Electron microscopy at atomic resolution

International Nuclear Information System (INIS)

Gronsky, R.

1983-11-01

The direct imaging of atomic structure in solids has become increasingly easier to accomplish with modern transmission electron microscopes, many of which have an information retrieval limit near 0.2 nm point resolution. Achieving better resolution, particularly with any useful range of specimen tilting, requires a major design effort. This presentation describes the new Atomic Resolution Microscope (ARM), recently put into operation at the Lawrence Berkeley Laboratory. Capable of 0.18 nm or better interpretable resolution over a voltage range of 400 kV to 1000 kV with +- 40 0 biaxial specimen tilting, the ARM features a number of new electron-optical and microprocessor-control designs. These are highlighted, and its atomic resolution performance demonstrated for a selection of inorganic crystals

The success story of crystallography.

Science.gov (United States)

Schwarzenbach, Dieter

2012-01-01

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

Macromolecular crystallography using synchrotron radiation

International Nuclear Information System (INIS)

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

1982-01-01

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

Recent advances in racemic protein crystallography.

Science.gov (United States)

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

2017-09-15

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

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

International Nuclear Information System (INIS)

Braam, A.W.M.

1981-01-01

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

Structure of HIV-1 protease determined by neutron crystallography

International Nuclear Information System (INIS)

Adachi, Motoyasu; Kuroki, Ryota

2009-01-01

HIV-1 protease is an aspartic protease, and plays an essential role in replication of HIV. To develop HIV-1 protease inhibitors through structure-based drug design, it is necessary to understand the catalytic mechanism and inhibitor recognition of HIV-1 protease. We have determined the crystal structure of HIV-1 protease in complex with KNI-272 to 1.9 A resolution by neutron crystallography in combination with 1.4 A resolution X-ray diffraction data. The results show that the carbonyl group of hydroxymethylcarbonyl (HMC) in KNI-272 forms a hydrogen bonding interaction with protonated Asp 25 and the hydrogen atom from the hydroxyl group of HMC forms a hydrogen bonding interaction with the deprotonated Asp125. This is the first neutron report for HIV-1/inhibitor complex and shows directly the locations of key hydrogen atoms in catalysis and in the binding of a transition-state analog. The results confirm key aspect of the presumed catalytic mechanism of HIV-1 protease and will aid in the further development of protease inhibitors. (author)

The founding and development of X-ray crystallography

International Nuclear Information System (INIS)

Mai Zhenhong

2014-01-01

2014 is the centennial of X-ray crystallography. Crystals have played an important 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 technology 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. (author)

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

International Nuclear Information System (INIS)

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

2014-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-09-01

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

Imaging Lithium Atoms at Sub-Angstrom Resolution

Energy Technology Data Exchange (ETDEWEB)

O' Keefe, Michael A.; Shao-Horn, Yang

2005-01-03

John Cowley and his group at ASU were pioneers in the use of transmission electron microscopy (TEM) for high-resolution imaging. Three decades ago they achieved images showing the crystal unit cell content at better than 4A resolution. Over the years, this achievement has inspired improvements in resolution that have enabled researchers to pinpoint the positions of heavy atom columns within the cell. More recently, this ability has been extended to light atoms as resolution has improved. Sub-Angstrom resolution has enabled researchers to image the columns of light atoms (carbon, oxygen and nitrogen) that are present in many complex structures. By using sub-Angstrom focal-series reconstruction of the specimen exit surface wave to image columns of cobalt, oxygen, and lithium atoms in a transition metal oxide structure commonly used as positive electrodes in lithium rechargeable batteries, we show that the range of detectable light atoms extends to lithium. HRTEM at sub-Angstrom resolution will provide the essential role of experimental verification for the emergent nanotech revolution. Our results foreshadow those to be expected from next-generation TEMs with CS-corrected lenses and monochromated electron beams.

40 keV atomic resolution TEM

International Nuclear Information System (INIS)

Bell, David C.; Russo, Christopher J.; Kolmykov, Dmitry V.

2012-01-01

Here we present the first atomic resolution TEM imaging at 40 keV using an aberration-corrected, monochromated source TEM. Low-voltage High-Resolution Electron Microscopy (LVHREM) has several advantages, including increased cross-sections for inelastic and elastic scattering, increased contrast per electron and improved spectroscopy efficiency, decreased delocalization effects and reduced knock-on damage. Together, these often improve the contrast to damage ratio obtained on a large class of samples. Third-order aberration correction now allows us to operate the TEM at low energies while retaining atomic resolution, which was previously impossible. At low voltage the major limitation to resolution becomes the chromatic aberration limit. We show that using a source monochromator we are able to reduce the effect of chromatic aberration and achieve a usable high-resolution limit at 40 keV to less than 1 Å. We show various materials' examples of the application of the technique to image graphene and silicon, and compare atomic resolution images with electron multislice simulations. -- Highlights: ► We present the first atomic resolution images recorded at 40 keV using an aberration-corrected, monochromated TEM. ► We show information transfer measured to better than 1 Å. ► At 40 keV an aberration-corrected monochromated TEM is limited by fifth-order spherical aberration. ► We show that using a monochromator the effect of chromatic aberration is reduced to enable high resolution imaging. ► Low voltage high resolution electron microscopy will be beneficial for imaging the organic/inorganic materials interface.

Crystallography: past and present

Science.gov (United States)

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

2007-12-01

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

'Seeing' Atoms: The Crystallographic Revolution.

Science.gov (United States)

Schwarzenbach, Dieter

2014-02-26

Laue's experiment in 1912 of the diffraction of X-rays by crystals led to one of the most influential discoveries in the history of science: the first determinations of crystal structures, NaCl and diamond in particular, by W. L. Bragg in 1913. For the first time, the visualisation of the structure of matter at the atomic level became possible. X-ray diffraction provided a sort of microscope with atomic resolution, atoms became observable physical objects and their relative positions in space could be seen. All branches of science concerned with matter, solid-state physics, chemistry, materials science, mineralogy and biology, could now be firmly anchored on the spatial arrangement of atoms. During the ensuing 100 years, structure determination by diffraction methods has matured into an indispensable method of chemical analysis. We trace the history of the development of 'small-structure' crystallography (excepting macromolecular structures) in Switzerland. Among the pioneers figure Peter Debye and Paul Scherrer with powder diffraction, and Paul Niggli and his Zurich School with space group symmetry and geometrical crystallography. Diffraction methods were applied early on by chemists at the Universities of Bern and Geneva. By the 1970s, X-ray crystallography was firmly established at most Swiss Universities, directed by full professors. Today, chemical analysis by structure determination is the task of service laboratories. However, the demand of diffraction methods to solve problems in all disciplines of science is still increasing and powerful radiation sources and detectors are being developed in Switzerland and worldwide.

Development of the Atomic-Resolution Environmental Transmission Electron Microscope

DEFF Research Database (Denmark)

Gai, Pratibha L.; Boyes, Edward D.; Yoshida, Kenta

2016-01-01

The development of the novel atomic-resolution environmental transmission electron microscope (atomic-resolution ETEM) for directly probing dynamic gas–solid reactions in situ at the atomic level under controlled reaction conditions consisting of gas environment and elevated temperatures is descr......The development of the novel atomic-resolution environmental transmission electron microscope (atomic-resolution ETEM) for directly probing dynamic gas–solid reactions in situ at the atomic level under controlled reaction conditions consisting of gas environment and elevated temperatures...... is used to study steels, graphene, nanowires, etc. In this chapter, the experimental setup of the microscope column and its peripherals are described....

HRTEM imaging of atoms at sub-Angstroem resolution

International Nuclear Information System (INIS)

O'Keefe, Michael A.; Allard, Lawrence F.; Blom, Douglas A.

2005-01-01

John Cowley and his group at Arizona State University pioneered the use of transmission electron microscopy for high-resolution imaging. Images were achieved three decades ago showing the crystal unit cell content at better than 4 A resolution. This achievement enabled researchers to pinpoint the positions of heavy atom columns within the unit cell. Lighter atoms appear as resolution is improved to sub-Angstroem levels. Currently, advanced microscopes can image the columns of the light atoms (carbon, oxygen, nitrogen) that are present in many complex structures, and even the lithium atoms present in some battery materials. Sub-Angstroem imaging, initially achieved by focal-series reconstruction of the specimen exit surface wave, will become commonplace for next-generation electron microscopes with C s -corrected lenses and monochromated electron beams. Resolution can be quantified in terms of peak separation and inter-peak minimum, but the limits imposed on the attainable resolution by the properties of the microscope specimen need to be considered. At extreme resolution the 'size' of atoms can mean that they will not be resolved even when spaced farther apart than the resolution of the microscope. (author)

HRTEM Imaging of Atoms at Sub-Angstrom Resolution

Energy Technology Data Exchange (ETDEWEB)

O' Keefe, Michael A.; Allard, Lawrence F.; Blom, Douglas A.

2005-04-06

John Cowley and his group at Arizona State University pioneered the use of transmission electron microscopy (TEM) for high-resolution imaging. Images were achieved three decades ago showing the crystal unit cell content at better than 4 Angstrom resolution. This achievement enabled researchers to pinpoint the positions of heavy atom columns within the unit cell. Lighter atoms appear as resolution is improved to sub-Angstrom levels. Currently, advanced microscopes can image the columns of the light atoms (carbon, oxygen, nitrogen) that are present in many complex structures, and even the lithium atoms present in some battery materials. Sub-Angstrom imaging, initially achieved by focal-series reconstruction of the specimen exit surface wave, will become common place for next-generation electron microscopes with CS-corrected lenses and monochromated electron beams. Resolution can be quantified in terms of peak separation and inter-peak minimum, but the limits imposed on the attainable resolution by the properties of the micro-scope specimen need to be considered. At extreme resolution the ''size'' of atoms can mean that they will not be resolved even when spaced farther apart than the resolution of the microscope.

Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules

Directory of Open Access Journals (Sweden)

Esko Oksanen

2017-04-01

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

Atomic-Resolution Spectrum Imaging of Semiconductor Nanowires.

Science.gov (United States)

Zamani, Reza R; Hage, Fredrik S; Lehmann, Sebastian; Ramasse, Quentin M; Dick, Kimberly A

2018-03-14

Over the past decade, III-V heterostructure nanowires have attracted a surge of attention for their application in novel semiconductor devices such as tunneling field-effect transistors (TFETs). The functionality of such devices critically depends on the specific atomic arrangement at the semiconductor heterointerfaces. However, most of the currently available characterization techniques lack sufficient spatial resolution to provide local information on the atomic structure and composition of these interfaces. Atomic-resolution spectrum imaging by means of electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) is a powerful technique with the potential to resolve structure and chemical composition with sub-angstrom spatial resolution and to provide localized information about the physical properties of the material at the atomic scale. Here, we demonstrate the use of atomic-resolution EELS to understand the interface atomic arrangement in three-dimensional heterostructures in semiconductor nanowires. We observed that the radial interfaces of GaSb-InAs heterostructure nanowires are atomically abrupt, while the axial interface in contrast consists of an interfacial region where intermixing of the two compounds occurs over an extended spatial region. The local atomic configuration affects the band alignment at the interface and, hence, the charge transport properties of devices such as GaSb-InAs nanowire TFETs. STEM-EELS thus represents a very promising technique for understanding nanowire physical properties, such as differing electrical behavior across the radial and axial heterointerfaces of GaSb-InAs nanowires for TFET applications.

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

Science.gov (United States)

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

Science.gov (United States)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

Fast resolution change in neutral helium atom microscopy

Science.gov (United States)

Flatabø, R.; Eder, S. D.; Ravn, A. K.; Samelin, B.; Greve, M. M.; Reisinger, T.; Holst, B.

2018-05-01

In neutral helium atom microscopy, a beam of atoms is scanned across a surface. Though still in its infancy, neutral helium microscopy has seen a rapid development over the last few years. The inertness and low energy of the helium atoms (less than 0.1 eV) combined with a very large depth of field and the fact that the helium atoms do not penetrate any solid material at low energies open the possibility for a non-destructive instrument that can measure topology on the nanoscale even on fragile and insulating surfaces. The resolution is determined by the beam spot size on the sample. Fast resolution change is an attractive property of a microscope because it allows different aspects of a sample to be investigated and makes it easier to identify specific features. However up till now it has not been possible to change the resolution of a helium microscope without breaking the vacuum and changing parts of the atom source. Here we present a modified source design, which allows fast, step wise resolution change. The basic design idea is to insert a moveable holder with a series of collimating apertures in front of the source, thus changing the effective source size of the beam and thereby the spot size on the surface and thus the microscope resolution. We demonstrate a design with 3 resolution steps. The number of resolution steps can easily be extended.

A neutron image plate quasi-Laue diffractometer for protein crystallography

Energy Technology Data Exchange (ETDEWEB)

Cipriani, F.; Castagna, J.C.; Wilkinson, C. [European Molecular Biology Laboratory, Grenoble (France)] [and others

1994-12-31

An instrument which is based on image plate technology has been constructed to perform cold neutron Laue crystallography on protein structures. The crystal is mounted at the center of a cylindrical detector which is 400mm long and has a circumference of 1000mm, with gadolinium oxide-containing image plates mounted on its exterior surface. Laue images registered on the plate are read out by rotating the drum and translating a laser read head parallel to the cylinder axis, giving a pixel size of 200{mu}m x 200{mu}m and a total read time of 5 minutes. Preliminary results indicate that it should be possible to obtain a complete data set from a protein crystal to atomic resolution in about two weeks.

Nanoflow electrospinning serial femtosecond crystallography

International Nuclear Information System (INIS)

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

2012-01-01

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

Nanoflow electrospinning serial femtosecond crystallography

Energy Technology Data Exchange (ETDEWEB)

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

2012-11-01

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

Atomic resolution images of graphite in air

Energy Technology Data Exchange (ETDEWEB)

Grigg, D.A.; Shedd, G.M.; Griffis, D.; Russell, P.E.

1988-12-01

One sample used for proof of operation for atomic resolution in STM is highly oriented pyrolytic graphite (HOPG). This sample has been imaged with many different STM`s obtaining similar results. Atomic resolution images of HOPG have now been obtained using an STM designed and built at the Precision Engineering Center. This paper discusses the theoretical predictions and experimental results obtained in imaging of HOPG.

Atomic Force Microscopy and Real Atomic Resolution. Simple Computer Simulations

NARCIS (Netherlands)

Koutsos, V.; Manias, E.; Brinke, G. ten; Hadziioannou, G.

1994-01-01

Using a simple computer simulation for AFM imaging in the contact mode, pictures with true and false atomic resolution are demonstrated. The surface probed consists of two f.c.c. (111) planes and an atomic vacancy is introduced in the upper layer. Changing the size of the effective tip and its

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

Science.gov (United States)

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

2014-09-01

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

Fab Chaperone-Assisted RNA Crystallography (Fab CARC).

Science.gov (United States)

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

2016-01-01

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

Effect of heavy atoms on the thermal stability of α-amylase from Aspergillus oryzae.

Directory of Open Access Journals (Sweden)

Michihiro Sugahara

Full Text Available Currently, there are no versatile and established methods for improving stability of proteins. In an entirely different approach from conventional techniques such as mutagenesis, we attempted to enhance enzyme stability of α-amylase from Aspergillus oryzae using a heavy-atom derivatization technique. We evaluated changes in stability using differential scanning calorimetry (DSC. Candidate heavy atoms were identified using the Heavy-Atom Database System HATODAS, a Web-based tool designed to assist in heavy-atom derivatization of proteins for X-ray crystallography. The denaturation temperature of α-amylase derivatized with gadolinium (Gd or samarium (Sm ions increased by 6.2 or 5.7°C, respectively, compared to that of the native protein (60.6°C. The binding of six Gd ions was confirmed by X-ray crystallography of the enzyme at 1.5 Å resolution. DSC and dynamic light-scattering data revealed a correlation between stability and the aggregation state upon addition of Gd ions. These results show that HATODAS search is an effective tool for selecting heavy atoms for stabilization of this protein.

Prospects of linear reconstruction in atomic resolution electron holographic tomography

International Nuclear Information System (INIS)

Krehl, Jonas; Lubk, Axel

2015-01-01

Tomography commonly requires a linear relation between the measured signal and the underlying specimen property; for Electron Holographic Tomography this is given by the Phase Grating Approximation (PGA). While largely valid at medium resolution, discrepancies arise at high resolution imaging conditions. We set out to investigate the artefacts that are produced if the reconstruction still assumes the PGA even with an atomic resolution tilt series. To forego experimental difficulties the holographic tilt series was simulated. The reconstructed electric potential clearly shows peaks at the positions of the atoms. These peaks have characterisitic deformations, which can be traced back to the defocus a particular atom has in the holograms of the tilt series. Exchanging an atom for one of a different atomic number results in a significant change in the reconstructed potential that is well contained within the atom's peak. - Highlights: • We simulate a holographic tilt series of a nanocrystal with atomic resolution. • Using PGA-based Holographic Tomography we reconstruct the atomic structure. • The reconstruction shows characteristic artefacts, chiefly caused by defocus. • Changing one atom's Z produces a well localised in the reconstruction

Prospects of linear reconstruction in atomic resolution electron holographic tomography

Energy Technology Data Exchange (ETDEWEB)

Krehl, Jonas, E-mail: Jonas.Krehl@triebenberg.de; Lubk, Axel

2015-03-15

Tomography commonly requires a linear relation between the measured signal and the underlying specimen property; for Electron Holographic Tomography this is given by the Phase Grating Approximation (PGA). While largely valid at medium resolution, discrepancies arise at high resolution imaging conditions. We set out to investigate the artefacts that are produced if the reconstruction still assumes the PGA even with an atomic resolution tilt series. To forego experimental difficulties the holographic tilt series was simulated. The reconstructed electric potential clearly shows peaks at the positions of the atoms. These peaks have characterisitic deformations, which can be traced back to the defocus a particular atom has in the holograms of the tilt series. Exchanging an atom for one of a different atomic number results in a significant change in the reconstructed potential that is well contained within the atom's peak. - Highlights: • We simulate a holographic tilt series of a nanocrystal with atomic resolution. • Using PGA-based Holographic Tomography we reconstruct the atomic structure. • The reconstruction shows characteristic artefacts, chiefly caused by defocus. • Changing one atom's Z produces a well localised in the reconstruction.

Functional analysis of biological matter across dimensions by atomic force microscopy (AFM): from tissues to molecules and, ultimately, atoms

OpenAIRE

Stolz, Martin

2004-01-01

For a detailed understanding of biological tissues and proteins and their dynamical processes the 3D structures of the components involved must be known. Most of the structural data have been obtained through the combination of three major techniques: X-ray crystallography, NMR and TEM. These three methods enable the determination of the structure of biological macromolecules at near atomic resolution and each of those was developed over many years to perfection. Nevertheless each one has its...

Application of electron crystallography to structure characterization of ZnS nanocrystals

Directory of Open Access Journals (Sweden)

Jin-Gyu Kim

2011-07-01

Full Text Available We chracterized the structure properties of two types of ZnS nanocrystals by electron crystallography. X-ray diffraction analysis for these ZnS nanocrystals was performed to determine their initial structures. Their crystallite sizes were about 5.9 nm and 8.1 nm and their crystal systems were hexagonal and cubic, respectively. Their atomic structures, however, could not be determined because of the weak diffraction intensities as well as the unexpected intensities from impurty. To overcome these problems, the structures of ZnS nanocrystals were resolved by electron crystallography using EF-EPD (energy-filtered electron powder diffraction and HRTEM (high resolution transmission electron microscopy methods. The structrues determined by Rietveld analysis are P63mc (a = 3.8452 Å, c = 18.5453 Å and F-43m (a = 5.4356 Å, respectively. Their crystallite shapes were nanorods and quasi-nanoparticles and the nanorod crystal were grown along the [001] direction. It was revealed that the phase transformation between the cubic sphalerite to the hexagonal wurtzite structure of ZnS nanocrytals was related to their shapes and growth mechanism. Electron cryststallogrpahy, employing EF-EPD and HRTEM methods together, has advantages for structure analysis and property chracterization of nano-sized materials.

Direct methods in protein crystallography.

Science.gov (United States)

Karle, J

1989-11-01

It is pointed out that the 'direct methods' of phase determination for small-structure crystallography do not have immediate applicability to macromolecular structures. The term 'direct methods in macromolecular crystallography' is suggested to categorize a spectrum of approaches to macromolecular structure determination in which the analyses are characterized by the use of two-phase and higher-order-phase invariants. The evaluation of the invariants is generally obtained by the use of heavy-atom techniques. The results of a number of the more recent algebraic and probabilistic studies involving isomorphous replacement and anomalous dispersion thus become valid subjects for discussion here. These studies are described and suggestions are also presented concerning future applicability. Additional discussion concerns the special techniques of filtering, the use of non-crystallographic symmetry, some features of maximum entropy and attempts to apply phase-determining formulas to the refinement of macromolecular structure. It is noted that, in addition to the continuing remarkable progress in macromolecular crystallography based on the traditional applications of isomorphous replacement and anomalous dispersion, recent valuable advances have been made in the application of non-crystallographic symmetry, in particular, to virus structures and in applications of filtering. Good progress has also been reported in the application of exact linear algebra to multiple-wavelength anomalous-dispersion investigations of structures containing anomalous scatterers of only moderate scattering power.

Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

Science.gov (United States)

Nakane, Takanori; Hanashima, Shinya; Suzuki, Mamoru; Saiki, Haruka; Hayashi, Taichi; Kakinouchi, Keisuke; Sugiyama, Shigeru; Kawatake, Satoshi; Matsuoka, Shigeru; Matsumori, Nobuaki; Nango, Eriko; Kobayashi, Jun; Shimamura, Tatsuro; Kimura, Kanako; Mori, Chihiro; Kunishima, Naoki; Sugahara, Michihiro; Takakyu, Yoko; Inoue, Shigeyuki; Masuda, Tetsuya; Hosaka, Toshiaki; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Inoue, Tsuyoshi; Nureki, Osamu; Iwata, So; Murata, Michio; Mizohata, Eiichi

2016-01-01

The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams. PMID:27799539

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

Science.gov (United States)

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

2010-10-01

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

Atomic-resolution neutron holography

International Nuclear Information System (INIS)

Cser, L.; Toeroek, Gy.; Krexner, G.

2001-01-01

Atomic-resolution neutron holography can be realised by two different schemes. In the frame of the first approach a point-like source of slow neutrons is produced inside the investigated crystal. Due to the extremely large value of the incoherent-scattering cross-section of the proton, hydrogen atoms imbedded in a metal single-crystal lattice may serve as point-like sources when the sample is irradiated by a monochromatic beam of slow neutrons. The second approach utilizes the registration of the interference between the incident and scattered waves by means of a point-like detector inserted in the lattice of the crystal under investigation. In addition, neutron-induced electron holography is considered. The feasibility of these ideas is discussed. (orig.)

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

Science.gov (United States)

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

2015-07-01

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

A high resolution ion microscope for cold atoms

International Nuclear Information System (INIS)

Stecker, Markus; Schefzyk, Hannah; Fortágh, József; Günther, Andreas

2017-01-01

We report on an ion-optical system that serves as a microscope for ultracold ground state and Rydberg atoms. The system is designed to achieve a magnification of up to 1000 and a spatial resolution in the 100 nm range, thereby surpassing many standard imaging techniques for cold atoms. The microscope consists of four electrostatic lenses and a microchannel plate in conjunction with a delay line detector in order to achieve single particle sensitivity with high temporal and spatial resolution. We describe the design process of the microscope including ion-optical simulations of the imaging system and characterize aberrations and the resolution limit. Furthermore, we present the experimental realization of the microscope in a cold atom setup and investigate its performance by patterned ionization with a structure size down to 2.7 μ m. The microscope meets the requirements for studying various many-body effects, ranging from correlations in cold quantum gases up to Rydberg molecule formation. (paper)

An atomic model of brome mosaic virus using direct electron detection and real-space optimization

Science.gov (United States)

Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah

2014-09-01

Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.

Racemic DNA Crystallography

OpenAIRE

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

2014-01-01

International audience; Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of Land D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propens...

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

Racemic DNA crystallography.

Science.gov (United States)

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

2014-12-22

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

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

Energy Technology Data Exchange (ETDEWEB)

Coquelle, Nicolas [Université Grenoble Alpes, IBS, 38044 Grenoble (France); CNRS, IBS, 38044 Grenoble (France); CEA, IBS, 38044 Grenoble (France); Brewster, Aaron S. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta [European Synchrotron Radiation Facility, BP 220, 38043 Grenoble (France); Burghammer, Manfred, E-mail: burgham@esrf.fr [European Synchrotron Radiation Facility, BP 220, 38043 Grenoble (France); Ghent University, Ghent B-9000 (Belgium); Colletier, Jacques-Philippe, E-mail: burgham@esrf.fr [Université Grenoble Alpes, IBS, 38044 Grenoble (France); CNRS, IBS, 38044 Grenoble (France); CEA, IBS, 38044 Grenoble (France)

2015-05-01

A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced. High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

Serial Millisecond Crystallography of Membrane Proteins.

Science.gov (United States)

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

2016-01-01

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

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.

Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

KAUST Repository

Zhu, Yihan

2012-08-28

The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex inhomogeneities. Here, we report an atomic structure study of an important MoVTeO complex metal oxide catalyst that is potentially useful for the industrially relevant propane-based BP/SOHIO process. We combined aberration-corrected scanning transmission electron microscopy with synchrotron powder X-ray crystallography to explore the structure at both nanoscopic and macroscopic scales. At the nanoscopic scale, this material exhibits structural and compositional order within nanosized "domains", while the domains show disordered distribution at the macroscopic scale. We proposed that the intradomain compositional ordering and the interdomain electric dipolar interaction synergistically induce the displacement of Te atoms in the Mo-V-O channels, which determines the geometry of the multifunctional metal oxo-active sites.

