epitaxially laterally overgrown (ELO) GaN films via hydride vapour phase epitaxy (HVPE) onsapphire substrates have been investigated by using the four-circle x-ray diffraction method. Three diffractionpeaks corresponding to the (0002) reflection of vertically epitaxial and tilted GaN domains are observable in thex-ray rocking curve. The angle separations △ω between the main peak and two lobes change with the azimuthangle φ. The dependence of △ω on φ and the crystal tilt angle θ has been calculated based on the standardkinetic x-ray diffraction model. The crystal tilt angle of a typical HVPE ELO GaN sample has been determinedto be 2.379°.

  10. 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.

  11. X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature

    Directory of Open Access Journals (Sweden)

    Christopher D. M. Hutchison

    2017-09-01

    Full Text Available The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on state at 1.9 Angstrom resolution and the trans (off state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.

  12. Macromolecular crystallization and crystal perfection

    CERN Document Server

    Chayen, Naomi E; Snell, Edward H

    2010-01-01

    Structural biology is key to our understanding of the mechanisms of biological processes. This text describes current methods and future frontiers in crystal growth and use of X-ray and neutron crystallography, in the context of automation of crystallization and generation of synchrotron X-ray and neutron beams.

  13. Laser-driven 6-16 keV x-ray imaging and backlighting with spherical crystals

    Science.gov (United States)

    Schollmeier, M.; Rambo, P. K.; Schwarz, J.; Smith, I. C.; Porter, J. L.

    2014-10-01

    Laser-driven x-ray self-emission imaging or backlighting of High Energy Density Physics experiments requires brilliant sources with keV energies and x-ray crystal imagers with high spatial resolution of about 10 μ m. Spherically curved crystals provide the required resolution when operated at near-normal incidence, which minimizes image aberrations due to astigmatism. However, this restriction dramatically limits the range of suitable crystal and spectral line combinations. We present a survey of crystals and spectral lines for x-ray backlighting and self-emission imaging with energies between 6 and 16 keV. Ray-tracing simulations including crystal rocking curves have been performed to predict image brightness and spatial resolution. Results have been benchmarked to experimental data using both Sandia's 4 kJ, ns Z-Beamlet and 200 J, ps Z-Petawatt laser systems. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. SAND NO. 2014-15552A.

  14. Imaging crystal spectrometer for high-resolution x-ray measurements on electron beam ion traps and tokamaks

    Science.gov (United States)

    Beiersdorfer, P.; Magee, E. W.; Hell, N.; Brown, G. V.

    2016-11-01

    We describe a crystal spectrometer implemented on the Livermore electron beam ion traps that employ two spherically bent quartz crystals and a cryogenically cooled back-illuminated charge-coupled device detector to measure x rays with a nominal resolving power of λ/Δλ ≥ 10 000. Its focusing properties allow us to record x rays either with the plane of dispersion perpendicular or parallel to the electron beam and, thus, to preferentially select one of the two linear x-ray polarization components. Moreover, by choice of dispersion plane and focussing conditions, we use the instrument either to image the distribution of the ions within the 2 cm long trap region, or to concentrate x rays of a given energy to a point on the detector, which optimizes the signal-to-noise ratio. We demonstrate the operation and utility of the new instrument by presenting spectra of Mo34+, which prepares the instrument for use as a core impurity diagnostic on the NSTX-U spherical torus and other magnetic fusion devices that employ molybdenum as plasma facing components.

  15. DNA binding, antioxidant, cytotoxicity (MTT, lactate dehydrogenase, NO), and cellular uptake studies of structurally different nickel(II) thiosemicarbazone complexes: synthesis, spectroscopy, electrochemistry, and X-ray crystallography.

    Science.gov (United States)

    Prabhakaran, R; Kalaivani, P; Huang, R; Poornima, P; Vijaya Padma, V; Dallemer, F; Natarajan, K

    2013-02-01

    Three new nickel(II) thiosemicarbazone complexes have been synthesized and characterized by analytical, spectral, and single-crystal X-ray diffraction studies. In complex 1, the ligand 2-hydroxy-1-naphthaldehydethiosemicarbazone coordinated as a monobasic tridentate donor, whereas in complexes 2 and 3, the ligands salicylaldehyde-4(N)-ethylthiosemicarbazone and 2-hydroxy-1-naphthaldehyde-4(N)-ethylthiosemicarbazone coordinated as a dibasic tridentate donor. The DNA binding ability of the complexes in calf thymus DNA was explored by absorption and emission titration experiments. The antioxidant property of the new complexes was evaluated to test their free-radical scavenging ability. In vitro cytotoxicity assays were performed for the new complexes in A549 and HepG2 cell lines. The new compounds overcome cisplatin resistance in the A549 cell line and they were also active in the HepG2 cell line. The cellular uptake study showed the accumulation of the complexes in tumor cells depended on the nature of the ligand attached to the nickel ion.

  16. Structure of a 14-3-3 coordinated hexamer of the plant plasma membrane H+ -ATPase by combining X-ray crystallography and electron cryomicroscopy.