Nanoflow electrospinning serial femtosecond crystallography

Science.gov (United States)

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

2012-01-01

An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14–3.1 µl min−1 to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min−1 and diffracted to beyond 4 Å resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption. PMID:23090408

Contribution of X-ray crystallography in energy related problems

International Nuclear Information System (INIS)

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

1995-01-01

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

3D structure determination from electron-microscope images: Electron crystallography of staurolite. [HFe[sub 2]Al[sub 9]Si[sub 4]O[sub 24

Energy Technology Data Exchange (ETDEWEB)

Wenk, H.R.; Hu Meisheng (California Univ., Berkeley, CA (United States). Dept. of Geology and Geophysics); Downing, K.H. (Lawrence Berkeley Lab., CA (United States). Donner Lab.); O' Keefe, M.A. (Lawrence Berkeley Lab., CA (United States). National Center for Electron Microscopy)

1992-09-01

Resolution of better than 2 A has been obtained in many crystals by high-resolution electron microscopy. Although this resolution is sufficient to resolve interatomic spacings, structures are traditionally interpreted by comparing experimental images with contrast calculations. A drawback of this method is that images are 2D projections in which information is invariably obscured by overlap of atoms. 3D electron crystallography, developed by biophysicists to study proteins, has been used to investigate the crystal structure of staurolite. Amplitudes and phases of structure factors are obtained experimentally from high-resolution images (JEOL ARM 1000 at the National Center for Electron Microscopy at LBL), taken in different directions from thin regions where dynamic scattering is minimal. From images in five orientations (containing 59 independent reflections to a resolution of 1.38 A), a 3D electron potential map is constructed which resolves clearly all cations (Al, Si, Fe, including those with partial occupancy) and all O atoms. This method has great potential in crystal structure determinations of small domains in heterogeneous crystals which are inaccessible to X-ray analysis. It is estimated that 3D structure determinations should be possible on regions only about ten unit cells wide and should resolve not only atom positions but also site occupancies. The method is also applicable to space-group determination. (orig.).

Atomic-resolution measurements with a new tunable diode laser-based interferometer

DEFF Research Database (Denmark)

Silver, R.M.; Zou, H.; Gonda, S.

2004-01-01

is lightweight and is mounted directly on an ultra-high vacuum scanning tunneling microscope capable of atomic resolution. We report the simultaneous acquisition of an atomic resolution image, while the relative lateral displacement of the tip along the sample distance is measured with the new tunable diode...

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

Watching proteins function with time-resolved x-ray crystallography

International Nuclear Information System (INIS)

Šrajer, Vukica; Schmidt, Marius

2017-01-01

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

Toward electron exit wave tomography of amorphous materials at atomic resolution

Energy Technology Data Exchange (ETDEWEB)

Borisenko, Konstantin B., E-mail: konstantin.borisenko@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Moldovan, Grigore [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Kirkland, Angus I., E-mail: angus.kirkland@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Van Dyck, Dirk [Department of Physics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Tang, Hsin-Yu; Chen, Fu-Rong [Department of Engineering and System Science, National Tsing Hua University, Kuang-Fu Road, 300 Hsinchu, Taiwan (China)

2012-09-25

Highlights: Black-Right-Pointing-Pointer We suggest a novel electron exit wave tomography approach to obtain three dimensional atomic structures of amorphous materials. Black-Right-Pointing-Pointer Theoretical tests using a model of amorphous Si doped with Au show that it is feasible to reconstruct both Si and Au atoms positions. Black-Right-Pointing-Pointer Reconstructions of the strongly scattering Au atoms positions appear to be insensitive to typical experimental errors. - Abstract: We suggest to use electron exit wave phase for tomographic reconstruction of structure of Au-doped amorphous Si with atomic resolution. In the present theoretical investigation into the approach it is found that the number of projections and the accuracy of defocus in the focal series restoration are the main factors that contribute to the final resolution. Although resolution is ultimately limited by these factors, phase shifts in the exit wave are sufficient to identify the position of Au atoms in an amorphous Si needle model, even when only 19 projections with defocus error of 4 nm are used. Electron beam damage will probably further limit the resolution of such tomographic reconstructions, however beam damage can be mitigated using lower accelerating voltages.

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

Directory of Open Access Journals (Sweden)

C. Mueller

2015-09-01

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

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

International Nuclear Information System (INIS)

Su Xiaodong; Cao Qin

2014-01-01

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

A history of experimental phasing in macromolecular crystallography

OpenAIRE

Isaacs, Neil

2016-01-01

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

On macromolecular refinement at subatomic resolution with interatomic scatterers

Energy Technology Data Exchange (ETDEWEB)

Afonine, Pavel V., E-mail: pafonine@lbl.gov; Grosse-Kunstleve, Ralf W.; Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 (United States); Lunin, Vladimir Y. [Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290 (Russian Federation); Urzhumtsev, Alexandre [IGMBC, 1 Rue L. Fries, 67404 Illkirch and IBMC, 15 Rue R. Descartes, 67084 Strasbourg (France); Faculty of Sciences, Nancy University, 54506 Vandoeuvre-lès-Nancy (France); Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 (United States)

2007-11-01

Modelling deformation electron density using interatomic scatters is simpler than multipolar methods, produces comparable results at subatomic resolution and can easily be applied to macromolecules. A study of the accurate electron-density distribution in molecular crystals at subatomic resolution (better than ∼1.0 Å) requires more detailed models than those based on independent spherical atoms. A tool that is conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8–1.0 Å, the number of experimental data is insufficient for full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented by additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark data sets gave results that were comparable in quality with the results of multipolar refinement and superior to those for conventional models. Applications to several data sets of both small molecules and macromolecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.

Protein crystal structure analysis using synchrotron radiation at atomic resolution

International Nuclear Information System (INIS)

Nonaka, Takamasa

1999-01-01

We can now obtain a detailed picture of protein, allowing the identification of individual atoms, by interpreting the diffraction of X-rays from a protein crystal at atomic resolution, 1.2 A or better. As of this writing, about 45 unique protein structures beyond 1.2 A resolution have been deposited in the Protein Data Bank. This review provides a simplified overview of how protein crystallographers use such diffraction data to solve, refine, and validate protein structures. (author)

Investigation of phosphorus atomization using high-resolution continuum source electrothermal atomic absorption spectrometry

International Nuclear Information System (INIS)

Dessuy, Morgana B.; Vale, Maria Goreti R.; Lepri, Fabio G.; Welz, Bernhard; Heitmann, Uwe

2007-01-01

The atomization of phosphorus in electrothermal atomic absorption spectrometry has been investigated using a high-resolution continuum source atomic absorption spectrometer and atomization from a graphite platform as well as from a tantalum boat inserted in a graphite tube. A two-step atomization mechanism is proposed for phosphorus, where the first step is a thermal dissociation, resulting in a fast atomization signal early in the atomization stage, and the second step is a slow release of phosphorus atoms from the graphite tube surface following the adsorption of molecular phosphorus at active sites of the graphite surface. Depending on experimental conditions only one of the mechanisms or both might be active. In the absence of a modifier and with atomization from a graphite or tantalum platform the second mechanism appears to be dominant, whereas in the presence of sodium fluoride as a modifier both mechanisms are observed. Intercalation of phosphorus into the graphite platform in the condensed phase has also been observed; this phosphorus, however, appears to be permanently trapped in the structure of the graphite and does not contribute to the absorption signal

Using the Plan View to Teach Basic Crystallography in General Chemistry

Science.gov (United States)

Cushman, Cody V.; Linford, Matthew R.

2015-01-01

The plan view is used in crystallography and materials science to show the positions of atoms in crystal structures. However, it is not widely used in teaching general chemistry. In this contribution, we introduce the plan view, and show these views for the simple cubic, body-centered cubic, face-centered cubic, hexagonal close packed, CsCl, NaCl,…

Visualising reacting single atoms under controlled conditions: Advances in atomic resolution in situ Environmental (Scanning) Transmission Electron Microscopy (E(S)TEM)

Science.gov (United States)

Boyes, Edward D.; Gai, Pratibha L.

2014-02-01

Advances in atomic resolution Environmental (Scanning) Transmission Electron Microscopy (E(S)TEM) for probing gas-solid catalyst reactions in situ at the atomic level under controlled reaction conditions of gas environment and temperature are described. The recent development of the ESTEM extends the capability of the ETEM by providing the direct visualisation of single atoms and the atomic structure of selected solid state heterogeneous catalysts in their working states in real-time. Atomic resolution E(S)TEM provides a deeper understanding of the dynamic atomic processes at the surface of solids and their mechanisms of operation. The benefits of atomic resolution-E(S)TEM to science and technology include new knowledge leading to improved technological processes with substantial economic benefits, improved healthcare, reductions in energy needs and the management of environmental waste generation. xml:lang="fr"

From electron microscopy to X-ray crystallography: molecular-replacement case studies

International Nuclear Information System (INIS)

Xiong, Yong

2008-01-01

Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement using various standard MR packages such as AMoRe, MOLREP and Phaser. Multi-component molecular complexes are increasingly being tackled by structural biology, bringing X-ray crystallography into the purview of electron-microscopy (EM) studies. X-ray crystallography can utilize a low-resolution EM map for structure determination followed by phase extension to high resolution. Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement (MR) using various standard MR packages such as AMoRe, MOLREP and Phaser. The results demonstrate that EM maps are viable models for molecular replacement. Possible difficulties in data analysis, such as the effects of the EM magnification error, and the effect of MR positional/rotational errors on phase extension are discussed

State of the art in atomic resolution off-axis electron holography

International Nuclear Information System (INIS)

Linck, Martin; Freitag, Bert; Kujawa, Stephan; Lehmann, Michael; Niermann, Tore

2012-01-01

As proposed by Hannes Lichte, to resolve structure–property relations not only the question “Which atom is where?” but also the question “Which fields are around?” has to be answered. High-resolution off-axis electron holography opens up an access to these key questions in that it allows accessing the complete exit-wave of the object provided within the information limit of the microscope, i.e. amplitude and phase including atomic details such as position and species, and moreover, information about large area electric potentials and magnetic fields, which a conventional transmission electron microscope is blind for—also when using a Cs-corrector. For an excellent object exit-wave reconstruction, special care has to be taken on the hologram quality, i.e. interference fringe contrast and electron dose. Severe restrictions are given to signal resolution by the limited brightness of the electron source. Utilizing a new high-brightness Schottky field electron emitter in a state-of-the-art transmission electron microscope operated at 300 kV, the phase signal resolution at atomic resolution can significantly be enhanced. An improvement by at least a factor of 2.88 compared to the most recently reported single hologram at atomic resolution is found. To proof the applicability of this setup to real materials science problems, a grain boundary of gold has been investigated holographically. -- Highlights: ► Impact of the brightness on the reconstructed signal in electron holography. ► Factor 2.8 gain in signal quality by setup with a high brightness electron gun. ► Investigation of a grain boundary in gold with a state-of-the-art holography setup. ► A-posteriori aberration fine-tuning for true one Angstrom resolution in the object wave. ► Mistilt analysis on the atomic scale by numerical wave optics.

Studying atomic-resolution by X-ray fluorescence holography

International Nuclear Information System (INIS)

Gao Hongyi; Chen Jianwen; Xie Honglan; Zhu Huafeng; Li Ruxin; Xu Zhizhan

2005-01-01

In this work, the results of numerical simulations of X-ray fluorescence holograms and the reconstructed atomic images for Fe single crystal are given. The influences of the recording angles ranges and the polarization effect on the reconstruction of the atomic images are discussed. The process for removing twin images by multiple energy fluorescence holography and expanding the energy range of the incident X-rays to improve the resolution of the reconstructed images is presented

Numerical simulation study for atomic-resolution x-ray fluorescence holography

International Nuclear Information System (INIS)

Xie Honglan; Gao Hongyi; Chen Jianwen; Xiong Shisheng; Xu Zhizhan; Wang Junyue; Zhu Peiping; Xian Dingchang

2003-01-01

Based on the principle of x-ray fluorescence holography, an iron single crystal model of a body-centred cubic lattice is numerically simulated. From the fluorescence hologram produced numerically, the Fe atomic images were reconstructed. The atomic images of the (001), (100), (010) crystallographic planes were consistent with the corresponding atomic positions of the model. The result indicates that one can obtain internal structure images of single crystals at atomic-resolution by using x-ray fluorescence holography

Crystallography beyond periodic Crystal perfection

International Nuclear Information System (INIS)

Estevez-Rams, E.

2008-01-01

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

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 ...

Macromolecular refinement by model morphing using non-atomic parameterizations.

Science.gov (United States)

Cowtan, Kevin; Agirre, Jon

2018-02-01

Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.

Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

Directory of Open Access Journals (Sweden)

Przemyslaw Nogly

2015-03-01

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

Crystallography: past and present

International Nuclear Information System (INIS)

Hodeau, J.L.; Guinebretiere, R.

2007-01-01

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

Ten Good Reasons for the Use of the Tellurium-Centered Anderson-Evans Polyoxotungstate in Protein Crystallography.

Science.gov (United States)

Bijelic, Aleksandar; Rompel, Annette

2017-06-20

Protein crystallography represents at present the most productive and most widely used method to obtain structural information on target proteins and protein-ligand complexes within the atomic resolution range. The knowledge obtained in this way is essential for understanding the biology, chemistry, and biochemistry of proteins and their functions but also for the development of compounds of high pharmacological and medicinal interest. Here, we address the very central problem in protein crystallography: the unpredictability of the crystallization process. Obtaining protein crystals that diffract to high resolutions represents the essential step to perform any structural study by X-ray crystallography; however, this method still depends basically on trial and error making it a very time- and resource-consuming process. The use of additives is an established process to enable or improve the crystallization of proteins in order to obtain high quality crystals. Therefore, a more universal additive addressing a wider range of proteins is desirable as it would represent a huge advance in protein crystallography and at the same time drastically impact multiple research fields. This in turn could add an overall benefit for the entire society as it profits from the faster development of novel or improved drugs and from a deeper understanding of biological, biochemical, and pharmacological phenomena. With this aim in view, we have tested several compounds belonging to the emerging class of polyoxometalates (POMs) for their suitability as crystallization additives and revealed that the tellurium-centered Anderson-Evans polyoxotungstate [TeW 6 O 24 ] 6- (TEW) was the most suitable POM-archetype. After its first successful application as a crystallization additive, we repeatedly reported on TEW's positive effects on the crystallization behavior of proteins with a particular focus on the protein-TEW interactions. As electrostatic interactions are the main force for TEW binding

Sub-nanometer resolution XPS depth profiling: Sensing of atoms

Energy Technology Data Exchange (ETDEWEB)

Szklarczyk, Marek, E-mail: szklarcz@chem.uw.edu.pl [Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw (Poland); Shim-Pol, ul. Lubomirskiego 5, 05-080 Izabelin (Poland); Macak, Karol; Roberts, Adam J. [Kratos Analytical Ltd, Wharfside, Trafford Wharf Road, Manchester, M17 1GP (United Kingdom); Takahashi, Kazuhiro [Kratos XPS Section, Shimadzu Corp., 380-1 Horiyamashita, Hadano, Kanagawa 259-1304 (Japan); Hutton, Simon [Kratos Analytical Ltd, Wharfside, Trafford Wharf Road, Manchester, M17 1GP (United Kingdom); Głaszczka, Rafał [Shim-Pol, ul. Lubomirskiego 5, 05-080 Izabelin (Poland); Blomfield, Christopher [Kratos Analytical Ltd, Wharfside, Trafford Wharf Road, Manchester, M17 1GP (United Kingdom)

2017-07-31

Highlights: • Angle resolved photoelectron depth profiling of nano thin films. • Sensing atomic position in SAM films. • Detection of direction position of adsorbed molecules. - Abstract: The development of a method capable of distinguishing a single atom in a single molecule is important in many fields. The results reported herein demonstrate sub-nanometer resolution for angularly resolved X-ray photoelectron spectroscopy (ARXPS). This is made possible by the incorporation of a Maximum Entropy Method (MEM) model, which utilize density corrected electronic emission factors to the X-ray photoelectron spectroscopy (XPS) experimental results. In this paper we report on the comparison between experimental ARXPS results and reconstructed for both inorganic and organic thin film samples. Unexpected deviations between experimental data and calculated points are explained by the inaccuracy of the constants and standards used for the calculation, e.g. emission factors, scattering intensity and atomic density through the studied thickness. The positions of iron, nitrogen and fluorine atoms were determined in the molecules of the studied self-assembled monolayers. It has been shown that reconstruction of real spectroscopic data with 0.2 nm resolution is possible.

Atomic resolution imaging of ferroelectric domains

International Nuclear Information System (INIS)

Bursill, L.A.

1997-01-01

Electron optical principles involved in obtaining atomic resolution images of ferroelectric domains are reviewed, including the methods available to obtain meaningful interpretation and analysis of the image detail in terms of the atomic structures. Recent work is concerned with establishing the relationship between the essentially static chemical nanodomains and the spatial and temporal fluctuations of the nanoscale polar domains present in the relaxor class of materials, including lead scandium tantalate (PST) and lead magnesium niobate (PMN). Correct interpretation of the images required use of Next Nearest Neighbour Ising model simulations for the chemical domain textures upon which we must superimpose the polar domain textures; an introduction to this work is presented. A thorough analysis of the atomic scale chemical inhomogeneities, based upon the HRTEM results, has lead to an improved formulation of the theory of the dielectric response of PMN and PST, which is capable to predict the observed temperature and frequency dependence. HRTEM may be combined with solid state and statistical physics principles to provide a deeper understanding of structure/property relationships. 15 refs., 6 figs

Ultrafast terahertz scanning tunneling microscopy with atomic resolution

DEFF Research Database (Denmark)

Jelic, Vedran; Iwaszczuk, Krzysztof; Nguyen, Peter H.

2016-01-01

We demonstrate that ultrafast terahertz scanning tunneling microscopy (THz-STM) can probe single atoms on a silicon surface with simultaneous sub-nanometer and sub-picosecond spatio-temporal resolution. THz-STM is established as a new technique for exploring high-field non-equilibrium tunneling...

The mechanisms underlying the enhanced resolution of atomic force microscopy with functionalized tips

International Nuclear Information System (INIS)

Moll, Nikolaj; Gross, Leo; Mohn, Fabian; Curioni, Alessandro; Meyer, Gerhard

2010-01-01

By functionalizing the tip of an atomic force microscope (AFM) with a molecule or an atom that significantly contributes to the tip-sample interaction, the resolution can be dramatically enhanced. The interaction and therefore the resolution crucially depend on the chemical nature of the tip termination. Employing a tip functionalized with a CO molecule, atomic resolution of a pentacene molecule was recently demonstrated. In this work, the interaction between the CO tip and the pentacene imaged are studied with first principles calculations. The calculated frequency shifts compare very well with the experiment. The different energy contributions are analyzed and the Pauli energy is computed. We demonstrate that the source of the high resolution is Pauli repulsion, whereas van der Waals and electrostatic interactions only add a diffuse attractive background.

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

Science.gov (United States)

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

2013-02-27

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

Application of the theory of martensite crystallography to displacive phase transformations in substitutional nonferrous alloys

International Nuclear Information System (INIS)

Muddle, B.C.; Nie, J.F.; Hugo, G.R.

1994-01-01

It has been demonstrated that the theory of martensite crystallography is capable of accounting successfully for the form and crystallography of a range of plate- or lath-shaped transformation products, even when the formation of the product phase involves significant substitutional diffusion. These transformations include the precipitation of metastable hexagonal γ' (Ag 2 Al) plates in disordered face-centered cubic (fcc) solid-solution Al-Ag alloys, the formation of ordered AuCu II plates from disordered fcc solid solution in equiatomic Au-Cu alloys, and the formation of metastable 9R α 1 plates in ordered (B2) Cu-Zn and Ag-Cd alloys. The application of the theory to these transformations is reviewed critically and the features common to them identified. It is confirmed that, in all three transformations, the product phase produces relief at a free surface consistent with an invariant plane-strain shape change and that the transformations are thus properly described as displacive. The agreement between experimental observations and theoretical predictions of the transformation crystallography is in all cases excellent. It is proposed that successful application of the theory implies a growth mechanism in which the coherent or semicoherent, planar interface between parent and product phases maintains its structural identity during migration and that growth proceeds atom by atom in a manner consistent with the maintenance of a correspondence of lattice sites

Data processing in neutron protein crystallography using position-sensitive detectors

International Nuclear Information System (INIS)

Schoenborn, B.P.

1982-01-01

Neutrons provide a unique probe for localizing hydrogen atoms and for distinguishing hydrogen from deuterons. Hydrogen atoms largely determine the three-dimensional structure of proteins and are responsible for many catalytic reactions. The study of hydrogen bonding and hydrogen exchange will therefore give insight into reaction mechanisms and conformational fluctuations. In addition, neutrons provide the ability to distinguish N from C and O and to allow correct orientation of groups such as histidine and glutamine. To take advantage of these unique features of neutron crystallography, one needs accurate Fourier maps depicting atomic structure to a high precision. In this paper, techniques are described for minimizing error in the observed structure factors by optimizing data collection and analysis procedures. Special attention is given to subtraction of the high background associated with hydrogen-containing molecules, which produces a disproportionately large statistical error

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

International Nuclear Information System (INIS)

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

1999-01-01

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

Smarter Drugs: How Protein Crystallography Revolutionizes Drug Design

International Nuclear Information System (INIS)

Smith, Clyde

2005-01-01

According to Smith, protein crystallography allows scientists to design drugs in a much more efficient way than the standard methods traditionally used by large drug companies, which can cost close to a billion dollars and take 10 to 15 years. 'A lot of the work can be compressed down,' Smith said. Protein crystallography enables researchers to learn the structure of molecules involved in disease and health. Seeing the loops, folds and placement of atoms in anything from a virus to a healthy cell membrane gives important information about how these things work - and how to encourage, sidestep or stop their functions. Drug design can be much faster when the relationship between structure and function tells you what area of a molecule to target. Smith will use a timeline to illustrate the traditional methods of drug development and the new ways it can be done now. 'It is very exciting work. There have been some failures, but many successes too.' A new drug to combat the flu was developed in a year or so. Smith will tell us how. He will also highlight drugs developed to combat HIV, Tuberculosis, hypertension and Anthrax.

Atomic-resolution transmission electron microscopy of electron beam–sensitive crystalline materials

Science.gov (United States)

Zhang, Daliang; Zhu, Yihan; Liu, Lingmei; Ying, Xiangrong; Hsiung, Chia-En; Sougrat, Rachid; Li, Kun; Han, Yu

2018-02-01

High-resolution imaging of electron beam–sensitive materials is one of the most difficult applications of transmission electron microscopy (TEM). The challenges are manifold, including the acquisition of images with extremely low beam doses, the time-constrained search for crystal zone axes, the precise image alignment, and the accurate determination of the defocus value. We develop a suite of methods to fulfill these requirements and acquire atomic-resolution TEM images of several metal organic frameworks that are generally recognized as highly sensitive to electron beams. The high image resolution allows us to identify individual metal atomic columns, various types of surface termination, and benzene rings in the organic linkers. We also apply our methods to other electron beam–sensitive materials, including the organic-inorganic hybrid perovskite CH3NH3PbBr3.

Atomic-resolution transmission electron microscopy of electron beam–sensitive crystalline materials

KAUST Repository

Zhang, Daliang

2018-01-18

High-resolution imaging of electron beam-sensitive materials is one of the most difficult applications of transmission electron microscopy (TEM). The challenges are manifold, including the acquisition of images with extremely low beam doses, the time-constrained search for crystal zone axes, the precise image alignment, and the accurate determination of the defocus value. We develop a suite of methods to fulfill these requirements and acquire atomic-resolution TEM images of several metal organic frameworks that are generally recognized as highly sensitive to electron beams. The high image resolution allows us to identify individual metal atomic columns, various types of surface termination, and benzene rings in the organic linkers. We also apply our methods to other electron beam–sensitive materials, including the organic-inorganic hybrid perovskite CH3NH3PbBr3.

History of protein crystallography in China.

Science.gov (United States)

Rao, Zihe

2007-06-29

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

High-resolution measurements of x rays from ion-atom collisions

International Nuclear Information System (INIS)

Knudson, A.R.

1974-01-01

High resolution measurements of K x-ray spectra produced by ion-atom collisions at MeV energies are presented. These measurements indicate that a distribution of L-shell vacancies accompanies K-shell excitation. The variation of these spectra as a function of incident ion energy and atomic number is discussed. Difficulties in the analysis of these spectra due to rearrangement of vacancies between the time of the collision and the time of x-ray emission are considered. The use of high resolution x-ray measurements to obtain information on projectile ion vacancy configurations is demonstrated by data for Ar ions in KCl. X-ray spectra from Al projectiles in a variety of targets were measured and the effect of target composition on these spectra is discussed

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.

Science.gov (United States)

Martin-Garcia, Jose M; Conrad, Chelsie E; Nelson, Garrett; Stander, Natasha; Zatsepin, Nadia A; Zook, James; Zhu, Lan; Geiger, James; Chun, Eugene; Kissick, David; Hilgart, Mark C; Ogata, Craig; Ishchenko, Andrii; Nagaratnam, Nirupa; Roy-Chowdhury, Shatabdi; Coe, Jesse; Subramanian, Ganesh; Schaffer, Alexander; James, Daniel; Ketwala, Gihan; Venugopalan, Nagarajan; Xu, Shenglan; Corcoran, Stephen; Ferguson, Dale; Weierstall, Uwe; Spence, John C H; Cherezov, Vadim; Fromme, Petra; Fischetti, Robert F; Liu, Wei

2017-07-01

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2A AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2A AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2A AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

Directory of Open Access Journals (Sweden)

Jose M. Martin-Garcia

2017-07-01

Full Text Available Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX is severely limited by the scarcity of X-ray free-electron laser (XFEL sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX. As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS, are reported. Microcrystals (5–20 µm of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2A adenosine receptor (A2AAR, the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP or a high-molecular-weight poly(ethylene oxide (PEO; molecular weight 8 000 000 were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the

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.

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

Science.gov (United States)

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

2016-01-01

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

Concept for room temperature single-spin tunneling force microscopy with atomic spatial resolution

Science.gov (United States)

Payne, Adam

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy (AFM) system noise. The results show that the approach could provide single-spin measurement of electrically isolated defect states with atomic spatial resolution at room temperature.

Atomic-resolution single-spin magnetic resonance detection concept based on tunneling force microscopy

Science.gov (United States)

Payne, A.; Ambal, K.; Boehme, C.; Williams, C. C.

2015-05-01

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single-electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy system noise. The results show that the approach could provide single-spin measurement of electrically isolated qubit states with atomic spatial resolution at room temperature.

Modeling noncontact atomic force microscopy resolution on corrugated surfaces

Directory of Open Access Journals (Sweden)

Kristen M. Burson

2012-03-01

Full Text Available Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO2 as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid. The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.

Data Management System at the Photon Factory Macromolecular Crystallography Beamline

International Nuclear Information System (INIS)

Yamada, Y; Matsugaki, N; Chavas, L M G; Hiraki, M; Igarashi, N; Wakatsuki, S

2013-01-01

Macromolecular crystallography is a very powerful tool to investigate three-dimensional structures of macromolecules at the atomic level, and is widely spread among structural biology researchers. Due to recent upgrades of the macromolecular crystallography beamlines at the Photon Factory, beamline throughput has improved, allowing more experiments to be conducted during a user's beam time. Although the number of beamlines has increased, so has the number of beam time applications. Consequently, both the experimental data from users' experiments and data derived from beamline operations have dramatically increased, causing difficulties in organizing these diverse and large amounts of data for the beamline operation staff and users. To overcome this problem, we have developed a data management system by introducing commercial middleware, which consists of a controller, database, and web servers. We have prepared several database projects using this system. Each project is dedicated to a certain aspect such as experimental results, beam time applications, beam time schedule, or beamline operation reports. Then we designed a scheme to link all the database projects.

Imaging three-dimensional surface objects with submolecular resolution by atomic force microscopy

Czech Academy of Sciences Publication Activity Database

Moreno, C.; Stetsovych, Oleksandr; Shimizu, T.K.; Custance, O.

2015-01-01

Roč. 15, č. 4 (2015), s. 2257-2262 ISSN 1530-6984 Institutional support: RVO:68378271 Keywords : noncontact atomic force microscopy (NC- AFM ) * submolecular resolution * three-dimensional dynamic force spectroscopy * high-resolution imaging Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 13.779, year: 2015

Racemic protein crystallography.

Science.gov (United States)

Yeates, Todd O; Kent, Stephen B H

2012-01-01

Although natural proteins are chiral and are all of one "handedness," their mirror image forms can be prepared by chemical synthesis. This opens up new opportunities for protein crystallography. A racemic mixture of the enantiomeric forms of a protein molecule can crystallize in ways that natural proteins cannot. Recent experimental data support a theoretical prediction that this should make racemic protein mixtures highly amenable to crystallization. Crystals obtained from racemic mixtures also offer advantages in structure determination strategies. The relevance of these potential advantages is heightened by advances in synthetic methods, which are extending the size limit for proteins that can be prepared by chemical synthesis. Recent ideas and results in the area of racemic protein crystallography are reviewed.

Facilities for small-molecule crystallography at synchrotron sources.

Science.gov (United States)

Barnett, Sarah A; Nowell, Harriott; Warren, Mark R; Wilcox, Andrian; Allan, David R

2016-01-01

Although macromolecular crystallography is a widely supported technique at synchrotron radiation facilities throughout the world, there are, in comparison, only very few beamlines dedicated to small-molecule crystallography. This limited provision is despite the increasing demand for beamtime from the chemical crystallography community and the ever greater overlap between systems that can be classed as either small macromolecules or large small molecules. In this article, a very brief overview of beamlines that support small-molecule single-crystal diffraction techniques will be given along with a more detailed description of beamline I19, a dedicated facility for small-molecule crystallography at Diamond Light Source.

Design and development of high-resolution atomic beam fluorescence spectroscopy facility for isotope shift and hyperfine structure measurements

International Nuclear Information System (INIS)

Acharyulu, G.V.S.G.; Sankari, M.; Kiran Kumar, P.V.; Suryanarayana, M.V.

2012-01-01

A high-resolution atomic beam fluorescence spectroscopy facility for the determination of isotope shifts and hyperfine structure in atomic species has been designed and developed. A resistively heated graphite tube atomic beam source was designed, tested and integrated into a compact interaction chamber for atomic beam fluorescence experiments. The design of the laser-atom interaction chamber and the source has been modified in a phased manner so as to achieve sub-Doppler resolution. The system has been used to record the hyperfine spectrum of the D2 transitions of Rb and K isotopes. The spectral resolution achieved is ∼ 26 MHz and is adequate to carry out high resolution measurement of isotope shifts and hyperfine structure of various atomic species. The other major advantage of the source is that it requires very small amounts of sample for achieving very good signal to noise ratio. (author)

Present needs and future trends in neutron crystallography and spectroscopy

International Nuclear Information System (INIS)

Williams, J.M.

1978-11-01

Topics covered include: structural investigation by neutron and x-ray diffraction; sources and characteristics of neutron radiation; time-of-flight techniques; overview of neutron crystallography and structural chemistry; hydrogen bonds; transition-metal hydride complexes; actinide and lanthanide complexes; carbon-hydrogen-metal interactions in organometallic chemistry and catalysis; metal clusters and catalysis; materials with unusual solid-state properties; biochemical molecules and biological systems; electron and spin density distributions in crystalline solids; incoherent neutron-scattering spectroscopy; and quasielastic neutron scattering and high resolution spectroscopy

UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions

International Nuclear Information System (INIS)

Siebert, Xavier; Navaza, Jorge

2009-01-01

UROX is software designed for the interactive fitting of atomic models into electron-microscopy reconstructions. The main features of the software are presented, along with a few examples. Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30–10 Å range and sometimes even beyond 10 Å. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/

The development of high-resolution spectroscopic methods and their use in atomic structure studies

International Nuclear Information System (INIS)

Poulsen, O.

1984-01-01

This thesis discusses work performed during the last nine years in the field of atomic spectroscopy. Several high-resolution techniques, ranging from quantum beats, level crossings, rf-laser double resonances to nonlinear field atom interactions, have been employed. In particular, these methods have been adopted and developed to deal with fast accelerated atomic or ionic beams, allowing studies of problems in atomic-structure theory. Fine- and hyperfine-structure determinations in the He I and Li I isoelectronic sequences, in 51 V I, and in 235 U I, II have permitted a detailed comparison with ab initio calculations, demonstrating the change in problems when going towards heavier elements or higher ionization stage. The last part of the thesis is concerned with the fundamental question of obtaining very high optical resolution in the interaction between a fast accelerated atom or ion beam and a laser field, this problem being the core in the continuing development of atomic spectroscopy necessary to challenge the more precise and sophisticated theories advanced. (Auth.)

LEED crystallography studies of the structure of clean and adsorbate-covered Ir, Pt and Rh crystal surfaces

International Nuclear Information System (INIS)

Koestner, R.J.

1982-08-01

There have only been a few Low Energy Electron Diffraction (LEED) intensity analyses carried out to determine the structure of molecules adsorbed on metal surfaces; most surface crystallography studies concentrated on the structure of clean unreconstructed or atomic adsorbate-covered transition metal faces. The few molecular adsorption systems already investigated by dynamical LEED are CO on Ni(100), Cu(100) and Pd(100) as well as C 2 H 2 and C 2 H 4 adsorbed on Pt(111). The emphasis of this thesis research has been to extend the applicability of LEED crystallography to the more complicated unit cells found in molecular overlayers on transition metals or in there constructed surfaces of clean transition metals

Lattice and strain analysis of atomic resolution Z-contrast images based on template matching

Energy Technology Data Exchange (ETDEWEB)

Zuo, Jian-Min, E-mail: jianzuo@uiuc.edu [Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801 (United States); Seitz Materials Research Laboratory, University of Illinois, Urbana, IL 61801 (United States); Shah, Amish B. [Center for Microanalysis of Materials, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Kim, Honggyu; Meng, Yifei; Gao, Wenpei [Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801 (United States); Seitz Materials Research Laboratory, University of Illinois, Urbana, IL 61801 (United States); Rouviére, Jean-Luc [CEA-INAC/UJF-Grenoble UMR-E, SP2M, LEMMA, Minatec, Grenoble 38054 (France)

2014-01-15

A real space approach is developed based on template matching for quantitative lattice analysis using atomic resolution Z-contrast images. The method, called TeMA, uses the template of an atomic column, or a group of atomic columns, to transform the image into a lattice of correlation peaks. This is helped by using a local intensity adjusted correlation and by the design of templates. Lattice analysis is performed on the correlation peaks. A reference lattice is used to correct for scan noise and scan distortions in the recorded images. Using these methods, we demonstrate that a precision of few picometers is achievable in lattice measurement using aberration corrected Z-contrast images. For application, we apply the methods to strain analysis of a molecular beam epitaxy (MBE) grown LaMnO{sub 3} and SrMnO{sub 3} superlattice. The results show alternating epitaxial strain inside the superlattice and its variations across interfaces at the spatial resolution of a single perovskite unit cell. Our methods are general, model free and provide high spatial resolution for lattice analysis. - Highlights: • A real space approach is developed for strain analysis using atomic resolution Z-contrast images and template matching. • A precision of few picometers is achievable in the measurement of lattice displacements. • The spatial resolution of a single perovskite unit cell is demonstrated for a LaMnO{sub 3} and SrMnO{sub 3} superlattice grown by MBE.

A history of experimental phasing in macromolecular crystallography.

Science.gov (United States)

Isaacs, Neil

2016-03-01

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

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

International Nuclear Information System (INIS)

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

2004-01-01

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

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.

NATO Advanced Study Institute on Electron Crystallography

CERN Document Server

Weirich, Thomas E; Zou, Xiaodong

2006-01-01

During the last decade we have been witness to several exciting achievements in electron crystallography. This includes structural and charge density studies on organic molecules complicated inorganic and metallic materials in the amorphous, nano-, meso- and quasi-crystalline state and also development of new software, tailor-made for the special needs of electron crystallography. Moreover, these developments have been accompanied by a now available new generation of computer controlled electron microscopes equipped with high-coherent field-emission sources, cryo-specimen holders, ultra-fast CCD cameras, imaging plates, energy filters and even correctors for electron optical distortions. Thus, a fast and semi-automatic data acquisition from small sample areas, similar to what we today know from imaging plates diffraction systems in X-ray crystallography, can be envisioned for the very near future. This progress clearly shows that the contribution of electron crystallography is quite unique, as it enables to r...

CO tip functionalization in subatomic resolution atomic force microscopy

International Nuclear Information System (INIS)

Kim, Minjung; Chelikowsky, James R.

2015-01-01

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule

MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron

International Nuclear Information System (INIS)

Cowieson, Nathan Philip; Aragao, David; Clift, Mark; Ericsson, Daniel J.; Gee, Christine; Harrop, Stephen J.; Mudie, Nathan; Panjikar, Santosh; Price, Jason R.; Riboldi-Tunnicliffe, Alan; Williamson, Rachel; Caradoc-Davies, Tom

2015-01-01

The macromolecular crystallography beamline MX1 at the Australian Synchrotron is described. MX1 is a bending-magnet crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range from 8 to 18 keV to a focal spot at the sample position of 120 µm FWHM. The beamline endstation and ancillary equipment facilitate local and remote access for both chemical and biological macromolecular crystallography. Here, the design of the beamline and endstation are discussed. The beamline has enjoyed a full user program for the last seven years and scientific highlights from the user program are also presented

Pharmaceutical crystallography: is there a devil in the details?

DEFF Research Database (Denmark)

Bond, A. D.

2012-01-01

Modern instruments for small-molecule crystallography continue to become more sophisticated and more automated. This technical progress provides a basis for frontier research in chemical and pharmaceutical crystallography, but it also encourages analytical crystallographers to become more...... are presented for pharmaceutical compounds, and the potential importance of the "details" in pharmaceutical crystallography is discussed....

Stacking it up: Exploring the limits of ultra-high resolution atomic force microscopy

NARCIS (Netherlands)

van der Heijden, N.J.

2017-01-01

Atomic force microscopy (AFM) is a technique wherein an atomically sharp needle raster scans across a surface, detecting forces between it and the sample. In state-of-the-art AFM experiments the measured forces are typically on the order of pico-Newtons, and the lateral resolution is on the order of

Celebrating macromolecular crystallography: A personal perspective

Directory of Open Access Journals (Sweden)

Abad-Zapatero, Celerino

2015-04-01

Full Text Available The twentieth century has seen an enormous advance in the knowledge of the atomic structures that surround us. The discovery of the first crystal structures of simple inorganic salts by the Braggs in 1914, using the diffraction of X-rays by crystals, provided the critical elements to unveil the atomic structure of matter. Subsequent developments in the field leading to macromolecular crystallography are presented with a personal perspective, related to the cultural milieu of Spain in the late 1950’s. The journey of discovery of the author, as he developed professionally, is interwoven with the expansion of macromolecular crystallography from the first proteins (myoglobin, hemoglobin to the ‘coming of age’ of the field in 1971 and the discoveries that followed, culminating in the determination of the structure of the ribosomes at the turn of the century. A perspective is presented exploring the future of the field and also a reflection about the future generations of Spanish scientists.El siglo XX ha sido testigo del increíble avance que ha experimentado el conocimiento de la estructura atómica de la materia que nos rodea. El descubrimiento de las primeras estructuras atómicas de sales inorgánicas por los Bragg en 1914, empleando difracción de rayos X con cristales, proporcionó los elementos clave para alcanzar tal conocimiento. Posteriores desarrollos en este campo, que condujeron a la cristalografía macromolecular, se presentan aquí desde una perspectiva personal, relacionada con el contexto cultural de la España de la década de los 50. La experiencia del descubrimiento científico, durante mi desarrollo profesional, se integra en el desarrollo de la cristalografía macromolecular, desde las primeras proteínas (míoglobina y hemoglobina, hasta su madurez en 1971 que, con los posteriores descubrimientos, culmina con la determinación del la estructura del ribosoma. Asimismo, se explora el futuro de esta disciplina y se

Crystallography taken to the extreme

Science.gov (United States)

Dubrovinskaia, Natalia; Dubrovinsky, Leonid

2018-06-01

This article is a brief autobiographical account of our life in science and the path that we took in performing the research for which we were awarded the Gregori Aminoff Prize in Crystallography 2017 by the Royal Swedish Academy of Sciences. We were invited to write it by the editor-in-chief of Physica Scripta, Suzy Lidström, who charged us with the task of contributing to a series of autobiographical articles published since 2014, the International Year of Crystallography, on the lives of the Aminoff Prize winners. As this series is intended to be of particular interest to young scientists, teachers and lecturers and those researching the history of science, we tried to adhere to this purpose while writing our story. It does not pretend to be a comprehensive review either of our own scientific results or, especially, of covering the complete history of the research field of high-pressure crystallography in which we are active.

LEED crystallography studies of the structure of clean and adsorbate-covered Ir, Pt and Rh crystal surfaces

Energy Technology Data Exchange (ETDEWEB)

Koestner, R.J.

1982-08-01

There have only been a few Low Energy Electron Diffraction (LEED) intensity analyses carried out to determine the structure of molecules adsorbed on metal surfaces; most surface crystallography studies concentrated on the structure of clean unreconstructed or atomic adsorbate-covered transition metal faces. The few molecular adsorption systems already investigated by dynamical LEED are CO on Ni(100), Cu(100) and Pd(100) as well as C/sub 2/H/sub 2/ and C/sub 2/H/sub 4/ adsorbed on Pt(111). The emphasis of this thesis research has been to extend the applicability of LEED crystallography to the more complicated unit cells found in molecular overlayers on transition metals or in there constructed surfaces of clean transition metals.

Visualization of arrangements of carbon atoms in graphene layers by Raman mapping and atomic-resolution TEM

KAUST Repository

Cong, Chunxiao

2013-02-01

In-plane and out-of-plane arrangements of carbon atoms in graphene layers play critical roles in the fundamental physics and practical applications of these novel two-dimensional materials. Here, we report initial results on the edge/crystal orientations and stacking orders of bi-and tri-layer graphene (BLG and TLG) from Raman spectroscopy and transmission electron microscopy (TEM) experiments performed on the same sample. We introduce a new method of transferring graphene flakes onto a normal TEM grid. Using this novel method, we probed the BLG and TLG flakes that had been previously investigated by Raman scattering with high-resolution (atomic) TEM.

Development of the protein crystallography by synchrotron radiation

International Nuclear Information System (INIS)

Yamamoto, Masaki

2014-01-01

Since crystal structure determination of the first protein by Kendrew in 1959, protein crystallography developed into the leading role of the protein structure study by various technology developments. Especially the utilization of synchrotron radiation from the 1990s brought innovative progress of protein crystallography on the data quality and the phasing method and had expanded the samples targets including membrane proteins and suprarmolecular complexes. Here I give the outline of the history and the future prospects of the protein crystallography from the role of synchrotron radiation. (author)

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

Science.gov (United States)

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

2018-03-01

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

The development of structural x-ray crystallography

Science.gov (United States)

Woolfson, M. M.

2018-03-01

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

X-ray spectroscopy and X-ray crystallography of metalloenzymes at XFELs

International Nuclear Information System (INIS)

Yano, Junko

2016-01-01

The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting crystallography data and X-ray emission spectra, using an energy dispersive spectrometer at ambient conditions. In addition, we have developed a way to collect metal L-edge data of dilute samples using soft X-rays at XFELs. The advantages and challenges of these methods will be described in this review. (author)

Electron dose dependence of signal-to-noise ratio, atom contrast and resolution in transmission electron microscope images

International Nuclear Information System (INIS)

Lee, Z.; Rose, H.; Lehtinen, O.; Biskupek, J.; Kaiser, U.

2014-01-01

In order to achieve the highest resolution in aberration-corrected (AC) high-resolution transmission electron microscopy (HRTEM) images, high electron doses are required which only a few samples can withstand. In this paper we perform dose-dependent AC-HRTEM image calculations, and study the dependence of the signal-to-noise ratio, atom contrast and resolution on electron dose and sampling. We introduce dose-dependent contrast, which can be used to evaluate the visibility of objects under different dose conditions. Based on our calculations, we determine optimum samplings for high and low electron dose imaging conditions. - Highlights: • The definition of dose-dependent atom contrast is introduced. • The dependence of the signal-to-noise ratio, atom contrast and specimen resolution on electron dose and sampling is explored. • The optimum sampling can be determined according to different dose conditions

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.

Macromolecular neutron crystallography at the Protein Crystallography Station (PCS)

OpenAIRE

Kovalevsky, Andrey; Fisher, Zoe; Johnson, Hannah; Mustyakimov, Marat; Waltman, Mary Jo; Langan, Paul

2010-01-01

The Protein Crystallography Station user facility at Los Alamos National Laboratory not only offers open access to a high-performance neutron beamline, but also actively supports and develops new methods in protein expression, deuteration, purification, robotic crystallization and the synthesis of substrates with stable isotopes and provides assistance with data-reduction and structure-refinement software and comprehensive neutron structure analysis.

High resolution atomic spectra of rare earths : progress report

International Nuclear Information System (INIS)

Saksena, G.D.; Ahmad, S.A.

1976-01-01

High resolution studies of atomic spectra of neodymium and gadolinium are being carried out on a recording Fabry-Perot spectrometer. The present progress report concerns work done on new assignments as well as confirmation of recently assigned electronic configurations and evaluation of isotope shifts of energy levels which have been possible from the isotope shift data obtained for several transitions of NdI, NdII and GdI, GdII respectively. (author)

Structure study of the tri-continuous mesoporous silica IBN-9 by electron crystallography

KAUST Repository

Zhang, Daliang

2011-12-01

High resolution electron microscopy (HRTEM) has unique advantages for structural determination of nano-sized porous materials compared to X-ray diffraction, because it provides the important structure factor phase information which is lost in diffraction. Here we demonstrate the structure determination of the first tri-continuous mesoporous silica IBN-9 by electron crystallography. IBN-9 has a hexagonal unit cell with the space group P6 3/mcm and a = 88.4 , c = 84.3 . HRTEM images taken along three main directions, [0 0 1], [11̄0] and [1 0 0] were combined to reconstruct the 3D electrostatic potential map, from which the tri-continuous pore structure of IBN-9 was discovered. The different steps of structure determination of unknown mesoporous structures by electron crystallography are described in details. Similar procedures can also be applied for structure determination of other porous and nonporous crystalline materials. © 2011 Elsevier Inc. All rights reserved.

A design for a subminiature, low energy scanning electron microscope with atomic resolution

International Nuclear Information System (INIS)

Eastham, D. A.; Edmondson, P.; Greene, S.; Donnelly, S.; Olsson, E.; Svensson, K.; Bleloch, A.

2009-01-01

We describe a type of scanning electron microscope that works by directly imaging the electron field-emission sites on a nanotip. Electrons are extracted from the nanotip through a nanoscale aperture, accelerated in a high electric field, and focused to a spot using a microscale Einzel lens. If the whole microscope (accelerating section and lens) and the focal length are both restricted in size to below 10 μm, then computer simulations show that the effects of aberration are extremely small and it is possible to have a system with approximately unit magnification at electron energies as low as 300 eV. Thus a typical emission site of 1 nm diameter will produce an image of the same size, and an atomic emission site will give a resolution of 0.1-0.2 nm (1-2 A). Also, because the beam is not allowed to expand beyond 100 nm in diameter, the depth of field is large and the contribution to the beam spot size from chromatic aberrations is less than 0.02 nm (0.2 A) for 500 eV electrons. Since it is now entirely possible to make stable atomic sized emitters (nanopyramids), it is expected that this instrument will have atomic resolution. Furthermore the brightness of the beam is determined only by the field emission and can be up to 1x10 6 times larger than in a typical (high energy) electron microscope. The advantages of this low energy, bright-beam electron microscope with atomic resolution are described and include the possibility of it being used to rapidly sequence the human genome from a single strand of DNA as well as being able to identify atomic species directly from the elastic scattering of electrons

History of protein crystallography in China

OpenAIRE

Rao, Zihe

2007-01-01

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

In situ macromolecular crystallography using microbeams.

Science.gov (United States)

Axford, Danny; Owen, Robin L; Aishima, Jun; Foadi, James; Morgan, Ann W; Robinson, James I; Nettleship, Joanne E; Owens, Raymond J; Moraes, Isabel; Fry, Elizabeth E; Grimes, Jonathan M; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S; Stuart, David I; Evans, Gwyndaf

2012-05-01

Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams. © 2012 International Union of Crystallography

Signal Tracking Beyond the Time Resolution of an Atomic Sensor by Kalman Filtering

Science.gov (United States)

Jiménez-Martínez, Ricardo; Kołodyński, Jan; Troullinou, Charikleia; Lucivero, Vito Giovanni; Kong, Jia; Mitchell, Morgan W.

2018-01-01

We study causal waveform estimation (tracking) of time-varying signals in a paradigmatic atomic sensor, an alkali vapor monitored by Faraday rotation probing. We use Kalman filtering, which optimally tracks known linear Gaussian stochastic processes, to estimate stochastic input signals that we generate by optical pumping. Comparing the known input to the estimates, we confirm the accuracy of the atomic statistical model and the reliability of the Kalman filter, allowing recovery of waveform details far briefer than the sensor's intrinsic time resolution. With proper filter choice, we obtain similar benefits when tracking partially known and non-Gaussian signal processes, as are found in most practical sensing applications. The method evades the trade-off between sensitivity and time resolution in coherent sensing.

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

Science.gov (United States)

Sakabe, N; Sakabe, K; Sasaki, K

2004-01-01

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

Streptavidin and its biotin complex at atomic resolution

International Nuclear Information System (INIS)

Le Trong, Isolde; Wang, Zhizhi; Hyre, David E.; Lybrand, Terry P.; Stayton, Patrick S.; Stenkamp, Ronald E.

2011-01-01

Analysis of atomic resolution crystal structures of wild-type streptavidin (1.03 Å) and its biotin complex (0.95 Å) indicate the range of conformational states taken on by this protein in the solid state. Most of the structural variation is found in the polypeptide loops between the strands in this β-sandwich protein. Atomic resolution crystallographic studies of streptavidin and its biotin complex have been carried out at 1.03 and 0.95 Å, respectively. The wild-type protein crystallized with a tetramer in the asymmetric unit, while the crystals of the biotin complex contained two subunits in the asymmetric unit. Comparison of the six subunits shows the various ways in which the protein accommodates ligand binding and different crystal-packing environments. Conformational variation is found in each of the polypeptide loops connecting the eight strands in the β-sandwich subunit, but the largest differences are found in the flexible binding loop (residues 45–52). In three of the unliganded subunits the loop is in an ‘open’ conformation, while in the two subunits binding biotin, as well as in one of the unliganded subunits, this loop ‘closes’ over the biotin–binding site. The ‘closed’ loop contributes to the protein’s high affinity for biotin. Analysis of the anisotropic displacement parameters included in the crystallographic models is consistent with the variation found in the loop structures and the view that the dynamic nature of the protein structure contributes to the ability of the protein to bind biotin so tightly

Chromatic Aberration Correction for Atomic Resolution TEM Imaging from 20 to 80 kV.