    Science.gov (United States)

    Ottmann, Christian; Marco, Sergio; Jaspert, Nina; Marcon, Caroline; Schauer, Nicolas; Weyand, Michael; Vandermeeren, Caroline; Duby, Geoffrey; Boutry, Marc; Wittinghofer, Alfred; Rigaud, Jean-Louis; Oecking, Claudia

    2007-02-09

    Regulatory 14-3-3 proteins activate the plant plasma membrane H(+)-ATPase by binding to its C-terminal autoinhibitory domain. This interaction requires phosphorylation of a C-terminal, mode III, recognition motif as well as an adjacent span of approximately 50 amino acids. Here we report the X-ray crystal structure of 14-3-3 in complex with the entire binding motif, revealing a previously unidentified mode of interaction. A 14-3-3 dimer simultaneously binds two H(+)-ATPase peptides, each of which forms a loop within the typical 14-3-3 binding groove and therefore exits from the center of the dimer. Several H(+)-ATPase mutants support this structure determination. Accordingly, 14-3-3 binding could result in H(+)-ATPase oligomerization. Indeed, by using single-particle electron cryomicroscopy, the 3D reconstruction of the purified H(+)-ATPase/14-3-3 complex demonstrates a hexameric arrangement. Fitting of 14-3-3 and H(+)-ATPase atomic structures into the 3D reconstruction map suggests the spatial arrangement of the holocomplex.

  17. Micro-crystallography comes of age.

    Science.gov (United States)

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

    2012-10-01

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

  18. Crystallization and preliminary X-ray diffraction of the Munc18c–syntaxin4{sub 1–29} complex

    Energy Technology Data Exchange (ETDEWEB)

    Latham, Catherine F.; Hu, Shu-Hong; Gee, Christine L.; Armishaw, Chris J.; Alewood, Paul F. [Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072 (Australia); James, David E. [Garvan Institute of Medical Research, Darlinghurst, NSW 2010 (Australia); Martin, Jennifer L., E-mail: j.martin@imb.uq.edu.au [Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072 (Australia)

    2007-06-01

    Cocrystallization with a peptide, free-interface diffusion crystal chips and crystal dehydration were important in the production of diffraction-quality crystals of the Munc18c protein that helps to regulate membrane fusion. The production of diffraction-quality crystals of Munc18c, a protein involved in regulating vesicular exocytosis in mammals, is reported. The diffraction resolution of Munc18c crystals was optimized by (i) cocrystallizing with a peptide fragment of the Munc18c functional binding partner syntaxin4, (ii) using nanolitre free-interface diffusion crystallization-screening chips and microlitre hanging-drop vapour diffusion and (iii) applying a post-crystallization dehydration treatment. Crystals belonging to the cubic space group P2{sub 1}3, with unit-cell parameters a = b = c = 170.8 Å, α = β = γ = 90°, were generated that diffract to 3.7 Å resolution on a laboratory X-ray source.

  19. X-Ray Diffraction.

    Science.gov (United States)

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

    1980-01-01

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

  20. X-Ray Diffraction.

    Science.gov (United States)

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

    1980-01-01

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

  1. X-ray diagnostics for TFTR

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Collimating Montel mirror as part of a multi-crystal analyzer system for resonant inelastic X-ray scattering.

    Science.gov (United States)

    Kim, Jungho; Shi, Xianbo; Casa, Diego; Qian, Jun; Huang, XianRong; Gog, Thomas

    2016-07-01

    Advances in resonant inelastic X-ray scattering (RIXS) have come in lockstep with improvements in energy resolution. Currently, the best energy resolution at the Ir L3-edge stands at ∼25 meV, which is achieved using a diced Si(844) spherical crystal analyzer. However, spherical analyzers are limited by their intrinsic reflection width. A novel analyzer system using multiple flat crystals provides a promising way to overcome this limitation. For the present design, an energy resolution at or below 10 meV was selected. Recognizing that the angular acceptance of flat crystals is severely limited, a collimating element is essential to achieve the necessary solid-angle acceptance. For this purpose, a laterally graded, parabolic, multilayer Montel mirror was designed for use at the Ir L3-absorption edge. It provides an acceptance larger than 10 mrad, collimating the reflected X-ray beam to smaller than 100 µrad, in both vertical and horizontal directions. The performance of this mirror was studied at beamline 27-ID at the Advanced Photon Source. X-rays from a diamond (111) monochromator illuminated a scattering source of diameter 5 µm, generating an incident beam on the mirror with a well determined divergence of 40 mrad. A flat Si(111) crystal after the mirror served as the divergence analyzer. From X-ray measurements, ray-tracing simulations and optical metrology results, it was established that the Montel mirror satisfied the specifications of angular acceptance and collimation quality necessary for a high-resolution RIXS multi-crystal analyzer system.

  3. Limit of hydrostaticity in He and Ne determined by means of in situ single crystal x-ray diffraction

    Science.gov (United States)

    Kurnosov, Alexander; Trots, Dmitro; Boffa Balaran, Tiziana; Frost, Daniel

    2010-05-01

    An ultrahigh-intensity rotating anode FR-E+ SuperBright from Rigaku coupled with a Huber four circle diffractometer and VariMaxTM focusing optics has been used to determine accurate and precise lattice parameters of very small single-crystals in diamond anvil cells at pressures above 40 GPa in a conventional laboratory. The optics are focusing the X-ray beam at the sample position (800 mm from the aperture of the optics) to the spot of about 200 μm size with high resolution (as measured by the sharp reflections line widths). The intensities of reflections from any crystal are at least 30 times larger than those obtained for the same sample with a similar x-ray diffractometer equipped with a conventional x-ray tube. However, accurate and precise lattice parameters at high pressure can be obtained only under hydrostatic or at least very close to hydrostatic conditions in order to avoid broadening of the reflections. To test the quasi-hydrostatic limits of He and Ne we have therefore performed a study of single crystals of quartz up to amorphisation of the sample and MgO single crystals. The study of these materials has also the advantage of being able to obtain compare the pressure scale of these two very well known materials with that of the ruby scale which appears to be dependent on the pressure medium used.