Science.gov (United States)

Linck, Martin; Hartel, Peter; Uhlemann, Stephan; Kahl, Frank; Müller, Heiko; Zach, Joachim; Haider, Max; Niestadt, Marcel; Bischoff, Maarten; Biskupek, Johannes; Lee, Zhongbo; Lehnert, Tibor; Börrnert, Felix; Rose, Harald; Kaiser, Ute

2016-08-12

Atomic resolution in transmission electron microscopy of thin and light-atom materials requires a rigorous reduction of the beam energy to reduce knockon damage. However, at the same time, the chromatic aberration deteriorates the resolution of the TEM image dramatically. Within the framework of the SALVE project, we introduce a newly developed C_{c}/C_{s} corrector that is capable of correcting both the chromatic and the spherical aberration in the range of accelerating voltages from 20 to 80 kV. The corrector allows correcting axial aberrations up to fifth order as well as the dominating off-axial aberrations. Over the entire voltage range, optimum phase-contrast imaging conditions for weak signals from light atoms can be adjusted for an optical aperture of at least 55 mrad. The information transfer within this aperture is no longer limited by chromatic aberrations. We demonstrate the performance of the microscope using the examples of 30 kV phase-contrast TEM images of graphene and molybdenum disulfide, showing unprecedented contrast and resolution that matches image calculations.

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.…

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

Science.gov (United States)

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

2012-10-08

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

Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls

Directory of Open Access Journals (Sweden)

Aaron J. Oakley

2012-10-01

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

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

Science.gov (United States)

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

2009-01-01

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

Neutron protein crystallography in JAERI

Indian Academy of Sciences (India)

results have clearly suggested that hydrogen atoms and water molecules around ... resolution (from 1.5 Å to 2.0 Å) structural analyses of several proteins. .... system like PDB is not sufficient to study hydrogen-related studies such as hydrogen.

High-pressure crystallography

Science.gov (United States)

Katrusiak, A.

2008-01-01

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

Building a pseudo-atomic model of the anaphase-promoting complex

International Nuclear Information System (INIS)

Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; Fonseca, Paula C. A. da; Barford, David

2013-01-01

This article describes an example of molecular replacement in which atomic models are used to interpret electron-density maps determined using single-particle electron-microscopy data. The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14–15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex

SPring-8 Structural Biology Beamlines / Current Status of Public Beamlines for Protein Crystallography at SPring-8

International Nuclear Information System (INIS)

Kawamoto, Masahide; Hasegawa, Kazuya; Shimizu, Nobutaka; Sakai, Hisanobu; Shimizu, Tetsuya; Nisawa, Atsushi; Yamamoto, Masaki

2007-01-01

SPring-8 has 2 protein crystallography beamlines for public use, BL38B1 (Structural Biology III) and BL41XU (Structural Biology I). The BL38B1 is a bending magnet beamline for routine data collection, and the BL41XU is an undulator beamline specially customized for micro beam and ultra-high resolutional experiment. The designs and the performances of each beamline are presented

Length-extension resonator as a force sensor for high-resolution frequency-modulation atomic force microscopy in air.

Science.gov (United States)

Beyer, Hannes; Wagner, Tino; Stemmer, Andreas

2016-01-01

Frequency-modulation atomic force microscopy has turned into a well-established method to obtain atomic resolution on flat surfaces, but is often limited to ultra-high vacuum conditions and cryogenic temperatures. Measurements under ambient conditions are influenced by variations of the dew point and thin water layers present on practically every surface, complicating stable imaging with high resolution. We demonstrate high-resolution imaging in air using a length-extension resonator operating at small amplitudes. An additional slow feedback compensates for changes in the free resonance frequency, allowing stable imaging over a long period of time with changing environmental conditions.

Macromolecular crystallography beamline X25 at the NSLS

Energy Technology Data Exchange (ETDEWEB)

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

2014-04-08

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

Macromolecular crystallography beamline X25 at the NSLS

International Nuclear Information System (INIS)

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

2014-01-01

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

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

Recent progress in structural biology: lessons from our research history.

Science.gov (United States)

Nitta, Ryo; Imasaki, Tsuyoshi; Nitta, Eriko

2018-05-16

The recent 'resolution revolution' in structural analyses of cryo-electron microscopy (cryo-EM) has drastically changed the research strategy for structural biology. In addition to X-ray crystallography and nuclear magnetic resonance spectroscopy, cryo-EM has achieved the structural analysis of biological molecules at near-atomic resolution, resulting in the Nobel Prize in Chemistry 2017. The effect of this revolution has spread within the biology and medical science fields affecting everything from basic research to pharmaceutical development by visualizing atomic structure. As we have used cryo-EM as well as X-ray crystallography since 2000 to elucidate the molecular mechanisms of the fundamental phenomena in the cell, here we review our research history and summarize our findings. In the first half of the review, we describe the structural mechanisms of microtubule-based motility of molecular motor kinesin by using a joint cryo-EM and X-ray crystallography method. In the latter half, we summarize our structural studies on transcriptional regulation by X-ray crystallography of in vitro reconstitution of a multi-protein complex.

Local crystallography analysis for atomically resolved scanning tunneling microscopy images

International Nuclear Information System (INIS)

Lin, Wenzhi; Li, Qing; Belianinov, Alexei; Gai, Zheng; Baddorf, Arthur P; Pan, Minghu; Jesse, Stephen; Kalinin, Sergei V; Sales, Brian C; Sefat, Athena

2013-01-01

Scanning probe microscopy has emerged as a powerful and flexible tool for atomically resolved imaging of surface structures. However, due to the amount of information extracted, in many cases the interpretation of such data is limited to being qualitative and semi-quantitative in nature. At the same time, much can be learned from local atom parameters, such as distances and angles, that can be analyzed and interpreted as variations of local chemical bonding, or order parameter fields. Here, we demonstrate an iterative algorithm for indexing and determining atomic positions that allows the analysis of inhomogeneous surfaces. This approach is further illustrated by local crystallographic analysis of several real surfaces, including highly ordered pyrolytic graphite and an Fe-based superconductor FeTe 0.55 Se 0.45 . This study provides a new pathway to extract and quantify local properties for scanning probe microscopy images. (paper)

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

Science.gov (United States)

Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

2014-01-01

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions

Towards a rational approach for heavy-atom derivative screening in protein crystallography

International Nuclear Information System (INIS)

Agniswamy, Johnson; Joyce, M. Gordon; Hammer, Carl H.; Sun, Peter D.

2008-01-01

Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity of more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity of more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Met-, Cys- and His-containing peptides were derivatized against Hg, Au and Pt compounds, while Tyr-, Glu-, Asp-, Asn- and Gln-containing peptides were assessed against Pb compounds. A total of 1668 reactive conditions were examined using mass spectrometry and were compiled into heavy-atom reactivity tables. The results showed that heavy-atom derivatization reactions are highly linked to buffer and pH, with the most accommodating buffer being MES at pH 6. A group of 21 compounds were identified as most successful irrespective of ligand or buffer/pH conditions. To assess the applicability of the peptide heavy-atom reactivity to proteins, lysozyme crystals were derivatized with a list of peptide-reactive compounds that included both known and new compounds for lysozyme derivatization. The results showed highly consistent heavy-atom reactivities between the peptides and lysozyme

Neutron diffractometer for bio-crystallography (BIX) with an imaging plate neutron detector

Energy Technology Data Exchange (ETDEWEB)

Niimura, Nobuo [Japan Atomic Energy Research Inst., Ibaraki-ken (Japan)

1994-12-31

We have constructed a dedicated diffractometer for neutron crystallography in biology (BIX) on the JRR-3M reactor at JAERI (Japan Atomic Energy Research Institute). The diffraction intensity from a protein crystal is weaker than that from most inorganic materials. In order to overcome the intensity problem, an elastically bent silicon monochromator and a large area detector system were specially designed. A preliminary result of diffraction experiment using BIX has been reported. An imaging plate neutron detector has been developed and a feasibility experiment was carried out on BIX. Results are reported. An imaging plate neutron detector has been developed and a feasibility test was carried out using BIX.

Experimental evaluation of interfaces using atomic-resolution high angle annular dark field (HAADF) imaging

International Nuclear Information System (INIS)

Robb, Paul D.; Finnie, Michael; Longo, Paolo; Craven, Alan J.

2012-01-01

Aberration-corrected high angle annular dark field (HAADF) imaging in scanning transmission electron microscopy (STEM) can now be performed at atomic-resolution. This is an important tool for the characterisation of the latest semiconductor devices that require individual layers to be grown to an accuracy of a few atomic layers. However, the actual quantification of interfacial sharpness at the atomic-scale can be a complicated matter. For instance, it is not clear how the use of the total, atomic column or background HAADF signals can affect the measured sharpness or individual layer widths. Moreover, a reliable and consistent method of measurement is necessary. To highlight these issues, two types of AlAs/GaAs interfaces were studied in-depth by atomic-resolution HAADF imaging. A method of analysis was developed in order to map the various HAADF signals across an image and to reliably determine interfacial sharpness. The results demonstrated that the level of perceived interfacial sharpness can vary significantly with specimen thickness and the choice of HAADF signal. Individual layer widths were also shown to have some dependence on the choice of HAADF signal. Hence, it is crucial to have an awareness of which part of the HAADF signal is chosen for analysis along with possible specimen thickness effects for future HAADF studies performed at the scale of a few atomic layers. -- Highlights: ► Quantification of interfaces using atomic-scale HAADF imaging is considered. ► The sharpness of AlAs/GaAs interfaces is investigated. ► A method of analysis was developed to map the various HAADF signals in an image. ► Measured sharpness varies with specimen thickness and HAADF signal type.

Atomic resolution chemical bond analysis of oxygen in La2CuO4

Science.gov (United States)

Haruta, M.; Nagai, T.; Lugg, N. R.; Neish, M. J.; Nagao, M.; Kurashima, K.; Allen, L. J.; Mizoguchi, T.; Kimoto, K.

2013-08-01

The distorted CuO6 octahedron in La2CuO4 was studied using aberration-corrected scanning transmission electron microscopy at atomic resolution. The near-edge structure in the oxygen K-edge electron energy-loss spectrum was recorded as a function of the position of the electron probe. After background subtraction, the measured spectrum image was processed using a recently developed inversion process to remove the mixing of signals on the atomic columns due to elastic and thermal scattering. The spectra were then compared with first-principles band structure calculations based on the local-density approximation plus on-site Coulomb repulsion (LDA + U) approach. In this article, we describe in detail not only anisotropic chemical bonding of the oxygen 2p state with the Cu 3d state but also with the Cu 4p and La 5d/4f states. Furthermore, it was found that buckling of the CuO2 plane was also detectable at the atomic resolution oxygen K-edge. Lastly, it was found that the effects of core-hole in the O K-edge were strongly dependent on the nature of the local chemical bonding, in particular, whether it is ionic or covalent.

Quantum crystallography: A perspective.

Science.gov (United States)

Massa, Lou; Matta, Chérif F

2018-06-30

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

Analytical evaluation of atomic form factors: Application to Rayleigh scattering

Energy Technology Data Exchange (ETDEWEB)

Safari, L., E-mail: laleh.safari@ist.ac.at [IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400 Klosterneuburg (Austria); Department of Physics, University of Oulu, Box 3000, FI-90014 Oulu (Finland); Santos, J. P. [Laboratório de Instrumentação, Engenharia Biomédica e Física da Radiação (LIBPhys-UNL), Departamento de Física, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Amaro, P. [Laboratório de Instrumentação, Engenharia Biomédica e Física da Radiação (LIBPhys-UNL), Departamento de Física, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Physikalisches Institut, Universität Heidelberg, D-69120 Heidelberg (Germany); Jänkälä, K. [Department of Physics, University of Oulu, Box 3000, FI-90014 Oulu (Finland); Fratini, F. [Department of Physics, University of Oulu, Box 3000, FI-90014 Oulu (Finland); Institute of Atomic and Subatomic Physics, TU Wien, Stadionallee 2, 1020 Wien (Austria); Departamento de Física, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG (Brazil)

2015-05-15

Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.

William Barlow and the Determination of Atomic Arrangement in Crystals.

Science.gov (United States)

Mauskopf, Seymour H

2015-04-01

William Barlow (1845-1934) was an important if unconventional scientist, known for having developed the 'closest-packing' atomic models of crystal structure. He resumed an early nineteenth-century tradition of utilizing crystallographical and chemical data to determine atomic arrangements in crystals. This essay recounts Barlow's career and scientific activity in three parts: (a) His place in the tradition of determining atomic arrangement in context of this earlier tradition and of contemporaneous developments of crystallography and chemistry, (b) his unconventional career, and (c) the 'success' of his program to determine atomic arrangements in crystals and its influence on the work of William Lawrence Bragg.

Midinfrared absorption measured at a lambda/400 resolution with an atomic force microscope.

Science.gov (United States)

Houel, Julien; Homeyer, Estelle; Sauvage, Sébastien; Boucaud, Philippe; Dazzi, Alexandre; Prazeres, Rui; Ortéga, Jean-Michel

2009-06-22

Midinfrared absorption can be locally measured using a detection combining an atomic force microscope and a pulsed excitation. This is illustrated for the midinfrared bulk GaAs phonon absorption and for the midinfrared absorption of thin SiO(2) microdisks. We show that the signal given by the cantilever oscillation amplitude of the atomic force microscope follows the spectral dependence of the bulk material absorption. The absorption spatial resolution achieved with microdisks is around 50 nanometer for an optical excitation around 22 micrometer wavelength.

Crystallography of quasicrystals concepts, methods and structures

CERN Document Server

Walter, Steurer

2009-01-01

From tilings to quasicrystal structures and from surfaces to the n-dimensional approach, this book gives a full, self-contained in-depth description of the crystallography of quasicrystals. It aims not only at conveying the concepts and a precise picture of the structures of quasicrystals, butit also enables the interested reader to enter the field of quasicrystal structure analysis. Going beyond metallic quasicrystals, it also describes the new, dynamically growing field of photonic quasicrystals. The readership will be graduate students and researchers in crystallography, solid-state physics, materials science, solid- state chemistry and applied mathematics.

Crystallography and Drug Design

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 12. Crystallography and Drug Design. K Suguna. General Article Volume 19 Issue 12 December 2014 pp 1093-1103. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/019/12/1093-1103. Keywords.

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

Science.gov (United States)

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

OCTOPUS: an innovative multimodal diffractometer for neutron macromolecular crystallography across the length scales

International Nuclear Information System (INIS)

Blakeley, M.P.; Andersen, K.; Kreuz, M.; Giroud, B.; McSweeney, S.; Mitchell, E.; Teixeira, S.C.M.; Forsyth, V.T.

2011-01-01

We propose to construct a novel protein diffractometer at position H112B. The new instrument will deliver major efficiency gains, as well as offering greatly extended flexibility through the option of several easily interchangeable modes of operation. This proposal builds on the demonstrable need to extend ILL's capacity for high resolution structural studies of protein systems, as well as a need to widen the scope of biological crystallography - in particular for monochromatic studies at both high and low resolution. The development will be carried out in close collaboration with structural biologists at the ESRF, and engineered in such a way that the user interface of the instrument (from sample to software) will be transparently identifiable to a large, dynamic, and driven community of European synchrotron X-ray macromolecular crystallographers. (authors)

Describing intrinsically disordered proteins at atomic resolution by NMR

International Nuclear Information System (INIS)

Ringkjobing Jensen, Malene; Blackledge, Martin; Ruigrok, Rob WH

2013-01-01

There is growing interest in the development of physical methods to study the conformational behaviour and biological activity of intrinsically disordered proteins (IDPs). In this review recent advances in the elucidation of quantitative descriptions of disordered proteins from nuclear magnetic resonance spectroscopy are presented. Ensemble approaches are particularly well adapted to map the conformational energy landscape sampled by the protein at atomic resolution. Significant advances in development of calibrated approaches to the statistical representation of the conformational behaviour of IDPs are presented, as well as applications to some biologically important systems where disorder plays a crucial role. (authors)

Atomic resolution electrostatic potential mapping of graphene sheets by off-axis electron holography

Energy Technology Data Exchange (ETDEWEB)

Cooper, David, E-mail: david.cooper@cea.fr [University Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054, Grenoble (France); Pan, Cheng-Ta; Haigh, Sarah [School of Materials, The University of Manchester, Manchester M13 9PL (United Kingdom)

2014-06-21

Off-axis electron holography has been performed at atomic resolution with the microscope operated at 80 kV to provide electrostatic potential maps from single, double, and triple layer graphene. These electron holograms have been reconstructed in order to obtain information about atomically resolved and mean inner potentials. We propose that off-axis electron holography can now be used to measure the electrical properties in a range of two-dimensional semiconductor materials and three dimensional devices comprising stacked layers of films to provide important information about their electrical properties.

Atomic resolution electrostatic potential mapping of graphene sheets by off-axis electron holography

International Nuclear Information System (INIS)

Cooper, David; Pan, Cheng-Ta; Haigh, Sarah

2014-01-01

Off-axis electron holography has been performed at atomic resolution with the microscope operated at 80 kV to provide electrostatic potential maps from single, double, and triple layer graphene. These electron holograms have been reconstructed in order to obtain information about atomically resolved and mean inner potentials. We propose that off-axis electron holography can now be used to measure the electrical properties in a range of two-dimensional semiconductor materials and three dimensional devices comprising stacked layers of films to provide important information about their electrical properties.

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.

Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

International Nuclear Information System (INIS)

Chen, Liqing; Wang, Yujun; Wells, David; Toh, Diana; Harold, Hunt; Zhou, Jing; DiGiammarino, Enrico; Meehan, Edward J.

2006-01-01

The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors

Atomic resolution imaging of YAlO{sub 3}: Ce in the chromatic and spherical aberration corrected PICO electron microscope

Energy Technology Data Exchange (ETDEWEB)

Jin, Lei [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich (Germany); Barthel, Juri [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich (Germany); Central Facility for Electron Microscopy, RWTH Aachen University, 52074 Aachen (Germany); Jia, Chun-Lin [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich (Germany); School of Electronic and Information Engineering and State Key Laboratory for Mechanical Behaviour of Materials, Xi' an Jiaotong University, Xi' an 710049 (China); Urban, Knut W., E-mail: k.urban@fz-juelich.de [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich, (Germany); School of Electronic and Information Engineering and State Key Laboratory for Mechanical Behaviour of Materials, Xi' an Jiaotong University, Xi' an 710049 (China)

2017-05-15

Highlights: • First time resolution of 57 pm atom separations by HRTEM with 200 keV electrons. • Quantification of the image spread by absolute matching of experiment and simulation. • An information limit of 52 pm is deduced from the determined image spread. • Substantial deviations from the bulk structure are observed for the ultra-thin sample. - Abstract: The application of combined chromatic and spherical aberration correction in high-resolution transmission electron microscopy enables a significant improvement of the spatial resolution down to 50 pm. We demonstrate that such a resolution can be achieved in practice at 200 kV. Diffractograms of images of gold nanoparticles on amorphous carbon demonstrate corresponding information transfer. The Y atom pairs in [010] oriented yttrium orthoaluminate are successfully imaged together with the Al and the O atoms. Although the 57 pm pair separation is well demonstrated separations between 55 pm and 80 pm are measured. This observation is tentatively attributed to structural relaxations and surface reconstruction in the very thin samples used. Quantification of the resolution limiting effective image spread is achieved based on an absolute match between experimental and simulated image intensity distributions.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

Analysis and Calibration of in situ scanning tunnelling microscopy Images with atomic Resolution Influenced by Surface Drift Phenomena

DEFF Research Database (Denmark)

Andersen, Jens Enevold Thaulov; Møller, Per

1994-01-01

The influence of surface drift velocities on in situ scanning tunnelling microscopy (STM) experiments with atomic resolution is analysed experimentally and mathematically. Constant drift velocities much smaller than the speed of scanning can in many in situ STM experiments with atomic resolution ...... as well as the vectors of the non-distorted surface lattice can be determined. The calibration of distances can thus be carried out also when the image is influenced by drift. Results with gold surfaces and graphite surfaces are analysed and discussed....

Investigation of chemical modifiers for phosphorus in a graphite furnace using high-resolution continuum source atomic absorption spectrometry

International Nuclear Information System (INIS)

Lepri, Fabio G.; Dessuy, Morgana B.; Vale, Maria Goreti R.; Borges, Daniel L.G.; Welz, Bernhard; Heitmann, Uwe

2006-01-01

Phosphorus is not one of the elements that are typically determined by atomic absorption spectrometry, but this technique nevertheless offers several advantages that make it attractive, such as the relatively great freedom from interferences. As the main resonance lines for phosphorus are in the vacuum-ultraviolet, inaccessible by conventional atomic absorption spectrometry equipment, L'vov and Khartsyzov proposed to use the non-resonance doublet at 213.5 / 213.6 nm. Later it turned out that with conventional equipment it is necessary to use a chemical modifier in order to get reasonable sensitivity, and lanthanum was the first one suggested for that purpose. In the following years more than 30 modifiers have been proposed for the determination of this element, and there is no consensus about the best one. In this work high-resolution continuum source atomic absorption spectrometry has been used to investigate the determination of phosphorus without a modifier and with the addition of selected modifiers of very different nature, including the originally recommended lanthanum modifier, several palladium-based modifiers and sodium fluoride. As high-resolution continuum source atomic absorption spectrometry is revealing the spectral environment of the analytical line at high resolution, it became obvious that without the addition of a modifier essentially no atomic phosphorus is formed, even at 2700 deg. C . The absorption measured with line source atomic absorption spectrometry in this case is due to the PO molecule, the spectrum of which is overlapping with the atomic line. Palladium, with or without the addition of calcium or ascorbic acid, was found to be the only modifier to produce almost exclusively atomic phosphorus. Lanthanum and particularly sodium fluoride produced a mixture of P and PO, depending on the atomization temperature. This fact can explain at least some of the discrepancies found in the literature and some of the phenomena observed in the

Serial Femtosecond Crystallography

OpenAIRE

Chapman, Henry N.

2015-01-01

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

Crystallography across the Sciences 2

NARCIS (Netherlands)

Schenk, H.

2008-01-01

This second commemorative compilation from the IUCr contains 24 invited articles, all refereed, from some of today's most eminent crystallographers. The articles describe state-of-the-art research in which crystallography has played a major role, and are intended to be attractive for a broad

Finding New Thermoelectric Compounds Using Crystallographic Data: Atomic Displacement Parameters

International Nuclear Information System (INIS)

Chakoumakos, B.C.; Mandrus, D.G.; Sales, B.C.; Sharp, J.W.

1999-01-01

A new structure-property relationship is discussed which links atomic displacement parameters (ADPs) and the lattice thermal conductivity of clathrate-like compounds. For many clathrate-like compounds, in which one of the atom types is weakly bound and ''rattles'' within its atomic cage, room temperature ADP information can be used to estimate the room temperature lattice thermal conductivity, the vibration frequency of the ''rattler'', and the temperature dependence of the heat capacity. Neutron data and X-ray crystallography data, reported in the literature, are used to apply this analysis to several promising classes of thermoelectric materials

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

Science.gov (United States)

Zhang, Tao; Gu, Yuanxin; Fan, Haifu

2016-06-01

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

Langmuir-Blodgett nanotemplates for protein crystallography.

Science.gov (United States)

Pechkova, Eugenia; Nicolini, Claudio

2017-12-01

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

Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

Science.gov (United States)

Robb, Paul D; Craven, Alan J

2008-12-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

Column ratio mapping: A processing technique for atomic resolution high-angle annular dark-field (HAADF) images

International Nuclear Information System (INIS)

Robb, Paul D.; Craven, Alan J.

2008-01-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [1 1 0]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 A-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

Quantitative atomic resolution elemental mapping via absolute-scale energy dispersive X-ray spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Chen, Z. [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia); Weyland, M. [Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800 (Australia); Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800 (Australia); Sang, X.; Xu, W.; Dycus, J.H.; LeBeau, J.M. [Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695 (United States); D' Alfonso, A.J.; Allen, L.J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Findlay, S.D., E-mail: scott.findlay@monash.edu [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia)

2016-09-15

Quantitative agreement on an absolute scale is demonstrated between experiment and simulation for two-dimensional, atomic-resolution elemental mapping via energy dispersive X-ray spectroscopy. This requires all experimental parameters to be carefully characterized. The agreement is good, but some discrepancies remain. The most likely contributing factors are identified and discussed. Previous predictions that increasing the probe forming aperture helps to suppress the channelling enhancement in the average signal are confirmed experimentally. It is emphasized that simple column-by-column analysis requires a choice of sample thickness that compromises between being thick enough to yield a good signal-to-noise ratio while being thin enough that the overwhelming majority of the EDX signal derives from the column on which the probe is placed, despite strong electron scattering effects. - Highlights: • Absolute scale quantification of 2D atomic-resolution EDX maps is demonstrated. • Factors contributing to remaining small quantitative discrepancies are identified. • Experiment confirms large probe-forming apertures suppress channelling enhancement. • The thickness range suitable for reliable column-by-column analysis is discussed.