  4. 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.

  5. Liquid sample delivery techniques for serial femtosecond crystallography.

    Science.gov (United States)

    Weierstall, Uwe

    2014-07-17

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

  6. Crystal growth of CZT and its properties for the application in X-ray and γ-ray detectors

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The paper reports the recent achievement of the research on CZT for the application of X-ray andγ-ray detectors in Northwestern Polytechnical University.The crystals of both un-doped and In doped were grown with a self-designed Bridgman furnace.The microstructure analyses show that the crystals possess high crystallinity.Through In doping,the electronic properties were greatly improved and as high as 5×10~(10)Ωcm resistivity was obtained.The detectors produced with our crystal exhibits high resolutions o...

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

    Energy Technology Data Exchange (ETDEWEB)

    Nagano, Celso S.; Gallego del Sol, Francisca [Instituto de Biomedicina de Valencia, CSIC, Valencia (Spain); Cavada, Benildo S.; Nascimento, Kyria Santiago Do [Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE 60451-970 (Brazil); Nunes, Eudismar Vale; Sampaio, Alexandre H. [Laboratorio de Bioquímica Marinha, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, CE 60451-970 (Brazil); Calvete, Juan J., E-mail: jcalvete@ibv.csic.es [Instituto de Biomedicina de Valencia, CSIC, Valencia (Spain)

    2005-11-01

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

  8. trans-Platinum(II) complex of 3-aminoflavone - synthesis, X-ray crystal structure and biological activities in vitro.

    Science.gov (United States)

    Fabijańska, Małgorzata; Studzian, Kazimierz; Szmigiero, Leszek; Rybarczyk-Pirek, Agnieszka J; Pfitzner, Arno; Cebula-Obrzut, Barbara; Smolewski, Piotr; Zyner, Elżbieta; Ochocki, Justyn

    2015-01-21

    This paper describes the synthesis of trans-bis-(3-aminoflavone)dichloridoplatinum(ii) (trans-Pt(3-af)2Cl2; TCAP) for use as a potential anticancer compound, and the evaluation of its structure by elemental and spectral analyses, and X-ray crystallography. The complex demonstrated a significant cytotoxic effect against human and murine cancer cell lines, as well as weaker toxicity towards healthy cells (human peripheral blood lymphocytes) in comparison with cisplatin. Various biochemical and morphological methods confirm that the proapoptotic activity of trans-Pt(3-af)2Cl2 is markedly higher than the reference cisplatin. Our results suggest that trans-Pt(3-af)2Cl2 may have a different antitumour specificity from that of cisplatin.

  9. Toward Low-Voltage and Bendable X-Ray Direct Detectors Based on Organic Semiconducting Single Crystals.

    Science.gov (United States)

    Ciavatti, Andrea; Capria, Ennio; Fraleoni-Morgera, Alessandro; Tromba, Giuliana; Dreossi, Diego; Sellin, Paul J; Cosseddu, Piero; Bonfiglio, Annalisa; Fraboni, Beatrice

    2015-11-25

    Organic materials have been mainly proposed as ionizing radiation detectors in the indirect conversion approach. The first thin and bendable X-ray direct detectors are realized (directly converting X-photons into an electric signal) based on organic semiconducting single crystals that possess enhanced sensitivity, low operating voltage (≈5 V), and a minimum detectable dose rate of 50 μGy s(-1) .

  10. Investigation on quality of cubic GaN/GaAs (100) by double-crystal X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    徐大鹏; 王玉田; 杨辉; 郑联喜; 李建斌; 段俐宏; 吴荣汉

    1999-01-01

    Cubic GaN was grown on GaAs (100) by low pressure metal organic chemical vapor deposition (MOCVD). X-ray diffraction, scanning electron microscope (SEM) and photoluminescence (PL) spectra were performed to characterize the quality of the GaN film. The PL spectra of cubic GaN thin films being thicker than 1.5 μm were reported. Triple-crystal diffraction to analyze orientation distributions and strain of the thin films was also demonstrated.

  11. Structures of an asymmetrically coupled double-well superlattice by double-crystal X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    马文全; 庄岩; 王玉田; 江德生

    1997-01-01

    An asymmetrically coupled ( GaAs/AlAs/GaAs/AlAs)/GaAs(001) double-well supperlattice isstudied by HRDCD (high resolution double-crystal X-ray diffractometry).The intensity of satellite peaks is modulated by wave packet of different sublayers.In the course of simulation,the satellite peaks in the vicinity of the node points of wave packet are very informative for precise determination of sublayer thickness and for improving accuracy.

  12. Non-invasive measurement of X-ray beam heating on a surrogate crystal sample.

    Science.gov (United States)

    Snell, Edward H; Bellamy, Henry D; Rosenbaum, Gerd; van der Woerd, Mark J

    2007-01-01

    Cryocooling is a technique routinely used to mitigate the effects of secondary radiation damage on macromolecules during X-ray data collection. Energy from the X-ray beam absorbed by the sample raises the temperature of the sample. How large is the temperature increase and does this reduce the effectiveness of cryocooling? Sample heating by the X-ray beam has been measured non-invasively for the first time by means of thermal imaging. Specifically, the temperature rise of 1 mm and 2 mm glass spheres (sample surrogates) exposed to an intense synchrotron X-ray beam and cooled in a laminar flow of nitrogen gas is experimentally measured. For the typical sample sizes, photon energies, fluxes, flux densities and exposure times used for macromolecular crystallographic data collection at third-generation synchrotron radiation sources and with the sample accurately centered in the cryostream, the heating by the X-ray beam is only a few degrees. This is not sufficient to raise the sample above the amorphous-ice/crystalline-ice transition temperature and, if the cryostream cools the sample to 100 K, not even enough to significantly enhance radiation damage from secondary effects.

  13. Structure of HI-6*sarin-acetylcholinesterase determined by X-ray crystallography and molecular dynamics simulation: reactivator mechanism and design.

    Directory of Open Access Journals (Sweden)

    Fredrik Ekström

    Full Text Available Organophosphonates such as isopropyl metylphosphonofluoridate (sarin are extremely toxic as they phosphonylate the catalytic serine residue of acetylcholinesterase (AChE, an enzyme essential to humans and other species. Design of effective AChE reactivators as antidotes to various organophosphonates requires information on how the reactivators interact with the phosphonylated AChEs. However, such information has not been available hitherto because of three main challenges. First, reactivators are generally flexible in order to change from the ground state to the transition state for reactivation; this flexibility discourages determination of crystal structures of AChE in complex with effective reactivators that are intrinsically disordered. Second, reactivation occurs upon binding of a reactivator to the phosphonylated AChE. Third, the phosphorous conjugate can develop resistance to reactivation. We have identified crystallographic conditions that led to the determination of a crystal structure of the sarin(nonaged-conjugated mouse AChE in complex with [(E-[1-[(4-carbamoylpyridin-1-ium-1-ylmethoxymethyl]pyridin-2-ylidene]methyl]-oxoazanium dichloride (HI-6 at a resolution of 2.2 A. In this structure, the carboxyamino-pyridinium ring of HI-6 is sandwiched by Tyr124 and Trp286, however, the oxime-pyridinium ring is disordered. By combining crystallography with microsecond molecular dynamics simulation, we determined the oxime-pyridinium ring structure, which shows that the oxime group of HI-6 can form a hydrogen-bond network to the sarin isopropyl ether oxygen, and a water molecule is able to form a hydrogen bond to the catalytic histidine residue and subsequently deprotonates the oxime for reactivation. These results offer insights into the reactivation mechanism of HI-6 and design of better reactivators.

  14. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures.

    Science.gov (United States)

    Mao, Binchen; Tejero, Roberto; Baker, David; Montelione, Gaetano T

    2014-02-05

    We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5-22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10-25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function.

  15. 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.

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

    Science.gov (United States)

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

    2000-01-01

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

  17. X-ray diffraction in temporally and spatially resolved biomolecular science.

    Science.gov (United States)

    Helliwell, John R; Brink, Alice; Kaenket, Surasak; Starkey, Victoria Laurina; Tanley, Simon W M

    2015-01-01

    Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a 'crystal lattice free' single molecule, with or without temporal resolved structural changes. This is altogether very challenging R&D. So as to assist this effort we have undertaken studies of metal clusters that bind to proteins, both 'fresh' and after repeated X-ray irradiation to assess their X-ray-photo-dynamics, namely Ta6Br12, K2PtI6 and K2PtBr6 bound to a test protein, hen egg white lysozyme. These metal complexes have the major advantage of being very recognisable shapes (pseudo spherical or octahedral) and thereby offer a start to (probably very difficult) single molecule electron density map interpretations, both static and dynamic. A further approach is to investigate the X-ray laser beam diffraction strength of a well scattering nano-cluster; an example from nature being the iron containing ferritin. Electron crystallography and single particle electron microscopy imaging offers alternatives to X-ray structural studies; our structural studies of crustacyanin, a 320 kDa protein carotenoid complex, can be extended either by electron based techniques or with the X-ray laser representing a fascinating range of options. General outlook remarks concerning X-ray, electron and neutron macromolecular crystallography as well as 'NMR crystallography' conclude the article.