Crystallography and structure of lath martensite of hexagonal α-phase in zirconium

International Nuclear Information System (INIS)

Dobromyslov, A.V.; Talits, N.I.

1989-01-01

Crystallography, morphology and substructural features of lath martensite produced in zirconium after quenching are studied using transmission electron microscopy and electron diffraction methods. It is shown that all lathes in the package as a rule have close oreintation, but sometimes lathes are met which are present in a twin position in relation to neighbouring ones. In this case twining plane between the lathes coincides with α-phase [1011] plane. Residual β-phase between lathes is not preserved. It is detected that threi types of habitus planes of lath martensite of hexagonal α-phase are observed: [1010], [1120], [1011]. Atom-crystallographic mechanism of lattice reconstruction at β → α-phase lath habitus planes produced on its base coincide with the ones experimentally determined

Status and prospects of macromolecular crystallography

Indian Academy of Sciences (India)

technique that could be completely automated in most cases. ... major challenge in macromolecular crystallography today is ... tial characterization of crystals in the home source and make a ... opportunities for a generation of structural biolo-.

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

International Nuclear Information System (INIS)

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

1978-01-01

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

Structure of Alzheimer’s disease amyloid precursor protein copper-binding domain at atomic resolution

Energy Technology Data Exchange (ETDEWEB)

Kong, Geoffrey Kwai-Wai; Adams, Julian J. [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Cappai, Roberto [Department of Pathology and Centre for Neuroscience, The University of Melbourne, Victoria 3010 (Australia); The Mental Health Research Institute of Victoria, Parkville, Victoria 3052 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia); Parker, Michael W., E-mail: mparker@svi.edu.au [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia)

2007-10-01

An atomic resolution structure of the copper-binding domain of the Alzheimer’s disease amyloid precursor protein is presented. Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer’s disease, as its cleavage generates the Aβ peptide that is toxic to cells. APP is able to bind Cu{sup 2+} and reduce it to Cu{sup +} through its copper-binding domain (CuBD). The interaction between Cu{sup 2+} and APP leads to a decrease in Aβ production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 Å) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu{sup 2+} reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Aβ production.

Precision controlled atomic resolution scanning transmission electron microscopy using spiral scan pathways

Science.gov (United States)

Sang, Xiahan; Lupini, Andrew R.; Ding, Jilai; Kalinin, Sergei V.; Jesse, Stephen; Unocic, Raymond R.

2017-03-01

Atomic-resolution imaging in an aberration-corrected scanning transmission electron microscope (STEM) can enable direct correlation between atomic structure and materials functionality. The fast and precise control of the STEM probe is, however, challenging because the true beam location deviates from the assigned location depending on the properties of the deflectors. To reduce these deviations, i.e. image distortions, we use spiral scanning paths, allowing precise control of a sub-Å sized electron probe within an aberration-corrected STEM. Although spiral scanning avoids the sudden changes in the beam location (fly-back distortion) present in conventional raster scans, it is not distortion-free. “Archimedean” spirals, with a constant angular frequency within each scan, are used to determine the characteristic response at different frequencies. We then show that such characteristic functions can be used to correct image distortions present in more complicated constant linear velocity spirals, where the frequency varies within each scan. Through the combined application of constant linear velocity scanning and beam path corrections, spiral scan images are shown to exhibit less scan distortion than conventional raster scan images. The methodology presented here will be useful for in situ STEM imaging at higher temporal resolution and for imaging beam sensitive materials.

Finding New Thermoelectric Compounds Using Crystallographic Data: Atomic Displacement Parameters

Energy Technology Data Exchange (ETDEWEB)

Chakoumakos, B.C.; Mandrus, D.G.; Sales, B.C.; Sharp, J.W.

1999-08-29

A new structure-property relationship is discussed which links atomic displacement parameters (ADPs) and the lattice thermal conductivity of clathrate-like compounds. For many clathrate-like compounds, in which one of the atom types is weakly bound and ''rattles'' within its atomic cage, room temperature ADP information can be used to estimate the room temperature lattice thermal conductivity, the vibration frequency of the ''rattler'', and the temperature dependence of the heat capacity. Neutron data and X-ray crystallography data, reported in the literature, are used to apply this analysis to several promising classes of thermoelectric materials.

The Beginnings of X-ray Crystallography

Indian Academy of Sciences (India)

IAS Admin

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

Automated data collection for macromolecular crystallography.

Science.gov (United States)

Winter, Graeme; McAuley, Katherine E

2011-09-01

An overview, together with some practical advice, is presented of the current status of the automation of macromolecular crystallography (MX) data collection, with a focus on MX beamlines at Diamond Light Source, UK. Copyright © 2011 Elsevier Inc. All rights reserved.

Optimizing the Recognition of Surface Crystallography

Czech Academy of Sciences Publication Activity Database

Frank, Luděk; Mika, Filip; Müllerová, Ilona

2015-01-01

Roč. 21, S4 (2015), s. 124-129 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LO1212 Institutional support: RVO:68081731 Keywords : surface crystallography Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.730, year: 2015

Tip radius preservation for high resolution imaging in amplitude modulation atomic force microscopy

Energy Technology Data Exchange (ETDEWEB)

Ramos, Jorge R., E-mail: jorge.rr@cea.cu [Instituto de Ciencia de Materiales de Madrid, Sor Juana Inés de la Cruz 3, Canto Blanco, 28049 Madrid, España (Spain)

2014-07-28

The acquisition of high resolution images in atomic force microscopy (AFM) is correlated to the cantilever's tip shape, size, and imaging conditions. In this work, relative tip wear is quantified based on the evolution of a direct experimental observable in amplitude modulation atomic force microscopy, i.e., the critical amplitude. We further show that the scanning parameters required to guarantee a maximum compressive stress that is lower than the yield/fracture stress of the tip can be estimated via experimental observables. In both counts, the optimized parameters to acquire AFM images while preserving the tip are discussed. The results are validated experimentally by employing IgG antibodies as a model system.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

Energy Technology Data Exchange (ETDEWEB)

Bhardwaj, Anshul [Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107 (United States); Casjens, Sherwood R. [University of Utah School of Medicine, Salt Lake City, UT 84112 (United States); Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu [Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107 (United States)

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

International Nuclear Information System (INIS)

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino

2014-01-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility

Structure of a tropomyosin N-terminal fragment at 0.98 Å resolution

International Nuclear Information System (INIS)

Meshcheryakov, Vladimir A.; Krieger, Inna; Kostyukova, Alla S.; Samatey, Fadel A.

2011-01-01

The crystal structure of the N-terminal fragment of the short nonmuscle α-tropomyosin has been determined at a resolution of 0.98 Å. Tropomyosin (TM) is an elongated two-chain protein that binds along actin filaments. Important binding sites are localized in the N-terminus of tropomyosin. The structure of the N-terminus of the long muscle α-TM has been solved by both NMR and X-ray crystallography. Only the NMR structure of the N-terminus of the short nonmuscle α-TM is available. Here, the crystal structure of the N-terminus of the short nonmuscle α-TM (αTm1bZip) at a resolution of 0.98 Å is reported, which was solved from crystals belonging to space group P3 1 with unit-cell parameters a = b = 33.00, c = 52.03 Å, α = β = 90, γ = 120°. The first five N-terminal residues are flexible and residues 6–35 form an α-helical coiled coil. The overall fold and the secondary structure of the crystal structure of αTM1bZip are highly similar to the NMR structure and the atomic coordinates of the corresponding C α atoms between the two structures superimpose with a root-mean-square deviation of 0.60 Å. The crystal structure validates the NMR structure, with the positions of the side chains being determined precisely in our structure

Structure of a tropomyosin N-terminal fragment at 0.98 Å resolution

Energy Technology Data Exchange (ETDEWEB)

Meshcheryakov, Vladimir A. [Okinawa Institute of Science and Technology, Okinawa (Japan); Krieger, Inna [Texas A& M University, College Station, Texas (United States); Kostyukova, Alla S. [Robert Wood Johnson Medical School, Piscataway, New Jersey (United States); Samatey, Fadel A., E-mail: f.a.samatey@oist.jp [Okinawa Institute of Science and Technology, Okinawa (Japan)

2011-09-01

The crystal structure of the N-terminal fragment of the short nonmuscle α-tropomyosin has been determined at a resolution of 0.98 Å. Tropomyosin (TM) is an elongated two-chain protein that binds along actin filaments. Important binding sites are localized in the N-terminus of tropomyosin. The structure of the N-terminus of the long muscle α-TM has been solved by both NMR and X-ray crystallography. Only the NMR structure of the N-terminus of the short nonmuscle α-TM is available. Here, the crystal structure of the N-terminus of the short nonmuscle α-TM (αTm1bZip) at a resolution of 0.98 Å is reported, which was solved from crystals belonging to space group P3{sub 1} with unit-cell parameters a = b = 33.00, c = 52.03 Å, α = β = 90, γ = 120°. The first five N-terminal residues are flexible and residues 6–35 form an α-helical coiled coil. The overall fold and the secondary structure of the crystal structure of αTM1bZip are highly similar to the NMR structure and the atomic coordinates of the corresponding C{sup α} atoms between the two structures superimpose with a root-mean-square deviation of 0.60 Å. The crystal structure validates the NMR structure, with the positions of the side chains being determined precisely in our structure.

Metalloprotein Crystallography: More than a Structure.

Science.gov (United States)

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

2016-04-19

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

Atomic resolution observation of conversion-type anode RuO 2 during the first electrochemical lithiation

KAUST Repository

Mao, Minmin; Nie, Anmin; Liu, Jiabin; Wang, Hongtao; Mao, Scott X; Wang, Qingxiao; Li, Kun; Zhang, Xixiang

2015-01-01

. In situ transmission electron microscopy reveals a two-step process during the initial lithiation of the RuO2 nanowire anode at atomic resolution. The first step is characterized by the formation of the intermediate phase LixRuO2 due to the Li

Two-energy twin image removal in atomic-resolution x-ray holography

International Nuclear Information System (INIS)

Nishino, Y.; Ishikawa, T.; Hayashi, K.; Takahashi, Y.; Matsubara, E.

2002-01-01

We propose a two-energy twin image removal algorithm for atomic-resolution x-ray holography. The validity of the algorithm is shown in a theoretical simulation and in an experiment of internal detector x-ray holography using a ZnSe single crystal. The algorithm, compared to the widely used multiple-energy algorithm, allows efficient measurement of holograms, and is especially important when the available x-ray energies are fixed. It enables twin image free holography using characteristic x rays from laboratory generators and x-ray pulses of free-electron lasers

The Cambridge crystallography subroutine library

International Nuclear Information System (INIS)

Brown, P.J.; Matthewman, J.C.

1981-06-01

This manual is an amalgamation of the original Cambridge Crystallography Subroutine Library Mark II manual and its supplement No I. The original Mark II system, a set of FORTRAN Subroutines which can be used for standard crystallographic calculations, has been extended to include facilities for conventional least squares refinement. Several new routines have also been added. (U.K.)

Instrumentation at the National Center for Electron Microscopy: the Atomic Resolution Microscope

International Nuclear Information System (INIS)

Gronsky, R.; Thomas, G.

1983-01-01

The Atomic Resolution Microscope (ARM) is one of two unique high voltage electron microscopes at the Lawrence Berkeley Laboratory's National Center for Electron Microscopy (NCEM). The latest results from this new instrument which was manufactured by JEOL, Ltd. to the performance specifications of the NCEM, delivered in January of 1983, and soon to be open to access by the entire microscopy community are given. Details of its history and development are given and its performance specifications are reviewed

Atomic scale resolution with correlation holography

International Nuclear Information System (INIS)

Csonka, P.L.

1979-01-01

For many atoms (including atoms of interest in biology) the elastic and inelastic photon scattering cross sections (denoted respectively by sigma/sub el/ and sigma/sub inel/) for photons in the wavelength region of interest, satisfy sigma/sub el/ << sigma/sub inel/. Therefore, the probability is high that when illuminated with photons, such an atom will decay before a holographic picture of it can be taken. On the other hand, if certain nonlinear phenomena: correlations between photons are taken into account, a hologram of such atoms can nevertheless be generated. Observation of small objects is compatible with the principles of quantum mechanics, even if the probability of disturbing the object as a result of observation is arbitrarily small

Atom-counting in High Resolution Electron Microscopy:TEM or STEM - That's the question.

Science.gov (United States)

Gonnissen, J; De Backer, A; den Dekker, A J; Sijbers, J; Van Aert, S

2017-03-01

In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the number of atoms in a projected atomic column. Recently, it has been demonstrated that HR TEM, when using negative spherical aberration imaging, is suitable for atom-counting as well. The capabilities of both imaging techniques are investigated and compared using the probability of error as a criterion. It is shown that for the same incoming electron dose, HR STEM outperforms HR TEM under common practice standards, i.e. when the decision is based on the probability function of the peak intensities in HR TEM and of the scattering cross-sections in HR STEM. If the atom-counting decision is based on the joint probability function of the image pixel values, the dependence of all image pixel intensities as a function of thickness should be known accurately. Under this assumption, the probability of error may decrease significantly for atom-counting in HR TEM and may, in theory, become lower as compared to HR STEM under the predicted optimal experimental settings. However, the commonly used standard for atom-counting in HR STEM leads to a high performance and has been shown to work in practice. Copyright © 2017 Elsevier B.V. All rights reserved.

Hydrogen bonds of DsrD protein revealed by neutron crystallography

International Nuclear Information System (INIS)

Chatake, Toshiyuki; Higuchi, Yoshiki; Mizuno, Nobuhiro; Tanaka, Ichiro; Niimura, Nobuo; Morimoto, Yukio

2008-01-01

Hydrogen bonds of DNA-binding protein DsrD have been determined by neutron diffraction. In terms of proton donors and acceptors, DsrD protein shows striking differences from other proteins. The features of hydrogen bonds in DsrD protein from sulfate-reducing bacteria have been investigated by neutron protein crystallography. The function of DsrD has not yet been elucidated clearly, but its X-ray crystal structure revealed that it comprises a winged-helix motif and shows the highest structural homology to the DNA-binding proteins. Since any neutron structure of a DNA recognition protein has not yet been obtained, here detailed information on the hydrogen bonds in the winged-helix-motif protein is given and the following features found. (i) The number of hydrogen bonds per amino acid of DsrD is relatively fewer than for other proteins for which neutron structures were determined previously. (ii) Hydrogen bonds are localized between main-chain and main-chain atoms; there are few hydrogen bonds between main-chain and side-chain atoms and between side-chain and side-chain atoms. (iii) Hydrogen bonds inducted by protonation of specific amino acid residues (Glu50) seem to play an essential role in the dimerization of DsrD. The former two points are related to the function of the DNA-binding protein; the three-dimensional structure was mainly constructed by hydrogen bonds in main chains, while the side chains appeared to be used for another role. The latter point would be expected to contribute to the crystal growth of DsrD

Chemical Crystallography· From Inception to Maturity

Indian Academy of Sciences (India)

design, charge density ... did not readily accept this first chemical crystallography experi- .... graphics. The packages clearly illustrate the complexity involved in both molecu- ... interactive online programs help to search, match and analyze.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

Science.gov (United States)

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Crystallography and Interphase Boundary of Martensite and Bainite in Steels

Science.gov (United States)

Furuhara, Tadashi; Chiba, Tadachika; Kaneshita, Takeshi; Wu, Huidong; Miyamoto, Goro

2017-06-01

Grain refinements in lath martensite and bainite structures are crucial for strengthening and toughening of high-strength structural steels. Clearly, crystallography of transformation plays an important role in determining the "grain" sizes in these structures. In the present study, crystallography and intrinsic boundary structure of martensite and bainite are described. Furthermore, various extrinsic factors affecting variant selection and growth kinetics, such as elastic/plastic strain and alloying effects on interphase boundary migration, are discussed.

Native chemical ligation at Asx-Cys, Glx-Cys: chemical synthesis and high-resolution X-ray structure of ShK toxin by racemic protein crystallography.

Science.gov (United States)

Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Kent, Stephen B H

2013-08-14

We have re-examined the utility of native chemical ligation at -Gln/Glu-Cys- [Glx-Cys] and -Asn/Asp-Cys- [Asx-Cys] sites. Using the improved thioaryl catalyst 4-mercaptophenylacetic acid (MPAA), native chemical ligation could be performed at -Gln-Cys- and Asn-Cys- sites without side reactions. After optimization, ligation at a -Glu-Cys- site could also be used as a ligation site, with minimal levels of byproduct formation. However, -Asp-Cys- is not appropriate for use as a site for native chemical ligation because of formation of significant amounts of β-linked byproduct. The feasibility of native chemical ligation at -Gln-Cys- enabled a convergent total chemical synthesis of the enantiomeric forms of the ShK toxin protein molecule. The D-ShK protein molecule was ~50,000-fold less active in blocking the Kv1.3 channel than the L-ShK protein molecule. Racemic protein crystallography was used to obtain high-resolution X-ray diffraction data for ShK toxin. The structure was solved by direct methods and showed significant differences from the previously reported NMR structures in some regions of the ShK protein molecule.

Why do We Trust X-ray Crystallography?

Indian Academy of Sciences (India)

IAS Admin

crystal X-ray diffraction pattern and good chemical sense that elevates X-ray crystallography to its position as the most trusted analytical technique. Suggested Reading. [1] William Clegg, Crystal Structure Determination, Oxford Chemistry Prim-.

Determining the resolution of scanning microwave impedance microscopy using atomic-precision buried donor structures

Science.gov (United States)

Scrymgeour, D. A.; Baca, A.; Fishgrab, K.; Simonson, R. J.; Marshall, M.; Bussmann, E.; Nakakura, C. Y.; Anderson, M.; Misra, S.

2017-11-01

To quantify the resolution limits of scanning microwave impedance microscopy (sMIM), we created scanning tunneling microscope (STM)-patterned donor nanostructures in silicon composed of 10 nm lines of highly conductive silicon buried under a protective top cap of silicon, and imaged them with sMIM. This dopant pattern is an ideal test of the resolution and sensitivity of the sMIM technique, as it is made with nm-resolution and offers minimal complications from topography convolution. It has been determined that typical sMIM tips can resolve lines down to ∼80 nm spacing, while resolution is independent of tip geometry as extreme tip wear does not change the resolving power, contrary to traditional scanning capacitance microscopy (SCM). Going forward, sMIM is an ideal technique for qualifying buried patterned devices, potentially allowing for quantitative post-fabrication characterization of donor structures, which may be an important tool for the study of atomic-scale transistors and state of the art quantum computation schemes.

The design of macromolecular crystallography diffraction experiments

International Nuclear Information System (INIS)

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

2011-01-01

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

Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design.

Science.gov (United States)

Gonnissen, J; De Backer, A; den Dekker, A J; Sijbers, J; Van Aert, S

2016-11-01

In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramér-Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms. Copyright © 2016 Elsevier B.V. All rights reserved.

Elemental mapping in achromatic atomic-resolution energy-filtered transmission electron microscopy

Energy Technology Data Exchange (ETDEWEB)

Forbes, B.D. [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia); Houben, L. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Mayer, J. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Central Facility for Electron Microscopy, RWTH Aachen University, D-52074 Aachen (Germany); Dunin-Borkowski, R.E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Allen, L.J., E-mail: lja@unimelb.edu.au [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia)

2014-12-15

We present atomic-resolution energy-filtered transmission electron microscopy (EFTEM) images obtained with the chromatic-aberration-corrected FEI Titan PICO at the Ernst-Ruska Centre, Jülich, Germany. We find qualitative agreement between experiment and simulation for the background-subtracted EFTEM images of the Ti–L{sub 2,3} and O–K edges for a specimen of SrTiO{sub 3} oriented down the [110] zone axis. The simulations utilize the transition potential formulation for inelastic scattering, which permits a detailed investigation of contributions to the EFTEM image. We find that energy-filtered images of the Ti–L{sub 2,3} and O–K edges are lattice images and that the background-subtracted core-loss maps may not be directly interpretable as elemental maps. Simulations show that this is a result of preservation of elastic contrast, whereby the qualitative details of the image are determined primarily by elastic, coherent scattering. We show that this effect places a constraint on the range of specimen thicknesses which could theoretically yield directly useful elemental maps. In general, interpretation of EFTEM images is ideally accompanied by detailed simulations. - Highlights: • Achromatic atomic-resolution EFTEM images were obtained for STO 〈110〉. • Simulations were in qualitative agreement with Ti–L{sub 2,3} and O–K edge maps. • The experimental EFTEM maps are not directly interpretable as elemental maps. • Image intensities are strongly determined by preservation of elastic contrast. • Interpretation of EFTEM images is ideally accompanied by detailed simulations.

The protein micro-crystallography beamlines for targeted protein research program

International Nuclear Information System (INIS)

Hirata, Kunio; Yamamoto, Masaki; Matsugaki, Naohiro; Wakatsuki, Soichi

2010-01-01

In order to collect proper diffraction data from outstanding micro-crystals, a brand-new data collection system should be designed to provide high signal-to noise ratio in diffraction images. SPring-8 and KEK-PF are currently developing two micro-beam beamlines for Targeted Proteins Research Program by MEXT of Japan. The program aims to reveal the structure and function of proteins that are difficult to solve but have great importance in both academic research and industrial application. At SPring-8, a new 1-micron beam beamline for protein micro-crystallography, RIKEN Targeted Proteins Beamline (BL32XU), is developed. At KEK-PF a new low energy micro-beam beamline, BL-1A, is dedicated for SAD micro-crystallography. The two beamlines will start operation in the end of 2010. The present status of the research and development for protein micro-crystallography will be presented. (author)

Neutron crystallographic studies of amino acids and nucleic acids

International Nuclear Information System (INIS)

Kashiwagi, Tatsuki

2014-01-01

Neutron crystallographic studies of two representative umami materials were executed utilizing iBLX at MLF/J-PARC. The results of them will be summarized in this report. At first, structure analysis of the alpha form crystal of L-glutamic acid was performed in order to assess the usefulness of neutron crystallography at iBIX to our company's R and D. Neutron crystal structure of it was successfully determined at 0.6 A resolution. All hydrogen atoms were clearly observed. Next, the mixed crystal of disodium Inosine-5'-phosphate (IMP · 2Na) and disodium Guanosine-5'-phosphate (GMP · 2Na) was analyzed by neutron crystallography. Neutron crystal structure of the mixed crystal of IMP and GMP (IM/GMP rate = 1.7) was successfully determined at 0.8 A resolution. In the neutron crystal structure of the mixed crystal, the hydrogen atom bonded to the C2 atom of purine base in IMP and the nitrogen atom bonded to the C2 atom of purine base in GMP were clearly observed in the nuclear density map, structurally demonstrating that this crystal is the mixed crystal. (author)

Choice and maintenance of equipment for electron crystallography.

Science.gov (United States)

Mills, Deryck J; Vonck, Janet

2013-01-01

The choice of equipment for an electron crystallography laboratory will ultimately be determined by the available budget; nevertheless, the ideal lab will have two electron microscopes: a dedicated 300 kV cryo-EM with a field emission gun and a smaller LaB(6) machine for screening. The high-end machine should be equipped with photographic film or a very large CCD or CMOS camera for 2D crystal data collection; the screening microscope needs a mid-size CCD for rapid evaluation of crystal samples. The microscope room installations should provide adequate space and a special environment that puts no restrictions on the collection of high-resolution data. Equipment for specimen preparation includes a carbon coater, glow discharge unit, light microscope, plunge freezer, and liquid nitrogen containers and storage dewars. When photographic film is to be used, additional requirements are a film desiccator, dark room, optical diffractometer, and a film scanner. Having the electron microscopes and ancillary equipment well maintained and always in optimum condition facilitates the production of high-quality data.

Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy.

Science.gov (United States)

Yan, Si; Guo, Changmiao; Hou, Guangjin; Zhang, Huilan; Lu, Xingyu; Williams, John Charles; Polenova, Tatyana

2015-11-24

Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

Nanoscale capacitance imaging with attofarad resolution using ac current sensing atomic force microscopy

International Nuclear Information System (INIS)

Fumagalli, L; Ferrari, G; Sampietro, M; Casuso, I; MartInez, E; Samitier, J; Gomila, G

2006-01-01

Nanoscale capacitance imaging with attofarad resolution (∼1 aF) of a nano-structured oxide thin film, using ac current sensing atomic force microscopy, is reported. Capacitance images are shown to follow the topographic profile of the oxide closely, with nanometre vertical resolution. A comparison between experimental data and theoretical models shows that the capacitance variations observed in the measurements can be mainly associated with the capacitance probed by the tip apex and not with positional changes of stray capacitance contributions. Capacitance versus distance measurements further support this conclusion. The application of this technique to the characterization of samples with non-voltage-dependent capacitance, such as very thin dielectric films, self-assembled monolayers and biological membranes, can provide new insight into the dielectric properties at the nanoscale

Nanoscale capacitance imaging with attofarad resolution using ac current sensing atomic force microscopy

Energy Technology Data Exchange (ETDEWEB)

Fumagalli, L [Dipartimento di Elettronica e Informazione, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 (Italy); Ferrari, G [Dipartimento di Elettronica e Informazione, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 (Italy); Sampietro, M [Dipartimento di Elettronica e Informazione, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 (Italy); Casuso, I [Departament d' Electronica, Universitat de Barcelona, C/MartIi Franques 1, 08028 Barcelona (Spain); MartInez, E [Plataforma de Nanotecnologia, Parc Cientific de Barcelona, C/ Josep Samitier 1-5, 08028-Barcelona (Spain); Samitier, J [Departament d' Electronica, Universitat de Barcelona, C/MartIi Franques 1, 08028 Barcelona (Spain); Gomila, G [Departament d' Electronica, Universitat de Barcelona, C/MartIi Franques 1, 08028 Barcelona (Spain)

2006-09-28

Nanoscale capacitance imaging with attofarad resolution ({approx}1 aF) of a nano-structured oxide thin film, using ac current sensing atomic force microscopy, is reported. Capacitance images are shown to follow the topographic profile of the oxide closely, with nanometre vertical resolution. A comparison between experimental data and theoretical models shows that the capacitance variations observed in the measurements can be mainly associated with the capacitance probed by the tip apex and not with positional changes of stray capacitance contributions. Capacitance versus distance measurements further support this conclusion. The application of this technique to the characterization of samples with non-voltage-dependent capacitance, such as very thin dielectric films, self-assembled monolayers and biological membranes, can provide new insight into the dielectric properties at the nanoscale.