  18. Structural characterization of three crystalline modifications of telmisartan by single crystal and high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Dinnebier, R E; Sieger, P; Nar, H; Shankland, K; David, W I

    2000-11-01

    Three crystalline modifications (A, B, and C) of 4'-[[2-n-propyl-4-methyl-6-(1-methyl-benzimidazol-2-yl)benzi midazol-1-yl]methyl]biphenyl-2-carboxylic acid (INN name, telmisartan) have been detected and their crystal structures have been determined by single-crystal X-ray diffraction (pseudopolymorph C) and the method of simulated annealing from high-resolution X-ray powder diffraction data (polymorphs A and B). The compound is of interest because of its use as an angiotensin II receptor antagonist. Polymorph A crystallizes in space group P2(I)/c, Z = 4, with unit cell parameters a = 18.7798(3), b = 18.1043(2), and c = 8.00578(7) A, beta = 97.066(1) degrees, and V = 2701.31 A(3). Polymorph B crystallizes in space group P2(I)/a, Z = 4, with unit cell parameters a = 16.0646(5), b = 13.0909(3), and c = 13.3231(3) A, beta = 99.402(1) degrees, and V = 2764.2(1) A(3). The solvated form C crystallizes in space group C2/c, Z = 8, with unit cell parameters a = 30.990(5), b = 13.130(3), and c = 16.381(3) A, beta = 95.02(2) degrees, and V = 6639(2) A(3). For the structure solutions of polymorphs A and B, 13 degrees of freedom (3 translational, 3 orientational, 7 torsion angles) were determined in approximately 2 h of computer time, demonstrating that the crystal packing and the molecular conformation of medium-sized (MW approximately 500) pharmaceutical compounds can now be solved quickly and routinely from high-resolution X-ray powder diffraction data.

  19. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.

    Science.gov (United States)

    Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett; Gati, Cornelius; Kimura, Tetsunari; Milne, Christopher; Milathianaki, Despina; Kubo, Minoru; Wu, Wenting; Conrad, Chelsie; Coe, Jesse; Bean, Richard; Zhao, Yun; Båth, Petra; Dods, Robert; Harimoorthy, Rajiv; Beyerlein, Kenneth R; Rheinberger, Jan; James, Daniel; DePonte, Daniel; Li, Chufeng; Sala, Leonardo; Williams, Garth J; Hunter, Mark S; Koglin, Jason E; Berntsen, Peter; Nango, Eriko; Iwata, So; Chapman, Henry N; Fromme, Petra; Frank, Matthias; Abela, Rafael; Boutet, Sébastien; Barty, Anton; White, Thomas A; Weierstall, Uwe; Spence, John; Neutze, Richard; Schertler, Gebhard; Standfuss, Jörg

    2016-08-22

    Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.

  20. X-ray and thermoluminescence of LiKB{sub 4}O{sub 7} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Adamiv, V.T. [Institute of Physical Optics, 23 Dragomanov Str., 79005 Lviv (Ukraine)], E-mail: adamiv@ifo.lviv.ua; Antonyak, O.T. [Physical Department, I. Franko Lviv State University, 8 Kyryla and Mefodiya Street, 79005 Lviv (Ukraine); Burak, Ya.V.; Teslyuk, I.M. [Institute of Physical Optics, 23 Dragomanov Str., 79005 Lviv (Ukraine)

    2008-03-15

    The thermoluminescent (TL) and X-ray luminescent (XL) spectra of undoped LiKB{sub 4}O{sub 7} (LKBO) single crystals had been investigated in the temperature range 80-300 K. It was found that in LKBO crystals, there are two intensive TL peaks at 112 and 132 K. The only one band emission spectra of sharply defined Gaussian shape, confirming the same mechanism of XL and TL by the radiation annihilation of the strongly localized self-trapped excitons (STE), had been observed in the TL and XL spectra. The possible models of these localization centers STE have been discussed.

  1. Crystal structure and tautomerism of Pigment Yellow 138 determined by X-ray powder diffraction and solid-state NMR

    DEFF Research Database (Denmark)

    Gumbert, Silke D.; Körbitzer, Meike; Alig, Edith;

    2016-01-01

    The crystal structure of C.I. Pigment Yellow 138 was determined from X-ray powder diffraction data using real-space methods with subsequent Rietveld refinements. The tautomeric state was investigated by solid-state 1D and 2D multinuclear NMR experiments. In the crystals, the compound exhibits...... the NH-tautomer with a hydrogen atom situated at the nitrogen of the quinoline moiety. Direct evidence of the presence of the NH-tautomer is provided by 1H–14N HMQC solid-state NMR at very fast MAS. Solid-state dispersion-corrected density functional theory calculations with BLYP-D3 confirm...

  2. High-sensitivity, portable, tunable imaging X-ray spectrometer based on a spherical crystal and MCP

    CERN Document Server

    Monot, P; Dobosz, S; D'Oliveira, P; Hulin, S; Bougeard, M; Faenov, A Y; Pikuz, T A; Skobelev, I Y

    2002-01-01

    A portable (200x100x100 mm sup 3), high-luminosity, spherically bent crystal spectrometer was designed to measure very low emissivity X-ray spectra of different elements with spatial resolution in a wide spectral range (1.2-19.6 A). A large (50x15 mm sup 2) open aperture mica spherically bent crystal with R=150 mm was used as dispersive and focusing element. This spectrometer was associated with a large sensitive area (phi=40 mm) micro-channel plates assembly. This apparatus provides simultaneously high spectral (lambda/delta lambda approx 1800) and spatial (100-200 mu m) resolutions. Its large tunability allowed, without any adjustment of the spectrometer set-up, to record spectra in the 1.38-17.5 A wavelength range. We used the X-ray emission of femtosecond laser-produced plasmas from different materials ((CF sub 2) sub n , CaF sub 2 , Cu, Al) to test the spectrometer. Thanks to the high sensitivity (high collection efficiency) of the system, high quality space-resolved X-ray spectra of Fluorine and Aluminu...