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.

Phase contrast scanning transmission electron microscopy imaging of light and heavy atoms at the limit of contrast and resolution.

Science.gov (United States)

Yücelen, Emrah; Lazić, Ivan; Bosch, Eric G T

2018-02-08

Using state of the art scanning transmission electron microscopy (STEM) it is nowadays possible to directly image single atomic columns at sub-Å resolution. In standard (high angle) annular dark field STEM ((HA)ADF-STEM), however, light elements are usually invisible when imaged together with heavier elements in one image. Here we demonstrate the capability of the recently introduced Integrated Differential Phase Contrast STEM (iDPC-STEM) technique to image both light and heavy atoms in a thin sample at sub-Å resolution. We use the technique to resolve both the Gallium and Nitrogen dumbbells in a GaN crystal in [[Formula: see text

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

International Nuclear Information System (INIS)

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

2015-01-01

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

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

International Nuclear Information System (INIS)

Tronrud, Dale E.; Karplus, P. Andrew

2011-01-01

A script was created to allow SHELXL to use the new CDL v.1.2 stereochemical library which defines the target values for main-chain bond lengths and angles as a function of the residue’s ϕ/ψ angles. Test refinements using this script show that the refinement behavior of structures at resolutions even better than 1 Å is substantially enhanced by the use of the new conformation-dependent ideal geometry paradigm. To utilize a new conformation-dependent backbone-geometry library (CDL) in protein refinements at atomic resolution, a script was written that creates a restraint file for the SHELXL refinement program. It was found that the use of this library allows models to be created that have a substantially better fit to main-chain bond angles and lengths without degrading their fit to the X-ray data even at resolutions near 1 Å. For models at much higher resolution (∼0.7 Å), the refined model for parts adopting single well occupied positions is largely independent of the restraints used, but these structures still showed much smaller r.m.s.d. residuals when assessed with the CDL. Examination of the refinement tests across a wide resolution range from 2.4 to 0.65 Å revealed consistent behavior supporting the use of the CDL as a next-generation restraint library to improve refinement. CDL restraints can be generated using the service at http://pgd.science.oregonstate.edu/cdl_shelxl/

Special issue on Chemical Crystallography Editorial

Indian Academy of Sciences (India)

Virtually, every invitation that we extended has translated into an article. We sincerely believe and wish that the collection of articles in this issue sufficiently showcases the panorama of chemical science involving X-ray crystallography in India. We note with pride that Prof. Gautam R. Desiraju, an eminent scientist who has.

Development of Control Applications for High-Throughput Protein Crystallography Experiments

International Nuclear Information System (INIS)

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

2007-01-01

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

Atomic resolution holography using advanced reconstruction techniques for two-dimensional detectors

Energy Technology Data Exchange (ETDEWEB)

Marko, M; Szakal, A; Cser, L [Neutron Spectroscopy Department, Research Institute for Solid State Physics and Optics, PO Box 49, H-1525 Budapest (Hungary); Krexner, G [Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna (Austria); Schefer, J, E-mail: marko@szfki.h [Laboratory for Neutron Scattering (LNS), Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland)

2010-06-15

Atomic resolution holography is based on two concepts. Either the emitter of the radiation used is embedded in the sample (internal source concept) or, on account of the optical reciprocity law, the detector forms part of the sample (internal detector concept). In many cases, holographic objects (atoms and nuclei) simultaneously adopt the roles of both source and detector. Thus, the recorded image contains a mixture of both inside source and inside detector holograms. When reconstructing one type of hologram, the presence of the other hologram causes serious distortions. In the present work, we propose a new method, the so-called double reconstruction (DR), which not only suppresses the mutual distortions but also exploits the information content of the measured hologram more effectively. This novel approach also decreases the level of distortion arising from diffraction and statistical noise. The efficiency of the DR technique is significantly enhanced by employing two-dimensional (2D) area detectors. The power of the method is illustrated here by applying it to a real measurement on a palladium-hydrogen sample.

Alcohol-Binding Sites in Distinct Brain Proteins: The Quest for Atomic Level Resolution

Science.gov (United States)

Howard, Rebecca J.; Slesinger, Paul A.; Davies, Daryl L.; Das, Joydip; Trudell, James R.; Harris, R. Adron

2011-01-01

Defining the sites of action of ethanol on brain proteins is a major prerequisite to understanding the molecular pharmacology of this drug. The main barrier to reaching an atomic-level understanding of alcohol action is the low potency of alcohols, ethanol in particular, which is a reflection of transient, low-affinity interactions with their targets. These mechanisms are difficult or impossible to study with traditional techniques such as radioligand binding or spectroscopy. However, there has been considerable recent progress in combining X-ray crystallography, structural modeling, and site-directed mutagenesis to define the sites and mechanisms of action of ethanol and related alcohols on key brain proteins. We review such insights for several diverse classes of proteins including inwardly rectifying potassium, transient receptor potential, and neurotransmit-ter-gated ion channels, as well as protein kinase C epsilon. Some common themes are beginning to emerge from these proteins, including hydrogen bonding of the hydroxyl group and van der Waals interactions of the methylene groups of ethanol with specific amino acid residues. The resulting binding energy is proposed to facilitate or stabilize low-energy state transitions in the bound proteins, allowing ethanol to act as a “molecular lubricant” for protein function. We discuss evidence for characteristic, discrete alcohol-binding sites on protein targets, as well as evidence that binding to some proteins is better characterized by an interaction region that can accommodate multiple molecules of ethanol. PMID:21676006

Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible "3He/10 T cryostat

International Nuclear Information System (INIS)

Allwörden, H. von; Ruschmeier, K.; Köhler, A.; Eelbo, T.; Schwarz, A.; Wiesendanger, R.

2016-01-01

The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped "3He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambers are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).

Atomic resolution structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A2

International Nuclear Information System (INIS)

Sekar, K.; Yogavel, M.; Gayathri, D.; Velmurugan, D.; Krishna, R.; Poi, M.-J.; Dauter, Z.; Dauter, M.; Tsai, M.-D.

2005-01-01

The atomic resolution crystal structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A 2 is reported. The structure of the double mutant K53,56M has previously been refined at 1.9 Å resolution using room-temperature data. The present paper reports the crystal structure of the same mutant K53,56M refined against 1.1 Å data collected using synchrotron radiation. A total of 116 main-chain atoms from 29 residues and 44 side chains are modelled in alternate conformations. Most of the interfacial binding residues are found to be disordered and alternate conformations could be recognized. The second calcium ion-binding site residue Glu92 adopts two alternate conformations. The minor and major conformations of Glu92 correspond to the second calcium ion bound and unbound states

The story of crystallography

International Nuclear Information System (INIS)

Nigam, G.D.

1976-01-01

The historical development of the very important field of crystallography has been narrated. The important land marks such as the first determination of the crystal structure of NaCl by Sir Poragy and that of DNA by Watson et al., etc. are mentioned. The important role played by this field and its role in bringing broad fields such as physics, chemistry and biology very close to each other are emphasised. Some of the outstanding contributions made by eminent crystallographers in India and abroad are mentioned. (K.B.)

PRIGo: a new multi-axis goniometer for macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Waltersperger, Sandro; Olieric, Vincent, E-mail: vincent.olieric@psi.ch; Pradervand, Claude [Paul Scherrer Institute, Villigen PSI (Switzerland); Glettig, Wayne [Centre Suisse d’Electronique et Microtechnique SA, Neuchâtel 2002 (Switzerland); Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias [Paul Scherrer Institute, Villigen PSI (Switzerland); Schulze-Briese, Clemens [Dectris Ltd, Baden 5400 (Switzerland); Wang, Meitian, E-mail: vincent.olieric@psi.ch [Paul Scherrer Institute, Villigen PSI (Switzerland)

2015-05-09

The design and performance of the new multi-axis goniometer PRIGo developed at the Swiss Light Source at Paul Scherrer Institute is described. The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0–90°), followed by a ϕ stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

High-Resolution Detector For X-Ray Diffraction

Science.gov (United States)

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

1988-01-01

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

In situ macromolecular crystallography using microbeams

International Nuclear Information System (INIS)

Axford, Danny; Owen, Robin L.; Aishima, Jun; Foadi, James; Morgan, Ann W.; Robinson, James I.; Nettleship, Joanne E.; Owens, Raymond J.; Moraes, Isabel; Fry, Elizabeth E.; Grimes, Jonathan M.; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S.; Stuart, David I.; Evans, Gwyndaf

2012-01-01

A sample environment for mounting crystallization trays has been developed on the microfocus beamline I24 at Diamond Light Source. The technical developments and several case studies are described. Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams

In situ macromolecular crystallography using microbeams

Energy Technology Data Exchange (ETDEWEB)

Axford, Danny; Owen, Robin L.; Aishima, Jun [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Morgan, Ann W.; Robinson, James I. [University of Leeds, Leeds LS9 7FT (United Kingdom); Nettleship, Joanne E.; Owens, Raymond J. [Research Complex at Harwell, Rutherford Appleton Laboratory R92, Didcot, Oxfordshire OX11 0DE (United Kingdom); Moraes, Isabel [Imperial College, London SW7 2AZ (United Kingdom); Fry, Elizabeth E.; Grimes, Jonathan M.; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S. [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

2012-04-17

A sample environment for mounting crystallization trays has been developed on the microfocus beamline I24 at Diamond Light Source. The technical developments and several case studies are described. Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams.

Atomic Resolution Imaging and Quantification of Chemical Functionality of Surfaces

Energy Technology Data Exchange (ETDEWEB)

Schwarz, Udo D. [Yale Univ., New Haven, CT (United States). Dept. of Mechanical Engineering and Materials Science; Altman, Eric I. [Yale Univ., New Haven, CT (United States). Dept. of Chemical and Environmental Engineering

2014-12-10

The work carried out from 2006-2014 under DoE support was targeted at developing new approaches to the atomic-scale characterization of surfaces that include species-selective imaging and an ability to quantify chemical surface interactions with site-specific accuracy. The newly established methods were subsequently applied to gain insight into the local chemical interactions that govern the catalytic properties of model catalysts of interest to DoE. The foundation of our work was the development of three-dimensional atomic force microscopy (3DAFM), a new measurement mode that allows the mapping of the complete surface force and energy fields with picometer resolution in space (x, y, and z) and piconewton/millielectron volts in force/energy. From this experimental platform, we further expanded by adding the simultaneous recording of tunneling current (3D-AFM/STM) using chemically well-defined tips. Through comparison with simulations, we were able to achieve precise quantification and assignment of local chemical interactions to exact positions within the lattice. During the course of the project, the novel techniques were applied to surface-oxidized copper, titanium dioxide, and silicon oxide. On these materials, defect-induced changes to the chemical surface reactivity and electronic charge density were characterized with site-specific accuracy.

Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design

Energy Technology Data Exchange (ETDEWEB)

Gonnissen, J.; De Backer, A. [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Dekker, A.J. den [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Delft Center for Systems and Control (DCSC), Delft University of Technology, Mekelweg 2, 2628 CD Delft (Netherlands); Sijbers, J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)

2016-11-15

In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramér–Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms. - Highlights: • The optimal detector design to detect and locate light atoms in HR STEM is derived. • The probability of error is quantified and used to detect light atoms. • The Cramér–Rao lower bound is calculated to determine the atomic column precision. • Both measures are evaluated and result in the single optimal LAADF detector regime. • The incoming electron dose is optimised for both research goals.

Quantitative atomic resolution mapping using high-angle annular dark field scanning transmission electron microscopy

International Nuclear Information System (INIS)

Van Aert, S.; Verbeeck, J.; Erni, R.; Bals, S.; Luysberg, M.; Dyck, D. Van; Tendeloo, G. Van

2009-01-01

A model-based method is proposed to relatively quantify the chemical composition of atomic columns using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. The method is based on a quantification of the total intensity of the scattered electrons for the individual atomic columns using statistical parameter estimation theory. In order to apply this theory, a model is required describing the image contrast of the HAADF STEM images. Therefore, a simple, effective incoherent model has been assumed which takes the probe intensity profile into account. The scattered intensities can then be estimated by fitting this model to an experimental HAADF STEM image. These estimates are used as a performance measure to distinguish between different atomic column types and to identify the nature of unknown columns with good accuracy and precision using statistical hypothesis testing. The reliability of the method is supported by means of simulated HAADF STEM images as well as a combination of experimental images and electron energy-loss spectra. It is experimentally shown that statistically meaningful information on the composition of individual columns can be obtained even if the difference in averaged atomic number Z is only 3. Using this method, quantitative mapping at atomic resolution using HAADF STEM images only has become possible without the need of simultaneously recorded electron energy loss spectra.

A high-pressure MWPC detector for crystallography

DEFF Research Database (Denmark)

Ortuno-Prados, F.; Bazzano, A.; Berry, A.

1999-01-01

The application of the Multi-Wire Proportional Counter (MWPC) as a potential detector for protein crystallography and other wide-angle diffraction experiments is presented. Electrostatic problems found with our large area MWPC when operated at high pressure are discussed. We suggest that a solution...

Crystallography of the Sb-Te-Ni system

Czech Academy of Sciences Publication Activity Database

Laufek, F.; Drábek, M.; Skála, Roman; Císařová, I.

2005-01-01

Roč. 12, č. 2 (2005), s. 153-154 ISSN 1211-5894 Grant - others:GAUK(CZ) 43-203391 Institutional research plan: CEZ:AV0Z30130516 Keywords : crystallography * antimony * tellurium Subject RIV: DB - Geology ; Mineralogy http:// xray .cz/ms/bul2005-2/student3.pdf

Status of the digital pixel array detector for protein crystallography

CERN Document Server

Datte, P; Beuville, E; Endres, N; Druillole, F; Luo, L; Millaud, J E; Xuong, N H

1999-01-01

A two-dimensional photon counting digital pixel array detector is being designed for static and time resolved protein crystallography. The room temperature detector will significantly enhance monochromatic and polychromatic protein crystallographic through-put data rates by more than three orders of magnitude. The detector has an almost infinite photon counting dynamic range and exhibits superior spatial resolution when compared to present crystallographic phosphor imaging plates or phosphor coupled CCD detectors. The detector is a high resistivity N-type Si with a pixel pitch of 150x150 mu m, and a thickness of 300 mu m, and is bump bonded to an application specific integrated circuit. The event driven readout of the detector is based on the column architecture and allows an independent pixel hit rate above 1 million photons/s/pixel. The device provides energy discrimination and sparse data readout which yields minimal dead-time. This type of architecture allows a continuous (frameless) data acquisition, a f...

Advanced double-biprism holography with atomic resolution

Energy Technology Data Exchange (ETDEWEB)

Genz, Florian, E-mail: florian.genz@physik.tu-berlin.de [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany); Niermann, Tore [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany); Buijsse, Bart; Freitag, Bert [FEI Company, Achtseweg Noord 5, 5651 GG Eindhoven (Netherlands); Lehmann, Michael [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany)

2014-12-15

The optimum biprism position as suggested by Lichte (Ultramicroscopy 64 (1996) 79 [10]) was implemented into a state-of-the-art transmission electron microscope. For a setup optimized for atomic resolution holograms with a width of 30 nm and a fringe spacing of 30 pm, we investigated the practical improvements on hologram quality. The setup is additionally supplemented by a second biprism as suggested by Harada et al. (Applied Physics Letters 84 (2004) 3229 [12]). In order to estimate the possibilities and limitations of the double biprism setup, geometric optics arguments lead to calculation of the exploitable shadow width, necessary for strong reduction of biprism-induced artefacts. Additionally, we used the double biprism setup to estimate the biprism vibration, yielding the most stable imaging conditions with lowest overall fringe contrast damping. Electron holograms of GaN demonstrate the good match between experiment and simulation, also as a consequence of the improved stability. - Highlights: • Investigation of optimum biprism position implementation into state-of-the-art TEM. • Reduction of artefacts, especially vignetting in double-biprism electron holography. • Biprism vibration and most stable imaging conditions in double-biprism holography. • Demonstration of the optimized double-biprism setup using a thin GaN-foil.

Solid-state NMR on complex biomolecules: novel methods and applications

NARCIS (Netherlands)

Nand, D.

2011-01-01

Solid-state NMR (ssNMR) represents a versatile technique in providing atomic-resolution information without the need for crystals or fast molecular motion required for X-ray crystallography and solution-state NMR, respectively. Recent past has witnessed the ability of this technique in providing

Seeing atoms with aberration-corrected sub-Angstroem electron microscopy

Energy Technology Data Exchange (ETDEWEB)

O' Keefe, Michael A. [Materials Science Division, Lawrence Berkeley National Laboratory, National Center for Electron Microscopy, 2R0200, 1 Cyclotron Road, Berkeley, CA 94720-8197 (United States)], E-mail: sub-Angstrom@comcast.net

2008-02-15

High-resolution electron microscopy is able to provide atomic-level characterization of many materials in low-index orientations. To achieve the same level of characterization in more complex orientations requires that instrumental resolution be improved to values corresponding to the sub-Angstroem separations of atom positions projected into these orientations. Sub-Angstroem resolution in the high-resolution transmission electron microscope has been achieved in the last few years by software aberration correction, electron holography, and hardware aberration correction; the so-called 'one-Angstroem barrier' has been left behind. Aberration correction of the objective lens currently allows atomic-resolution imaging at the sub-0.8 A level and is advancing towards resolutions in the deep sub-Angstroem range (near 0.5 A). At current resolution levels, images with sub-Rayleigh resolution require calibration in order to pinpoint atom positions correctly. As resolution levels approach the 'sizes' of atoms, the atoms themselves will produce a limit to resolution, no matter how much the instrumental resolution is improved. By arranging imaging conditions suitably, each atom peak in the image can be narrower, so atoms are imaged smaller and may be resolved at finer separations.

Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible {sup 3}He/10 T cryostat

Energy Technology Data Exchange (ETDEWEB)

Allwörden, H. von; Ruschmeier, K.; Köhler, A.; Eelbo, T.; Schwarz, A., E-mail: aschwarz@physnet.uni-hamburg.de; Wiesendanger, R. [Department of Physics, University of Hamburg, Jungiusstrasse 11, 20355 Hamburg (Germany)

2016-07-15

The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped {sup 3}He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambers are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).

Sources, instrumentation and detectors for protein crystallography

CERN Document Server

Nave, C

2001-01-01

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

Detecting and locating light atoms from high-resolution STEM images : The quest for a single optimal design

NARCIS (Netherlands)

Gonnissen, J; De Backer, A; den Dekker, A.J.; Sijbers, J.; Van Aert, S.

2016-01-01

In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of

A rapid and rational approach to generating isomorphous heavy-atom phasing derivatives.

Science.gov (United States)

Lu, Jinghua; Sun, Peter D

2014-09-01

In attempts to replace the conventional trial-and-error heavy-atom derivative search method with a rational approach, we previously defined heavy metal compound reactivity against peptide ligands. Here, we assembled a composite pH- and buffer-dependent peptide reactivity profile for each heavy metal compound to guide rational heavy-atom derivative search. When knowledge of the best-reacting heavy-atom compound is combined with mass spectrometry assisted derivatization, and with a quick-soak method to optimize phasing, it is likely that the traditional heavy-atom compounds could meet the demand of modern high-throughput X-ray crystallography. As an example, we applied this rational heavy-atom phasing approach to determine a previously unknown mouse serum amyloid A2 crystal structure. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Observations of silicon carbide by high resolution transmission electron microscopy

International Nuclear Information System (INIS)

Smith, D.J.; Jepps, N.W.; Page, T.F.

1978-01-01

High resolution transmission electron microscopy techniques, principally involving direct lattice imaging, have been used as part of a study of the crystallography and phase transformation mechanics of silicon carbide polytypes. In particular, the 3C (cubic) and 6H (hexagonal) polytypes have been examined together with partially transformed structural mixtures. Although direct observation of two-dimensional atomic structures was not possible at an operating voltage of 100 kV, considerable microstructural information has been obtained by careful choice of the experimental conditions. In particular, tilted beam observations of the 0.25 nm lattice fringes have been made in the 3C polytype for two different brace 111 brace plane arrays in order to study the dimensions and coherency of finely-twinned regions together with brace 0006 brace and brace 1 0 bar1 2 brace lattice images in the 6H polytype which allow the detailed stacking operations to be resolved. Lower resolution lattice images formed with axial illumination have also been used to study the nature of the 3C → 6H transformation and results are presented showing that the transformation interface may originate with fine twinning of the 3C structure followed by growth of the resultant 6H regions. Observations have been made of the detailed stepped structure of this interface together with the stacking fault distribution in the resultant 6H material. (author)

Crystallography and Morphology of Niobium Carbide in As-Cast HP-Niobium Reformer Tubes

Science.gov (United States)

Buchanan, Karl G.; Kral, Milo V.

2012-06-01

The microstructures of two as-cast heats of niobium-modified HP stainless steels were characterized. Particular attention was paid to the interdendritic niobium-rich carbides formed during solidification of these alloys. At low magnifications, these precipitates are grouped in colonies of similar lamellae. Higher magnifications revealed that the lamellae actually obtain two distinct morphologies. The type I morphology exhibits broad planar interfaces with a smooth platelike shape. Type II lamellae have undulating interfaces and an overall reticulated shape. To provide further insight into the origin of these two different morphologies, the microstructure and crystallography of each have been studied in detail using high resolution scanning electron microscopy, transmission electron microscopy, various electron diffraction methods (electron backscatter diffraction (EBSD), selected area diffraction (SAD), and convergent beam electron diffraction (CBED)), and energy dispersive X-ray spectroscopy.

High Resolution Numerical Simulations of Primary Atomization in Diesel Sprays with Single Component Reference Fuels

Science.gov (United States)

2015-09-01

NC. 14. ABSTRACT A high-resolution numerical simulation of jet breakup and spray formation from a complex diesel fuel injector at diesel engine... diesel fuel injector at diesel engine type conditions has been performed. A full understanding of the primary atomization process in diesel fuel... diesel liquid sprays the complexity is further compounded by the physical attributes present including nozzle turbulence, large density ratios

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.

Electric field imaging of single atoms

Science.gov (United States)

Shibata, Naoya; Seki, Takehito; Sánchez-Santolino, Gabriel; Findlay, Scott D.; Kohno, Yuji; Matsumoto, Takao; Ishikawa, Ryo; Ikuhara, Yuichi

2017-01-01

In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures. PMID:28555629

Influence of spatial and temporal coherences on atomic resolution high angle annular dark field imaging

Energy Technology Data Exchange (ETDEWEB)

Beyer, Andreas, E-mail: andreas.beyer@physik.uni-marburg.de; Belz, Jürgen; Knaub, Nikolai; Jandieri, Kakhaber; Volz, Kerstin

2016-10-15

Aberration-corrected (scanning) transmission electron microscopy ((S)TEM) has become a widely used technique when information on the chemical composition is sought on an atomic scale. To extract the desired information, complementary simulations of the scattering process are inevitable. Often the partial spatial and temporal coherences are neglected in the simulations, although they can have a huge influence on the high resolution images. With the example of binary gallium phosphide (GaP) we elucidate the influence of the source size and shape as well as the chromatic aberration on the high angle annular dark field (HAADF) intensity. We achieve a very good quantitative agreement between the frozen phonon simulation and experiment for different sample thicknesses when a Lorentzian source distribution is assumed and the effect of the chromatic aberration is considered. Additionally the influence of amorphous layers introduced by the preparation of the TEM samples is discussed. Taking into account these parameters, the intensity in the whole unit cell of GaP, i.e. at the positions of the different atomic columns and in the region between them, is described correctly. With the knowledge of the decisive parameters, the determination of the chemical composition of more complex, multinary materials becomes feasible. - Highlights: • Atomic resolution high angle annular dark field images of gallium phosphide are compared quantitatively with simulated ones. • The influence of partial spatial and temporal coherence on the HAADF-intensity is investigated. • The influence of amorphous layers introduced by the sample preparation is simulated.

Measurement of transient atomic displacements in thin films with picosecond and femtometer resolution

Directory of Open Access Journals (Sweden)

M. Kozina

2014-05-01

Full Text Available We report measurements of the transient structural response of weakly photo-excited thin films of BiFeO3, Pb(Zr,TiO3, and Bi and time-scales for interfacial thermal transport. Utilizing picosecond x-ray diffraction at a 1.28 MHz repetition rate with time resolution extending down to 15 ps, transient changes in the diffraction angle are recorded. These changes are associated with photo-induced lattice strains within nanolayer thin films, resolved at the part-per-million level, corresponding to a shift in the scattering angle three orders of magnitude smaller than the rocking curve width and changes in the interlayer lattice spacing of fractions of a femtometer. The combination of high brightness, repetition rate, and stability of the synchrotron, in conjunction with high time resolution, represents a novel means to probe atomic-scale, near-equilibrium dynamics.