  3. A high resolution X-ray crystal spectrometer to study electron and heavy-ion impact atomic collisions

    Indian Academy of Sciences (India)

    Ajay Kumar; D Misra; A H Kelkar; U R Kadhane; K V Thulasiram; Lokesh C Tribedi

    2007-06-01

    We have studied fast ion–atom and electron–atom collision processes using a reconditioned high resolution X-ray spectrometer. The X-rays, generated by the collisions, are dispersed by a curved ADP crystal (Johansson geometry) and detected by a gas proportional counter. A self-written LabVIEW based program has been used to give precise and controlled movement to the crystal and for data acquisition. The performance was tested by detecting the K diagram and satellite lines of several elements. The K satellite lines of Al have been studied in collision with 3–12 keV electrons and 40 MeV C4+ ions. In ion collisions as large as four L-vacancies are created simultaneously with the K-vacancy, compared to two satellites in case of the e-impact. In addition, we have measured the X-rays from H-, He- and Li-like Si ions which arise due to the electron loss/capture process in highly charged 80 MeV Si7+ ions in collision with thin carbon foil. Approximate charge state distribution has been obtained using this new technique.

  4. Interactions between X-ray induced transient defects and pre-existing damage precursors in DKDP crystals

    Energy Technology Data Exchange (ETDEWEB)

    Negres, R A; Saw, C K; Demos, S G

    2008-10-24

    Large-aperture laser systems, currently designed to achieve high energy densities at the target location (exceeding {approx} 10{sup 11} J/m{sup 3}), will enable studies of the physics of matter and radiation under extreme conditions. As a result, their optical components, such as the frequency conversion crystals (KDP/DKDP), may be exposed to X-rays and other ionizing radiation. This in turn may lead to a change in the damage performance of these materials as they may be affected by radiation-induced effects by either forming new damage initiation centers or interacting with the pre-existing damage initiating defects (so-called damage precursors). We present an experimental study on the laser-induced bulk damage performance at 355-nm of DKDP crystals following X-ray irradiation at room temperature. Results indicate that the damage performance of the material is affected by exposure to X-rays. We attribute this behavior to a change in the physical properties of the precursors which, in turn, affect their individual damage threshold.

  5. X-ray Crystal Structure of the B Component of Hemolysin BL from Bacillus cereus

    Energy Technology Data Exchange (ETDEWEB)

    Madegowda,M.; Eswaramoorthy, S.; Burley, S.; Swaminathan, S.

    2008-01-01

    Bacillus cereus Hemolysin BL enterotoxin, a ternary complex of three proteins, is the causative agent of food poisoning and requires all three components for virulence. The X-ray structure of the binding domain of HBL suggests that it may form a pore similar to other soluble channel forming proteins. A putative pathway of pore formation is discussed.

  6. X-ray crystal structure of divalent metal-activated ß-xyloisdase, RS223BX

    Science.gov (United States)

    We report the first X-ray structure of a glycoside hydrolase family 43 ß-xylosidase, RS223BX, which is strongly activated by the addition of divalent metal cations. The 2.69 Å structure reveals that the Ca2+ cation is located at the back of the active site pocket. The Ca2+ coordinates to H274 to sta...

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

  9. Purification, crystallization and preliminary X-ray diffraction analysis of water-soluble chlorophyll-binding protein from Chenopodium album

    Energy Technology Data Exchange (ETDEWEB)

    Ohtsuki, Takayuki [Department of Bimolecular Science, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510 (Japan); Ohshima, Shigeru [Department of Environmental Science, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510 (Japan); Uchida, Akira, E-mail: auchida@biomol.sci.toho-u.ac.jp [Department of Bimolecular Science, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510 (Japan)

    2007-09-01

    A water-soluble chlorophyll-binding protein with photoconvertibility from C. album was extracted, purified and crystallized in a darkroom. The crystal diffracted to around 2.0 Å resolution. A water-soluble chlorophyll-binding protein (WSCP) with photoconvertibility from Chenopodium album was extracted, purified and crystallized in a darkroom. Green crystals suitable for data collection appeared in about 10 d. A native data set was collected to 2.0 Å resolution at 100 K. The space group of the crystal was determined to be orthorhombic I222 or I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 48.13, b = 60.59, c = 107.21 Å. Preliminary analysis of the X-ray data indicated that there is one molecule per asymmetric unit.

  10. Non-destructive analysis of didymium and praseodymium molybdate crystals using energy dispersive X-ray fluorescence technique

    Science.gov (United States)

    Bhat, C. K.; Joseph, Daisy; Pandita, Sanjay; Kotru, P. N.

    2016-08-01

    Analysis of didymium (Di) and praseodymium molybdate crystals were carried out using energy dispersive X-ray fluorescence (EDXRF). The assigned empirical chemical formulae of the composites were tested and verified by the EDXRF technique by estimating experimental major elemental concentration ratios. On the Basis of these ratios, the established formulae for some of the composite materials have been verified and suggestions made for their refinement. Non-destructive technique used in this analysis enables to retain the original crystal samples and makes rapid simultaneous scan of major elements such as La, Pr, Ned and Mo as well as impurities such as Ce. Absence of samarium(Sm) in the spectrum during analysis of didymium molybdate crystals indicated an incomplete growth of mixed rare earth single crystal. These crystals (e.g.,Di) are shown to be of modified stoichiometry with Ce as trace impurity.