Composition measurement in substitutionally disordered materials by atomic resolution energy dispersive X-ray spectroscopy in scanning transmission electron microscopy.

Science.gov (United States)

Chen, Z; Taplin, D J; Weyland, M; Allen, L J; Findlay, S D

2017-05-01

The increasing use of energy dispersive X-ray spectroscopy in atomic resolution scanning transmission electron microscopy invites the question of whether its success in precision composition determination at lower magnifications can be replicated in the atomic resolution regime. In this paper, we explore, through simulation, the prospects for composition measurement via the model system of Al x Ga 1-x As, discussing the approximations used in the modelling, the variability in the signal due to changes in configuration at constant composition, and the ability to distinguish between different compositions. Results are presented in such a way that the number of X-ray counts, and thus the expected variation due to counting statistics, can be gauged for a range of operating conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Energy Technology Data Exchange (ETDEWEB)

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

2011-01-01

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

Peak-shape analysis for protein neutron crystallography with position-sensitive detectors

International Nuclear Information System (INIS)

Schoenborn, B.P.

1983-01-01

In neutron protein crystallography, the use of position-sensitive detectors controlled by a modern data-acquisition system permits new approaches to data-collection strategies. Instead of dealing with conventional scans, like the theta-2theta scan, that provide an integrated intensity as a function of a rotational parameter, the computer-linked counter can be used to produce a three-dimensional reflection profile. As the crystal steps (δ#betta#) through a reflection, the observed data for each step are stored in an external memory as a function of extent in 2theta and height (y) of a reflection. In this space, the reflection will be a three-dimensional distribution with dimensions determined by such basic geometrical conditions as δlambda, crystal size, mosaic spread, counter-resolution, and beam-collimation parameters. Knowledge of the interaction of these basic parameters will allow the design of optimal beam optics and will permit the delineation of the reflection from the background and permit, therefore, an accurate intensity determination. (Auth.)

Determination of cobalt in biological samples by line-source and high-resolution continuum source graphite furnace atomic absorption spectrometry using solid sampling or alkaline treatment

International Nuclear Information System (INIS)

Ribeiro, Anderson Schwingel; Vieira, Mariana Antunes; Furtado da Silva, Alessandra; Borges, Daniel L. Gallindo; Welz, Bernhard; Heitmann, Uwe; Curtius, Adilson Jose

2005-01-01

Two procedures for the determination of Co in biological samples by graphite furnace atomic absorption spectrometry (GF AAS) were compared: solid sampling (SS) and alkaline treatment with tetramethylammonium hydroxide (TMAH) using two different instruments for the investigation: a conventional line-source (LS) atomic absorption spectrometer and a prototype high-resolution continuum source atomic absorption spectrometer. For the direct introduction of the solid samples, certified reference materials (CRM) were ground to a particle size ≤50 μm. Alkaline treatment was carried out by placing about 250 mg of the sample in polypropylene flasks, adding 2 mL of 25% m/v tetramethylammonium hydroxide and de-ionized water. Due to its unique capacity of providing a 3-D spectral plot, a high-resolution continuum source (HR-CS) graphite furnace atomic absorption spectrometry was used as a tool to evaluate potential spectral interferences, including background absorption for both sample introduction procedures, revealing that a continuous background preceded the atomic signal for pyrolysis temperatures lower than 700 deg. C. Molecular absorption bands with pronounced rotational fine structure appeared for atomization temperatures >1800 deg. C probably as a consequence of the formation of PO. After optimization had been carried out using high resolution continuum source atomic absorption spectrometry, the optimized conditions were adopted also for line-source atomic absorption spectrometry. Six biological certified reference materials were analyzed, with calibration against aqueous standards, resulting in agreement with the certified values (according to the t-test for a 95% confidence level) and in detection limits as low as 5 ng g -1

Atomic-resolution studies of In2O3-ZnO compounds on aberration-corrected electron microscopes

International Nuclear Information System (INIS)

Yu, Wentao

2009-01-01

In this work, the characteristic inversion domain microstructures of In 2 O 3 (ZnO) m (m=30) compounds were investigated by TEM methods. At bright-atom contrast condition, atomically resolved HR-TEM images of In 2 O 3 (ZnO) 30 were successfully acquired in [1 anti 100] zone axis of ZnO, with projected metal columns of ∝1.6 A well resolved. From contrast maxima in the TEM images, local lattice distortions at the pyramidal inversion domain boundaries were observed for the first time. Lattice displacements and the strain field in two-dimensions were visualized and measured using the 'DALI' algorithm. Atomically resolved single shot and focal series images of In 2 O 3 (ZnO) 30 were achieved in both zone axes of ZnO, [1 anti 100] and [2 anti 1 anti 10], respectively. The electron waves at the exit-plane were successfully reconstructed using the software package 'TrueImage'. Finally, a three dimensional atomic structure model for the pyramidal IDB was proposed, with an In distribution of 10%, 20%, 40%, 20% and 10% of In contents over 5 atom columns along basal planes, respectively. Through a detailed structural study of In 2 O 3 (ZnO) m compounds by using phase-contrast and Z-contrast imaging at atomic resolution, In 3+ atoms are determined with trigonal bi-pyramidal co-ordination and are distributed at the pyramidal IDBs. (orig.)

'Big Bang' tomography as a new route to atomic-resolution electron tomography.

Science.gov (United States)

Van Dyck, Dirk; Jinschek, Joerg R; Chen, Fu-Rong

2012-06-13

Until now it has not been possible to image at atomic resolution using classical electron tomographic methods, except when the target is a perfectly crystalline nano-object imaged along a few zone axes. The main reasons are that mechanical tilting in an electron microscope with sub-ångström precision over a very large angular range is difficult, that many real-life objects such as dielectric layers in microelectronic devices impose geometrical constraints and that many radiation-sensitive objects such as proteins limit the total electron dose. Hence, there is a need for a new tomographic scheme that is able to deduce three-dimensional information from only one or a few projections. Here we present an electron tomographic method that can be used to determine, from only one viewing direction and with sub-ångström precision, both the position of individual atoms in the plane of observation and their vertical position. The concept is based on the fact that an experimentally reconstructed exit wave consists of the superposition of the spherical waves that have been scattered by the individual atoms of the object. Furthermore, the phase of a Fourier component of a spherical wave increases with the distance of propagation at a known 'phase speed'. If we assume that an atom is a point-like object, the relationship between the phase and the phase speed of each Fourier component is linear, and the distance between the atom and the plane of observation can therefore be determined by linear fitting. This picture has similarities with Big Bang cosmology, in which the Universe expands from a point-like origin such that the distance of any galaxy from the origin is linearly proportional to the speed at which it moves away from the origin (Hubble expansion). The proof of concept of the method has been demonstrated experimentally for graphene with a two-layer structure and it will work optimally for similar layered materials, such as boron nitride and molybdenum disulphide.

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

International Nuclear Information System (INIS)

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

2009-01-01

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

Ion-atom collisions with laser-prepared target: High resolution study of single charge exchange process

International Nuclear Information System (INIS)

Leredde, Arnaud

2012-01-01

Single charge transfer in low-energy Na"++"8"7Rb(5s,5p) collisions is investigated using magneto-optically trapped Rb atoms and high-resolution recoil-ion momentum spectroscopy. The three-dimensional reconstruction of the recoil-ion momentum provides accurate relative cross-sections for the active channels and the projectile scattering angle distributions. Thanks to the high experimental resolution, scattering structures such as diffraction-like oscillations in angular distributions are clearly observed. The measurements are compared with molecular close-coupling calculations and an excellent agreement is found. To go further in the test of the theory, the target is prepared in an oriented state. It is the first time that such collision experiments with oriented target is performed with such a high resolution. The right-left asymmetry expected for the scattering angle distribution is evidenced. The agreement between MOCC calculations and experiments is very good. Simple models developed for collisions with oriented target are also discussed. (author) [fr

Atom optics

International Nuclear Information System (INIS)

Balykin, V. I.; Jhe, W.

1999-01-01

Atom optics, in analogy to neutron and electron optics, deals with the realization of as a traditional elements, such as lenes, mirrors, beam splitters and atom interferometers, as well as a new 'dissipative' elements such as a slower and a cooler, which have no analogy in an another types of optics. Atom optics made the development of atom interferometer with high sensitivity for measurement of acceleration and rotational possible. The practical interest in atom optics lies in the opportunities to create atom microprobe with atom-size resolution and minimum damage of investigated objects. (Cho, G. S.)

Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

Energy Technology Data Exchange (ETDEWEB)

A Soares; D Schneider; J Skinner; M Cowan; R Buono; H Robinson; A Heroux; M Carlucci-Dayton; A Saxena; R Sweet

2011-12-31

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

International Nuclear Information System (INIS)

Soares, A.; Schneider, D.; Skinner, J.; Cowan, M.; Buono, R.; Robinson, H.; Heroux, A.; Carlucci-Dayton, M.; Saxena, A.; Sweet, R.

2008-01-01

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

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

Energy Technology Data Exchange (ETDEWEB)

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

2006-10-15

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

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

International Nuclear Information System (INIS)

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

2006-01-01

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

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

Science.gov (United States)

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

2006-09-06

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

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

Science.gov (United States)

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

2014-01-01

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

Atomic resolution three-dimensional electron diffraction microscopy

International Nuclear Information System (INIS)

Miao Jianwei; Ohsuna, Tetsu; Terasaki, Osamu; Hodgson, Keith O.; O'Keefe, Michael A.

2002-01-01

We report the development of a novel form of diffraction-based 3D microscopy to overcome resolution barriers inherent in high-resolution electron microscopy and tomography. By combining coherent electron diffraction with the oversampling phasing method, we show that the 3D structure of a nanocrystal can be determined ab initio at a resolution of 1 Angstrom from 29 simulated noisy diffraction patterns. This new form of microscopy can be used to image the 3D structures of nanocrystals and noncrystalline samples, with resolution limited only by the quality of sample diffraction

Investigation of an alternating current plasma as an element selective atomic emission detector for high-resolution capillary gas chromatography and as a source for atomic absorption and atomic emission spectrometry

Science.gov (United States)

Ombaba, Jackson M.

This thesis deals with the construction and evaluation of an alternating current plasma (ACP) as an element-selective detector for high resolution capillary gas chromatography (GC) and as an excitation source for atomic absorption spectrometry (AAS) and atomic emission spectrometry (AES). The plasma, constrained in a quartz discharge tube at atmospheric pressure, is generated between two copper electrodes and utilizes helium as the plasma supporting gas. The alternating current plasma power source consists of a step-up transformer with a secondary output voltage of 14,000 V at a current of 23 mA. The device exhibits a stable signal because the plasma is self-seeding and reignites itself every half cycle. A tesla coil is not required to commence generation of the plasma if the ac voltage applied is greater than the breakdown voltage of the plasma-supporting gas. The chromatographic applications studied included the following: (1) the separation and selective detection of the organotin species, tributyltin chloride (TBT) and tetrabutyltin (TEBT), in environmental matrices including mussels (Mvutilus edullus) and sediment from Boston Harbor, industrial waste water and industrial sludge, and (2) the detection of methylcyclopentadienyl manganesetricarbonyl (MMT) and similar compounds used as gasoline additives. An ultrasonic nebulizer (common room humidifier) was utilized as a sample introduction device for aqueous solutions when the ACP was employed as an atomization source for atomic absorption spectrometry and as an excitation source for atomic emission spectrometry. Plasma diagnostic parameters studied include spatial electron number density across the discharge tube, electronic, excitation and ionization temperatures. Interference studies both in absorption and emission modes were also considered. Figures of merits of selected elements both in absorption and emission modes are reported. The evaluation of a computer-aided optimization program, Drylab GC, using

A pixel detector for the protein crystallography beamline at the SLS

CERN Document Server

Brönnimann, C; Eikenberry, E F; Fischer, P; Florin, S; Horisberger, R P; Lindner, Manfred; Schmitt, B; Schulze, C

2002-01-01

At the Paul Scherrer Institute a new synchrotron light source is currently under construction, the Swiss Light Source (SLS), which will be operational in summer 2001. Among the first beamlines is a high brightness, micro-focusing protein crystallography beamline. It will be equipped with a pixel detector, which has several features of interest for the next generation of protein crystallography detectors. The point spread function and the effect of charge sharing was measured with a prototype detector in a test experiment at the European Synchrotron Radiation Facility in Grenoble. The concepts of the SLS pixel detector is presented as well as test results from radiation hard prototype chips.

On the possibilities of high-resolution continuum source graphite furnace atomic absorption spectrometry for the simultaneous or sequential monitoring of multiple atomic lines

International Nuclear Information System (INIS)

Resano, M.; Rello, L.; Florez, M.; Belarra, M.A.

2011-01-01

This paper explores the potential of commercially available high-resolution continuum source graphite furnace atomic absorption spectrometry instrumentation for the simultaneous or sequential monitoring of various atomic lines, in an attempt to highlight the analytical advantages that can be derived from this strategy. In particular, it is demonstrated how i) the monitoring of multiplets may allow for the simple expansion of the linear range, as shown for the measurement of Ni using the triplet located in the vicinity of 234.6 nm; ii) the use of a suitable internal standard may permit improving the precision and help in correcting for matrix-effects, as proved for the monitoring of Ni in different biological samples; iii) direct and multi-element analysis of solid samples may be feasible on some occasions, either by monitoring various atomic lines that are sufficiently close (truly simultaneous monitoring, as demonstrated in the determination of Co, Fe and Ni in NIST 1566a Oyster tissue) or, alternatively, by opting for a selective and sequential atomization of the elements of interest during every single replicate. Determination of Cd and Ni in BCR 679 White cabbage is attempted using both approaches, which permits confirming that both methods can offer very similar and satisfactory results. However, it is important to stress that the second approach provides more flexibility, since analysis is no longer limited to those elements that show very close atomic lines (closer than 0.3 nm in the ultraviolet region) with a sensitivity ratio similar to the concentration ratio of the analytes in the samples investigated.

Experimental realization of suspended atomic chains composed of different atomic species

International Nuclear Information System (INIS)

Bettini, Jefferson; Ugarte, Daniel; Sato, Fernando; Galvao, Douglas Soares; Coura, Pablo Zimmerman; Dantas, Socrates de Oliveira

2006-01-01

We report high resolution transmission electron microscopy (HRTEM) and molecular dynamics results of the first experimental test of suspended atomic chains composed of different atomic species formed from spontaneous stretching of metallic nanowires. (author)

A rational approach to heavy-atom derivative screening

International Nuclear Information System (INIS)

Joyce, M. Gordon; Radaev, Sergei; Sun, Peter D.

2010-01-01

In order to overcome the difficulties associated with the ‘classical’ heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom-derivative screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. Despite the development in recent times of a range of techniques for phasing macromolecules, the conventional heavy-atom derivatization method still plays a significant role in protein structure determination. However, this method has become less popular in modern high-throughput oriented crystallography, mostly owing to its trial-and-error nature, which often results in lengthy empirical searches requiring large numbers of well diffracting crystals. In addition, the phasing power of heavy-atom derivatives is often compromised by lack of isomorphism or even loss of diffraction. In order to overcome the difficulties associated with the ‘classical’ heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom derivative-screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. The method includes three basic steps: (i) the selection of likely reactive compounds for a given protein and specific crystallization conditions based on pre-defined heavy-atom compound reactivity profiles, (ii) screening of the chosen heavy-atom compounds for their ability to form protein adducts using mass spectrometry and (iii) derivatization of crystals with selected heavy-metal compounds using the quick-soak method to maximize diffraction quality and minimize non-isomorphism. Overall, this system streamlines the process of heavy-atom compound identification and minimizes the problem of non-isomorphism in phasing

A rational approach to heavy-atom derivative screening

Energy Technology Data Exchange (ETDEWEB)

Joyce, M. Gordon; Radaev, Sergei; Sun, Peter D., E-mail: psun@nih.gov [Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, Maryland 20852 (United States)

2010-04-01

In order to overcome the difficulties associated with the ‘classical’ heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom-derivative screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. Despite the development in recent times of a range of techniques for phasing macromolecules, the conventional heavy-atom derivatization method still plays a significant role in protein structure determination. However, this method has become less popular in modern high-throughput oriented crystallography, mostly owing to its trial-and-error nature, which often results in lengthy empirical searches requiring large numbers of well diffracting crystals. In addition, the phasing power of heavy-atom derivatives is often compromised by lack of isomorphism or even loss of diffraction. In order to overcome the difficulties associated with the ‘classical’ heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom derivative-screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. The method includes three basic steps: (i) the selection of likely reactive compounds for a given protein and specific crystallization conditions based on pre-defined heavy-atom compound reactivity profiles, (ii) screening of the chosen heavy-atom compounds for their ability to form protein adducts using mass spectrometry and (iii) derivatization of crystals with selected heavy-metal compounds using the quick-soak method to maximize diffraction quality and minimize non-isomorphism. Overall, this system streamlines the process of heavy-atom compound identification and minimizes the problem of non-isomorphism in phasing.

Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.

Science.gov (United States)

Organtini, Lindsey J; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E; Makhov, Alexander M; Conway, James F; Parrish, Colin R; Hafenstein, Susan

2016-11-01

Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Crystallography of waxes - an electron diffraction study of refined and natural products

Science.gov (United States)

Dorset, Douglas L.

1997-02-01

The crystal structure of four waxes has been investigated by electron crystallography. Two of these waxes, including a refined petroleum product (Gulfwax) and a material from lignite (montan wax), form well ordered crystals and their structure could be solved quantitatively from the observed 0022-3727/30/3/018/img1 diffraction patterns. As also found previously for simpler binary n-paraffin solid solutions, the average structure resembles that of a pure paraffin (e.g. n-0022-3727/30/3/018/img2) but with a Gaussian distribution of atomic occupancies near the chain ends to account for the statistical distribution of chain lengths within a lamella. Two other waxes from living organisms, South African bee honeycomb and the leaves of the Brazilian carnauba palm, are much less ordered, even though they share the same methylene subcell packing of the most crystalline parts of the previous materials. It appears that these waxes cannot fully separate into distinct lamellae, perhaps due to the presence of very long `tie' molecules, and are therefore `frustrated' crystal structures.

Optimal thickness of a monocrystal line object in atomic plane visualization on its image in a high-resolution electron microscope

International Nuclear Information System (INIS)

Grishina, T.A.; Sviridova, V.Yu.

1983-01-01

Theoretical and experimental investigation of the influence of the FCC-lattice crystal (gold, nickel) thickness on conditions of visulization of atomic plane projections (APP) on the crystal image in a transmission high-resolution electron microscope (THREM) is reported. Results of electron diffraction theory are used for theoretical investigation. Calculation analysis of the influence of the monocrystal thickness and orientation on conitions of visualization of APP and atomic columns in monocrystal images formed in THREM in multibeam regimes with inclined and axial illumination is conducted. It is shown that, to visualize the atomic column projections in a crystal image formed in the multibeam regime with axial illumination, optimal are the thicknesses from 0.1 xisub(min) to 0.25 xisub(min) and at some object orientations also the thicknesses from 0.8 xisub(min) to 0.9 xisub(min), where xisub(min) is the extinction length minimum for the given orientation. It is shown that, to realize the ultimate resolutions in multibeam regimes both with inclined and axial illumination the optimal thickness of the object is 0.63 xisub(min). Satisfactory coincidence of theoretical and experimental data is obtained

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

CERN Document Server

Kawamoto, M; Kamiya, N

2001-01-01

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

High-resolution and large dynamic range nanomechanical mapping in tapping-mode atomic force microscopy

International Nuclear Information System (INIS)

Sahin, Ozgur; Erina, Natalia

2008-01-01

High spatial resolution imaging of material properties is an important task for the continued development of nanomaterials and studies of biological systems. Time-varying interaction forces between the vibrating tip and the sample in a tapping-mode atomic force microscope contain detailed information about the elastic, adhesive, and dissipative response of the sample. We report real-time measurement and analysis of the time-varying tip-sample interaction forces with recently introduced torsional harmonic cantilevers. With these measurements, high-resolution maps of elastic modulus, adhesion force, energy dissipation, and topography are generated simultaneously in a single scan. With peak tapping forces as low as 0.6 nN, we demonstrate measurements on blended polymers and self-assembled molecular architectures with feature sizes at 1, 10, and 500 nm. We also observed an elastic modulus measurement range of four orders of magnitude (1 MPa to 10 GPa) for a single cantilever under identical feedback conditions, which can be particularly useful for analyzing heterogeneous samples with largely different material components.

Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

Energy Technology Data Exchange (ETDEWEB)

Brewster, Aaron S. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Sawaya, Michael R. [University of California, Los Angeles, CA 90095-1570 (United States); University of California, Los Angeles, CA 90095-1570 (United States); University of California, Los Angeles, CA 90095-1570 (United States); Rodriguez, Jose [University of California, Los Angeles, CA 90095-1570 (United States); University of California, Los Angeles, CA 90095-1570 (United States); Hattne, Johan; Echols, Nathaniel [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); McFarlane, Heather T. [University of California, Los Angeles, CA 90095-1570 (United States); University of California, Los Angeles, CA 90095-1570 (United States); Cascio, Duilio [University of California, Los Angeles, CA 90095-1570 (United States); University of California, Los Angeles, CA 90095-1570 (United States); University of California, Los Angeles, CA 90095-1570 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California, Berkeley, CA 94720 (United States); Eisenberg, David S. [University of California, Los Angeles, CA 90095-1570 (United States); University of California, Los Angeles, CA 90095-1570 (United States); University of California, Los Angeles, CA 90095-1570 (United States); Sauter, Nicholas K., E-mail: nksauter@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

2015-02-01

Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions. Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.

A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits.

Science.gov (United States)

Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

2014-09-01

As a contribution to the celebration of the year 2014, declared by the United Nations to be 'The International Year of Crystallography', the FEBS Journal is dedicating this issue to papers showcasing the intimate union between macromolecular crystallography and structural biology, both in historical perspective and in current research. Instead of a formal editorial piece, by way of introduction, this review discusses the most important, often iconic, achievements of crystallographers that led to major advances in our understanding of the structure and function of biological macromolecules. We identified at least 42 scientists who received Nobel Prizes in Physics, Chemistry or Medicine for their contributions that included the use of X-rays or neutrons and crystallography, including 24 who made seminal discoveries in macromolecular sciences. Our spotlight is mostly, but not only, on the recipients of this most prestigious scientific honor, presented in approximately chronological order. As a summary of the review, we attempt to construct a genealogy tree of the principal lineages of protein crystallography, leading from the founding members to the present generation. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Missed opportunities in crystallography.

Science.gov (United States)

Dauter, Zbigniew; Jaskolski, Mariusz

2014-09-01

Scrutinized from the perspective of time, the giants in the history of crystallography more than once missed a nearly obvious chance to make another great discovery, or went in the wrong direction. This review analyzes such missed opportunities focusing on macromolecular crystallographers (using Perutz, Pauling, Franklin as examples), although cases of particular historical (Kepler), methodological (Laue, Patterson) or structural (Pauling, Ramachandran) relevance are also described. Linus Pauling, in particular, is presented several times in different circumstances, as a man of vision, oversight, or even blindness. His example underscores the simple truth that also in science incessant creativity is inevitably connected with some probability of fault. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

On R factors for dynamic structure crystallography

DEFF Research Database (Denmark)

Coppens, Philip; Kaminski, Radoslaw; Schmøkel, Mette Stokkebro

2010-01-01

In studies of dynamic changes in crystals in which induced metastable species may have lifetimes of microseconds or less, refinements are most sensitive if based on the changes induced in the measured intensities. Agreement factors appropriate for such refinements, based on the ratios of the inte...... of the intensities before and after the external perturbation is applied, are discussed and compared with R factors commonly applied in static structure crystallography....

The basics of crystallography and diffraction

CERN Document Server

Hammond, C

2015-01-01

This title provides a clear and very broadly based introduction to crystallography, light, X-ray, and electron diffraction; a knowledge of which is essential to students in a wide range of scientific disciplines but which is otherwise generally covered in subject-specific and more mathematically detailed texts. The book is also designed to appeal to the more general reader since it shows, by historical and biographical references, how the subject has developed from the work and insights of successive generations of crystallographers and scientists.

The 3.2 Angstrom Resolution Structure of the Polymorphic Cowpea Chlorotic Mottle Virus Ribonucleoprotein Particle

Science.gov (United States)

Speir, Jeffrey Alan

in the atomic structures of the DNA tumor papovaviruses (SV40 and polyoma). The swollen structure is closely similar to the expanded form of tomato bushy stunt virus (TBSV) previously determined at 8A resolution by X-ray crystallography.