  11. The x-ray reflection efficiencies of planes (III) in germanium silicon and fluorite analyzing crystals. Experimental data

    Energy Technology Data Exchange (ETDEWEB)

    Bermudez Polonio, J.

    1964-07-01

    Integrated and peak reflection efficiency curves relative to a LiF crystal are presented. K{sub {alpha}} fluorescent radiations between (22) Ti and (41) Nb were used for both germanium and silicon crystals: the interval was extended to CaK{sub {alpha}} radiation in the short wavelength region with the fluorite crystal. Reflection efficiency curves show sharp declines in the region around the K absorption edges of germanium and calcium. For CuK{sub {alpha}} radiation, the experimental reflection efficiencies at the peak for germanium, silicon and fluorite crystals are 52, 38.5 and 17 percent, whereas the integrated reflection efficiencies are 65.5, 38 and 14 percent respectively. The data were obtained from untreated crystals, using a standard Norelco non-focussing X-ray spectrometer. Experimental procedures are presented. Some considerations about the (222) missing reflections are made. (Author) 12 refs.

  12. Specular and non-specular X-ray reflection from a single-crystal molybdenum mirror surface

    CERN Document Server

    Mizusawa, M

    2003-01-01

    The surface morphology of a super-polished mirror of single-crystal molybdenum has been studied by grazing-incidence X-ray reflection. It yields a rather high specular reflectivity (82.0%) for 16.0 keV X-rays below the critical angle. The data suggest that the mirror has a small roughness (0.7 nm rms) unlike other metal mirrors, but, on the other hand, strongly damaged layers (6.35 nm in total) exist at the near surface. It has been also found that the surface has a large correlation length (>3 mu m) and a small Hurst parameter (0.2-0.3) from the non-specular reflection.

  13. Assessing two-dimensional crystallization trials of small membrane proteins for structural biology studies by electron crystallography.

    Science.gov (United States)

    Johnson, Matthew C; Rudolph, Frederik; Dreaden, Tina M; Zhao, Gengxiang; Barry, Bridgette A; Schmidt-Krey, Ingeborg

    2010-10-29

    Electron crystallography has evolved as a method that can be used either alternatively or in combination with three-dimensional crystallization and X-ray crystallography to study structure-function questions of membrane proteins, as well as soluble proteins. Screening for two-dimensional (2D) crystals by transmission electron microscopy (EM) is the critical step in finding, optimizing, and selecting samples for high-resolution data collection by cryo-EM. Here we describe the fundamental steps in identifying both large and ordered, as well as small 2D arrays, that can potentially supply critical information for optimization of crystallization conditions. By working with different magnifications at the EM, data on a range of critical parameters is obtained. Lower magnification supplies valuable data on the morphology and membrane size. At higher magnifications, possible order and 2D crystal dimensions are determined. In this context, it is described how CCD cameras and online-Fourier Transforms are used at higher magnifications to assess proteoliposomes for order and size. While 2D crystals of membrane proteins are most commonly grown by reconstitution by dialysis, the screening technique is equally applicable for crystals produced with the help of monolayers, native 2D crystals, and ordered arrays of soluble proteins. In addition, the methods described here are applicable to the screening for 2D crystals of even smaller as well as larger membrane proteins, where smaller proteins require the same amount of care in identification as our examples and the lattice of larger proteins might be more easily identifiable at earlier stages of the screening.

  14. Detection of the X-ray spectra of imploding neon Z-pinch with elliptically bent mica crystal spectrometer

    Institute of Scientific and Technical Information of China (English)

    Jun Shi; Shali Xiao; Hongjian Wang; Xianbin Huang; Libing Yang; Shenye Liu

    2008-01-01

    A wide variety of X-ray and extreme ultraviolet diagnostics are being developed to study on Yang acceler- ator. An elliptically bent crystal spectrometer is designed with a focal length of 1350 mm. A mica crystal with an interplanar spacing of 1.984 nm bent onto an elliptical substrate with eccentricity of 0.9485 is used. The crystal analyzer covers the Bragg angle range from 30° to 60°. The mica crystal can efficiently reflect radiation in multiple orders, covering the entire spectral range from 0.1 to 1.73 nm except for a gap from 0.86 to 1.0 nm. The application experiment is performed on Yang accelerator using the bent mica crystal analyzer. Spectra of neon-puff Z-pinch plasmas are recorded with a X-ray film, showing the H-like and the He-like lines of neon. Each spectrum has been identified and used for the wavelength calibration, and most of the line radiation is contained in the He-α and the L-α lines. The experimental results have demonstrated that the spectral resolution approximates 379.

  15. 7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source.

    Science.gov (United States)

    Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark S; Zatsepin, Nadia A; Barty, Anton; Benner, W Henry; Boutet, Sébastien; Feld, Geoffrey K; Hau-Riege, Stefan P; Kirian, Richard A; Kupitz, Christopher; Messerschmitt, Marc; Ogren, John I; Pardini, Tommaso; Segelke, Brent; Williams, Garth J; Spence, John C H; Abela, Rafael; Coleman, Matthew; Evans, James E; Schertler, Gebhard F X; Frank, Matthias; Li, Xiao-Dan

    2014-07-17

    Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump-probe experiments at subpicosecond time resolution. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  16. Purification, crystallization and preliminary X-ray diffraction studies of C-phycocyanin and allophycocyanin from Spirulina platensis.

    Science.gov (United States)

    Moreno, A; Bermejo, R; Talavera, E; Alvarez-Pez, J M; Sanz-Aparicio, J; Romero-Garrido, A

    1997-05-01

    C-phycocyanin and allophycocyanin from the green alga Spirulina platensis were isolated and crystallized by gel-acupuncture techniques. A novel two-step chromatographic procedure was used for purification. Blue hexagonal crystals were obtained by diffusing magnesium chloride into the protein solution for a week, followed by diffusion of PEG 6000 in order to complete the reduction of the solubility of the protein in the capillary tube used as a growth cell. In the case of allophycocyanin, crystals with a size of 0.4 x 0.3 x 0.3 mm were characterized by X-ray diffraction. They belong to space group P6(3)22 with unit-cell parameters a = b = 102.04, c = 131.22 A. The crystals of C-phycocyanin belong to either space group P6 or P6(3) with unit-cell constants a = b = 182.38, c = 60.87 A, alpha = beta = 90, gamma = 120 degrees. The crystals diffract beyond 2.4 and 2.5 A resolution, respectively, using a rotating anode as an X-ray source.

  17. A novel approach for structure analysis of two-dimensional membrane protein crystals using x-ray powder diffraction data

    CERN Document Server

    Dilanian, Ruben A; Varghese, Jose N; Wilkins, Steve W; Oka, Toshihiko; Yagi, Naoto; Quiney, Harry M; Nugent, Keith A

    2010-01-01

    The application of powder diffraction methods in two-dimensional crystallography is regarded as intractable because of the uncertainties associated with overlapping reflections. Here, we report an approach that resolves these ambiguities and provides reliable low-resolution phase information directly from powder diffraction data. We apply our method to the recovery of the structure of the bacteriorhodopsin (bR) molecule to a resolution of 7 angstroms using only powder diffraction data obtained from two-dimensional purple membrane (PM) crystals.

  18. [Study on the hydrolysis distribution of ferric saline by infrared spectrophotometry and single crystal X-ray diffraction method].

    Science.gov (United States)

    Zheng, Huai-Li; Xie, Li-Guo; Gao, Chao-Yong; Sun, Xiu-Ping; Yang, You; Tang, Xue

    2009-02-01

    The hydrolytic stability of Fe(a), Fe(b) and Fe(c) in different pH values of poly-ferric-flocculants was studied by using Fe-ferron time by time complexation colorimetry. The research results showed that Fe(b) was unstable, and all Fe(b) was transformed to Fe(c) after 10-15 d placement. The content of Fe(c) tended towards stability after 10-15 d. Also, the content of Fe(a) tended towards stability after 10 d. The single crystal was synthesized by the method of direct crystallization in Fe(III)-SO4(2-) water solution at normal temperature and its structure characteristic was studied by single crystal X ray diffraction method and IR (infrared spectrophotometry). The research results showed that there was no group of Fe-OH-Fe, Fe-OH and binary ferric complexed with two hydroxyl groups in the single crystal synthesized from the ferric aqueous solution in low pH (pH was about 0.5). The form of Fe in single crystal was all Fe(III). The chemical formula of the single crystal was Fe(H2O)6 (SO4)2NH4 x 6H2O when the ammonia water was used as the alkalinizing agent. One reason was that with the evaporation of water, these single crystals were synthesized at pH 0. 5 despite of different initial pH and different initial alkalinizing agents. Another reason was that the hydrolysis distribution of ferric saline was unstable. Therefore, it was not easy to obtain the single crystal of Fe(III)-hydroxy complexes or Fe(III)-polymer at low pH value. The study showed that infrared spectrophotometry and single crystal X ray diffraction method have a good prospect in the research on hydrolysis distribution of flocculants.

  19. On the Use of Wide-Angle Energy-Sensitive Detectors in White-Beam X-Ray Single-Crystal Diffraction

    DEFF Research Database (Denmark)

    Buras, B.; Staun Olsen, J.; Gerward, Leif

    1980-01-01

    The possible applications of multiple-element or large-area semiconductor detectors in single-crystal X-ray diffraction are discussed on the basis of experimental results using Bremsstrahlung as well as synchrotron radiation.......The possible applications of multiple-element or large-area semiconductor detectors in single-crystal X-ray diffraction are discussed on the basis of experimental results using Bremsstrahlung as well as synchrotron radiation....

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

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yi-Hung [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Peng, Wen-Yan [Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Huang, Yen-Chieh [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Guan, Hong-Hsiang; Hsieh, Ying-Cheng [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Liu, Ming-Yih [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Chang, Tschining [Department of Hospitality Management, Nan Jeon Institute of Technology, Yen-Shui, Tainan 73746,Taiwan (China); Chen, Chun-Jung, E-mail: cjchen@nsrrc.org.tw [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Department of Physics, National Tsing-Hua University, Hsinchu 30013,Taiwan (China)

    2006-08-01

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