Recent Major Improvements to the ALS Sector 5 Macromolecular Crystallography Beamlines

International Nuclear Information System (INIS)

Morton, Simon A.; Glossinger, James; Smith-Baumann, Alexis; McKean, John P.; Trame, Christine; Dickert, Jeff; Rozales, Anthony; Dauz, Azer; Taylor, John; Zwart, Petrus; Duarte, Robert; Padmore, Howard; McDermott, Gerry; Adams, Paul

2007-01-01

Although the Advanced Light Source (ALS) was initially conceived primarily as a low energy (1.9GeV) 3rd generation source of VUV and soft x-ray radiation it was realized very early in the development of the facility that a multipole wiggler source coupled with high quality, (brightness preserving), optics would result in a beamline whose performance across the optimal energy range (5-15keV) for macromolecular crystallography (MX) would be comparable to, or even exceed, that of many existing crystallography beamlines at higher energy facilities. Hence, starting in 1996, a suite of three beamlines, branching off a single wiggler source, was constructed, which together formed the ALS Macromolecular Crystallography Facility. From the outset this facility was designed to cater equally to the needs of both academic and industrial users with a heavy emphasis placed on the development and introduction of high throughput crystallographic tools, techniques, and facilities--such as large area CCD detectors, robotic sample handling and automounting facilities, a service crystallography program, and a tightly integrated, centralized, and highly automated beamline control environment for users. This facility was immediately successful, with the primary Multiwavelength Anomalous Diffraction beamline (5.0.2) in particular rapidly becoming one of the foremost crystallographic facilities in the US--responsible for structures such as the 70S ribosome. This success in-turn triggered enormous growth of the ALS macromolecular crystallography community and spurred the development of five additional ALS MX beamlines all utilizing the newly developed superconducting bending magnets ('superbends') as sources. However in the years since the original Sector 5.0 beamlines were built the performance demands of macromolecular crystallography users have become ever more exacting; with growing emphasis placed on studying larger complexes, more difficult structures, weakly diffracting or smaller

Dynamically polarized samples for neutron protein crystallography at the Spallation Neutron Source

International Nuclear Information System (INIS)

Zhao, Jinkui; Pierce, Josh; Robertson, J. L.; Herwig, Kenneth W.; Myles, Dean; Cuneo, Matt; Li, Le; Meilleur, Flora; Standaert, Bob

2016-01-01

To prepare for the next generation neutron scattering instruments for the planned second target station at the Spallation Neutron Source (SNS) and to broaden the scientific impact of neutron protein crystallography at the Oak Ridge National Laboratory, we have recently ramped up our efforts to develop a dynamically polarized target for neutron protein crystallography at the SNS. Proteins contain a large amount of hydrogen which contributes to incoherent diffraction background and limits the sensitivity of neutron protein crystallography. This incoherent background can be suppressed by using polarized neutron diffraction, which in the same time also improves the coherent diffraction signal. Our plan is to develop a custom Dynamic Nuclear Polarization (DNP) setup tailored to neutron protein diffraction instruments. Protein crystals will be polarized at a magnetic field of 5 T and temperatures of below 1 K. After the dynamic polarization process, the sample will be brought to a frozen-spin mode in a 0.5 T holding field and at temperatures below 100 mK. In a parallel effort, we are also investigating various ways of incorporating polarization agents needed for DNP, such as site specific spin labels, into protein crystals. (paper)

Single-atom-resolved fluorescence imaging of an atomic Mott insulator

DEFF Research Database (Denmark)

Sherson, Jacob; Weitenberg, Christof; Andres, Manuel

2010-01-01

in situ images of a quantum fluid in which each underlying quantum particle is detected. Here we report fluorescence imaging of strongly interacting bosonic Mott insulators in an optical lattice with single-atom and single-site resolution. From our images, we fully reconstruct the atom distribution...

The gating cycle of a K+ channel at atomic resolution

Energy Technology Data Exchange (ETDEWEB)

Cuello, Luis G. [Center for Membrane Protein Research, Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, United States; Cortes, D. Marien [Center for Membrane Protein Research, Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, United States; Perozo, Eduardo [Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States

2017-11-22

C-type inactivation in potassium channels helps fine-tune long-term channel activity through conformational changes at the selectivity filter. Here, through the use of cross-linked constitutively open constructs, we determined the structures of KcsA’s mutants that stabilize the selectivity filter in its conductive (E71A, at 2.25 Å) and deep C-type inactivated (Y82A at 2.4 Å) conformations. These structural snapshots represent KcsA’s transient open-conductive (O/O) and the stable open deep C-type inactivated states (O/I), respectively. The present structures provide an unprecedented view of the selectivity filter backbone in its collapsed deep C-type inactivated conformation, highlighting the close interactions with structural waters and the local allosteric interactions that couple activation and inactivation gating. Together with the structures associated with the closed-inactivated state (C/I) and in the well-known closed conductive state (C/O), this work recapitulates, at atomic resolution, the key conformational changes of a potassium channel pore domain as it progresses along its gating cycle.

X-ray holography with an atomic scatterer

Energy Technology Data Exchange (ETDEWEB)

Mityureva, A.A.; Smirnov, V.V., E-mail: valery_smirnov@mail.ru

2016-08-15

X-ray holography scheme with reference scatterer consisting of heavy atom as reference center and its link to an object consisting of several light atoms and using controlled variation of the alignment is represented. The scheme can reproduce an object in three dimensions with atomic resolution. The distorting factors of reconstruction are considered. - Highlights: • X-ray holography scheme with a reference wave formed by atomic scatterer. • 3D object reconstruction with atomic resolution from the set of holograms. • Simple formula for the distorting factor in reconstruction.

High-resolution continuum-source atomic absorption spectrometry: what can we expect?

Directory of Open Access Journals (Sweden)

Welz Bernhard

2003-01-01

Full Text Available A new instrumental concept has been developed for atomic absorption spectrometry (AAS, using a high-intensity xenon short-arc lamp as continuum radiation source, a high-resolution double-echelle monochromator and a CCD array detector, providing a resolution of ~2 pm per pixel. Among the major advantages of the system are: i an improved signal-to-noise ratio because of the high intensity of the radiation source, resulting in improved photometric precision and detection limits; ii for the same reason, there are no more 'weak' lines, i.e. secondary lines can be used without compromises; iii new elements might be determined, for which no radiation source has been available; iv the entire spectral environment around the analytical line becomes 'visible', giving a lot more information than current AAS instruments; v the CCD array detector allows a truly simultaneous background correction close to the analytical line; vi the software is capable of storing reference spectra, e.g. of a molecular absorption with rotational fine structure, and of subtracting such spectra from the spectra recorded for a sample, using a least squares algorithm; vii although not yet realized, the system makes possible a truly simultaneous multi-element AAS measurement when an appropriate two-dimensional detector is used, as is already common practice in optical emission spectrometry; vii preliminary experiments have indicated that the instrumental concept could result in a more rugged analytical performance in the determination of trace elements in complex matrices.

Structural dynamics of surfaces by ultrafast electron crystallography: experimental and multiple scattering theory.

Science.gov (United States)

Schäfer, Sascha; Liang, Wenxi; Zewail, Ahmed H

2011-12-07

Recent studies in ultrafast electron crystallography (UEC) using a reflection diffraction geometry have enabled the investigation of a wide range of phenomena on the femtosecond and picosecond time scales. In all these studies, the analysis of the diffraction patterns and their temporal change after excitation was performed within the kinematical scattering theory. In this contribution, we address the question, to what extent dynamical scattering effects have to be included in order to obtain quantitative information about structural dynamics. We discuss different scattering regimes and provide diffraction maps that describe all essential features of scatterings and observables. The effects are quantified by dynamical scattering simulations and examined by direct comparison to the results of ultrafast electron diffraction experiments on an in situ prepared Ni(100) surface, for which structural dynamics can be well described by a two-temperature model. We also report calculations for graphite surfaces. The theoretical framework provided here allows for further UEC studies of surfaces especially at larger penetration depths and for those of heavy-atom materials. © 2011 American Institute of Physics

An alternative approach to determine attainable resolution directly from HREM images

International Nuclear Information System (INIS)

Wang, A.; Turner, S.; Van Aert, S.; Van Dyck, D.

2013-01-01

The concept of resolution in high-resolution electron microscopy (HREM) is the power to resolve neighboring atoms. Since the resolution is related to the width of the point spread function of the microscope, it could in principle be determined from the image of a point object. However, in electron microscopy there are no ideal point objects. The smallest object is an individual atom. If the width of an atom is much smaller than the resolution of the microscope, this atom can still be considered as a point object. As the resolution of the microscope enters the sub-Å regime, information about the microscope is strongly entangled with the information about the atoms in HREM images. Therefore, we need to find an alternative method to determine the resolution in an object-independent way. In this work we propose to use the image wave of a crystalline object in zone axis orientation. Under this condition, the atoms of a column act as small lenses so that the electron beam channels through the atom column periodically. Because of this focusing, the image wave of the column can be much more peaked than the constituting atoms and can thus be a much more sensitive probe to measure the resolution. Our approach is to use the peakiness of the image wave of the atom column to determine the resolution. We will show that the resolution can be directly linked to the total curvature of the atom column wave. Moreover, we can then directly obtain the resolution of the microscope given that the contribution from the object is known, which is related to the bounding energy of the atom. The method is applied on an experimental CaTiO 3 image wave. - Highlights: • Microscope aberrations and the size of the atoms influence the resolution at the sub-Å level. • In channeling condition the atoms in the column focus the electron beam into a narrow peak at the exit face. • The shape of this peak can be used to determine the resolution in an object independent way. • This results in a

A smooth and differentiable bulk-solvent model for macromolecular diffraction

Energy Technology Data Exchange (ETDEWEB)

Fenn, T. D. [Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California (United States); Schnieders, M. J. [Department of Chemistry, Stanford, California (United States); Brunger, A. T., E-mail: brunger@stanford.edu [Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California (United States); Departments of Neurology and Neurological Sciences, Structural Biology and Photon Science, Stanford, California (United States)

2010-09-01

A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R{sub free} and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography.

A smooth and differentiable bulk-solvent model for macromolecular diffraction

International Nuclear Information System (INIS)

Fenn, T. D.; Schnieders, M. J.; Brunger, A. T.

2010-01-01

A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R free and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography

The Joint Structural Biology Group beam lines at the ESRF: Modern macromolecular crystallography

CERN Document Server

Mitchell, E P

2001-01-01

Macromolecular crystallography has evolved considerably over the last decade. Data sets in under an hour are now possible on high throughput beam lines leading to electron density and, possibly, initial models calculated on-site. There are five beam lines currently dedicated to macromolecular crystallography: the ID14 complex and BM-14 (soon to be superseded by ID-29). These lines handle over five hundred projects every six months and demand is increasing. Automated sample handling, alignment and data management protocols will be required to work efficiently with this demanding load. Projects developing these themes are underway within the JSBG.

Low-resolution continuum source simultaneous multi-element electrothermal atomic absorption spectrometry: steps into practice

International Nuclear Information System (INIS)

Katskov, Dmitri

2015-01-01

The theory and practical problems of continuum source simultaneous multi-element electrothermal atomic absorption spectrometry (SMET AAS) are discussed by the example of direct analysis of underground water. The experimental methodology is based on pulse vaporization of the sample in a fast heated graphite tube and measurement of transient absorption of continuum spectrum radiation from D 2 and Xe lamps within 200–400 nm wavelengths range with a low resolution spectral instrument and linear charge-coupled device. The setup permits the acquisition of 200 spectra during 1 s atomization pulse. Respective data matrix absorbance vs wavelength/time is employed for the quantification of elements in the sample. The calculation algorithm developed includes broad band and continuum background correction, linearization of function absorbance vs. concentration of atomic vapor and integration of thus modified absorbance at the resonance lines of the elements to be determined. Practical application shows that the method can be employed for the direct simultaneous determination of about 20 elements above microgram per liter level within 3–5 orders of the magnitude concentration range. The investigated sources of measurement errors are mainly associated with the atomization and vapor transportation problems, which are aggravated for the simultaneous release of major and minor sample constituents. Respective corrections concerning the selection of analytical lines, optimal sampling volume, matrix modification and cleaning of the atomizer have been introduced in the SMET AAS analytical technology. Under the optimized experimental conditions the calibration curves in Log-Log coordinates for all the investigated analytes in the single or multi-element reference solutions are approximated by the first order equations. The use of these equations as permanent characteristics of the setup enables instant quantification of Al, Ca, Co, Cr, Cu, Fe, Mg, Mn and Ni in the underground water

Low-resolution continuum source simultaneous multi-element electrothermal atomic absorption spectrometry: steps into practice

Energy Technology Data Exchange (ETDEWEB)

Katskov, Dmitri, E-mail: katskovda@tut.ac.za

2015-03-01

The theory and practical problems of continuum source simultaneous multi-element electrothermal atomic absorption spectrometry (SMET AAS) are discussed by the example of direct analysis of underground water. The experimental methodology is based on pulse vaporization of the sample in a fast heated graphite tube and measurement of transient absorption of continuum spectrum radiation from D{sub 2} and Xe lamps within 200–400 nm wavelengths range with a low resolution spectral instrument and linear charge-coupled device. The setup permits the acquisition of 200 spectra during 1 s atomization pulse. Respective data matrix absorbance vs wavelength/time is employed for the quantification of elements in the sample. The calculation algorithm developed includes broad band and continuum background correction, linearization of function absorbance vs. concentration of atomic vapor and integration of thus modified absorbance at the resonance lines of the elements to be determined. Practical application shows that the method can be employed for the direct simultaneous determination of about 20 elements above microgram per liter level within 3–5 orders of the magnitude concentration range. The investigated sources of measurement errors are mainly associated with the atomization and vapor transportation problems, which are aggravated for the simultaneous release of major and minor sample constituents. Respective corrections concerning the selection of analytical lines, optimal sampling volume, matrix modification and cleaning of the atomizer have been introduced in the SMET AAS analytical technology. Under the optimized experimental conditions the calibration curves in Log-Log coordinates for all the investigated analytes in the single or multi-element reference solutions are approximated by the first order equations. The use of these equations as permanent characteristics of the setup enables instant quantification of Al, Ca, Co, Cr, Cu, Fe, Mg, Mn and Ni in the underground

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

African Journals Online (AJOL)

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

Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.

Science.gov (United States)

Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen-Hsiang; Parks, Jerry M; Smith, Jeremy C; Weiss, Kevin L; Keen, David A; Blakeley, Matthew P; Louis, John M; Langan, Paul; Weber, Irene T; Kovalevsky, Andrey

2016-04-11

Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bandgap modulation in photoexcited topological insulator Bi{sub 2}Te{sub 3} via atomic displacements

Energy Technology Data Exchange (ETDEWEB)

Hada, Masaki, E-mail: hadamasaki@okayama-u.ac.jp [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Materials and Structures Laboratory, Tokyo Institute of Technology, Yokohama 226-8503 (Japan); PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012 (Japan); Norimatsu, Katsura; Tsuruta, Tetsuya; Igarashi, Kyushiro; Kayanuma, Yosuke; Sasagawa, Takao; Nakamura, Kazutaka G. [Materials and Structures Laboratory, Tokyo Institute of Technology, Yokohama 226-8503 (Japan); Tanaka, Sei' ichi; Ishikawa, Tadahiko; Koshihara, Shin-ya [Department of Chemistry and Materials Science, Tokyo Institute of Technology, Tokyo 152-8551 (Japan); Keskin, Sercan [The Max Planck Institute for the Structure and Dynamics of Matter, The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg 22761 (Germany); Miller, R. J. Dwayne [The Max Planck Institute for the Structure and Dynamics of Matter, The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg 22761 (Germany); Departments of Chemistry and Physics, University of Toronto, Toronto M5S 3H6 (Canada); Onda, Ken [PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012 (Japan); Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama 226-8502 (Japan)

2016-07-14

The atomic and electronic dynamics in the topological insulator (TI) Bi{sub 2}Te{sub 3} under strong photoexcitation were characterized with time-resolved electron diffraction and time-resolved mid-infrared spectroscopy. Three-dimensional TIs characterized as bulk insulators with an electronic conduction surface band have shown a variety of exotic responses in terms of electronic transport when observed under conditions of applied pressure, magnetic field, or circularly polarized light. However, the atomic motions and their correlation between electronic systems in TIs under strong photoexcitation have not been explored. The artificial and transient modification of the electronic structures in TIs via photoinduced atomic motions represents a novel mechanism for providing a comparable level of bandgap control. The results of time-domain crystallography indicate that photoexcitation induces two-step atomic motions: first bismuth and then tellurium center-symmetric displacements. These atomic motions in Bi{sub 2}Te{sub 3} trigger 10% bulk bandgap narrowing, which is consistent with the time-resolved mid-infrared spectroscopy results.

Directed Atom-by-Atom Assembly of Dopants in Silicon.

Science.gov (United States)

Hudak, Bethany M; Song, Jiaming; Sims, Hunter; Troparevsky, M Claudia; Humble, Travis S; Pantelides, Sokrates T; Snijders, Paul C; Lupini, Andrew R

2018-05-17

The ability to controllably position single atoms inside materials is key for the ultimate fabrication of devices with functionalities governed by atomic-scale properties. Single bismuth dopant atoms in silicon provide an ideal case study in view of proposals for single-dopant quantum bits. However, bismuth is the least soluble pnictogen in silicon, meaning that the dopant atoms tend to migrate out of position during sample growth. Here, we demonstrate epitaxial growth of thin silicon films doped with bismuth. We use atomic-resolution aberration-corrected imaging to view the as-grown dopant distribution and then to controllably position single dopants inside the film. Atomic-scale quantum-mechanical calculations corroborate the experimental findings. These results indicate that the scanning transmission electron microscope is of particular interest for assembling functional materials atom-by-atom because it offers both real-time monitoring and atom manipulation. We envision electron-beam manipulation of atoms inside materials as an achievable route to controllable assembly of structures of individual dopants.

Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution

Energy Technology Data Exchange (ETDEWEB)

Tu, Chao [Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702 (United States); Tan, Yu-Hong [Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697 (United States); Shaw, Gary [Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702 (United States); Zhou, Zheng; Bai, Yawen [Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892 (United States); Luo, Ray [Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697 (United States); Ji, Xinhua, E-mail: jix@ncifcrf.gov [Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702 (United States)

2008-05-01

The impact of hotspot mutation R282Q on the structure of human p53 DNA-binding domain has been characterized by X-ray crystallography and molecular-dynamics simulations. Tumor suppressor p53 is a sequence-specific DNA-binding protein and its central DNA-binding domain (DBD) harbors six hotspots (Arg175, Gly245, Arg248, Arg249, Arg273 and Arg282) for human cancers. Here, the crystal structure of a low-frequency hotspot mutant, p53DBD(R282Q), is reported at 1.54 Å resolution together with the results of molecular-dynamics simulations on the basis of the structure. In addition to eliminating a salt bridge, the R282Q mutation has a significant impact on the properties of two DNA-binding loops (L1 and L3). The L1 loop is flexible in the wild type, but it is not flexible in the mutant. The L3 loop of the wild type is not flexible, whereas it assumes two conformations in the mutant. Molecular-dynamics simulations indicated that both conformations of the L3 loop are accessible under biological conditions. It is predicted that the elimination of the salt bridge and the inversion of the flexibility of L1 and L3 are directly or indirectly responsible for deactivating the tumor suppressor p53.

Atomic-resolution studies of In{sub 2}O{sub 3}-ZnO compounds on aberration-corrected electron microscopes

Energy Technology Data Exchange (ETDEWEB)

Yu, Wentao

2009-10-23

In this work, the characteristic inversion domain microstructures of In{sub 2}O{sub 3}(ZnO){sub m} (m=30) compounds were investigated by TEM methods. At bright-atom contrast condition, atomically resolved HR-TEM images of In{sub 2}O{sub 3}(ZnO){sub 30} were successfully acquired in [1 anti 100] zone axis of ZnO, with projected metal columns of {proportional_to}1.6 A well resolved. From contrast maxima in the TEM images, local lattice distortions at the pyramidal inversion domain boundaries were observed for the first time. Lattice displacements and the strain field in two-dimensions were visualized and measured using the 'DALI' algorithm. Atomically resolved single shot and focal series images of In{sub 2}O{sub 3}(ZnO){sub 30} were achieved in both zone axes of ZnO, [1 anti 100] and [2 anti 1 anti 10], respectively. The electron waves at the exit-plane were successfully reconstructed using the software package 'TrueImage'. Finally, a three dimensional atomic structure model for the pyramidal IDB was proposed, with an In distribution of 10%, 20%, 40%, 20% and 10% of In contents over 5 atom columns along basal planes, respectively. Through a detailed structural study of In{sub 2}O{sub 3}(ZnO){sub m} compounds by using phase-contrast and Z-contrast imaging at atomic resolution, In{sup 3+} atoms are determined with trigonal bi-pyramidal co-ordination and are distributed at the pyramidal IDBs. (orig.)

Advances in powder diffraction crystallography

International Nuclear Information System (INIS)

Magneli, A.

1986-01-01

This is the first conference to be arranged within the framework of an agreement on scientific exchange and co-operation between l Academie des Sciences de l Institut de France and the Royal Swedish Academy of Sciences. The responsibility for the scientific program of the conference has been shared between members of the two Academies. The contributions include glimpses of the historical background and broad reviews of the present status of development and of recent work in powder crystallography. Reports are given on a number of studies, basic as well as applied in character, currently conducted in the two countries in a large variety of fields. Prospects of further developments in the area are also presented

Macromolecular crystallography research at Trombay

International Nuclear Information System (INIS)

Kannan, K.K.; Chidamrabam, R.

1983-01-01

Neutron diffraction studies of hydrogen positions in small molecules of biological interest at Trombay have provided valuable information that has been used in protein and enzyme structure model-building and in developing hydrogen bond potential functions. The new R-5 reactor is expected to provide higher neutron fluxes and also make possible small-angle neutron scattering studies of large biomolecules and bio-aggregates. In the last few years infrastructure facilities have also been established for macromolecular x-ray crystallography research. Meanwhile, the refinement of carbonic hydrases and lyysozyme structures have been carried out and interesting results obtained on protein dynamics and structure-function relationships. Some interesting presynaptic toxin phospholipases have also taken up for study. (author)

Progress in atomic spectroscopy

International Nuclear Information System (INIS)

Beyer, H.J.; Kleinpoppen, H.

1984-01-01

This book presents reviews by leading experts in the field covering areas of research at the forefront of atomic spectroscopy. Topics considered include the k ordering of atomic structure, multiconfiguration Hartree-Fock calculations for complex atoms, new methods in high-resolution laser spectroscopy, resonance ionization spectroscopy (inert atom detection), trapped ion spectroscopy, high-magnetic-field atomic physics, the effects of magnetic and electric fields on highly excited atoms, x rays from superheavy collision systems, recoil ion spectroscopy with heavy ions, investigations of superheavy quasi-atoms via spectroscopy of electron rays and positrons, impact ionization by fast projectiles, and amplitudes and state parameters from ion- and atom-atom excitation processes

Neutron protein crystallography hydrogen protons and hydration in bio-macromolecules

CERN Document Server

Niimura, Nobuo

2011-01-01

This text is dedicated to the emerging field of neutron protein crystallography (NPC). It covers all of the practical aspects of NPC and demonstrates how NPC can explore protein features such as hydrogen bonds, protonation and deprotonation of amino acid residues, and hydration structures.

Chiral Gold Nanoclusters: Atomic Level Origins of Chirality.

Science.gov (United States)

Zeng, Chenjie; Jin, Rongchao

2017-08-04

Chiral nanomaterials have received wide interest in many areas, but the exact origin of chirality at the atomic level remains elusive in many cases. With recent significant progress in atomically precise gold nanoclusters (e.g., thiolate-protected Au n (SR) m ), several origins of chirality have been unveiled based upon atomic structures determined by using single-crystal X-ray crystallography. The reported chiral Au n (SR) m structures explicitly reveal a predominant origin of chirality that arises from the Au-S chiral patterns at the metal-ligand interface, as opposed to the chiral arrangement of metal atoms in the inner core (i.e. kernel). In addition, chirality can also be introduced by a chiral ligand, manifested in the circular dichroism response from metal-based electronic transitions other than the ligand's own transition(s). Lastly, the chiral arrangement of carbon tails of the ligands has also been discovered in a very recent work on chiral Au 133 (SR) 52 and Au 246 (SR) 80 nanoclusters. Overall, the origins of chirality discovered in Au n (SR) m nanoclusters may provide models for the understanding of chirality origins in other types of nanomaterials and also constitute the basis for the development of various applications of chiral nanoparticles. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic resolution scanning tunneling microscopy in a cryogen free dilution refrigerator at 15 mK

International Nuclear Information System (INIS)

Haan, A. M. J. den; Wijts, G. H. C. J.; Galli, F.; Oosterkamp, T. H.; Usenko, O.; Baarle, G. J. C. van; Zalm, D. J. van der

2014-01-01

Pulse tube refrigerators are becoming more common, because they are cost efficient and demand less handling than conventional (wet) refrigerators. However, a downside of a pulse tube system is the vibration level at the cold-head, which is in most designs several micrometers. We implemented vibration isolation techniques which significantly reduced vibration levels at the experiment. These optimizations were necessary for the vibration sensitive magnetic resonance force microscopy experiments at milli-kelvin temperatures for which the cryostat is intended. With these modifications we show atomic resolution scanning tunneling microscopy on graphite. This is promising for scanning probe microscopy applications at very low temperatures

State-selective imaging of cold atoms

NARCIS (Netherlands)

Sheludko, D.V.; Bell, S.C.; Anderson, R.; Hofmann, C.S.; Vredenbregt, E.J.D.; Scholten, R.E.

2008-01-01

Atomic coherence phenomena are usually investigated using single beam techniques without spatial resolution. Here we demonstrate state-selective imaging of cold 85Rb atoms in a three-level ladder system, where the atomic refractive index is sensitive to the quantum coherence state of the atoms. We

Ultrafast electron crystallography of the cooperative reaction path in vanadium dioxide

Directory of Open Access Journals (Sweden)

Ding-Shyue Yang

2016-05-01

Full Text Available Time-resolved electron diffraction with atomic-scale spatial and temporal resolution was used to unravel the transformation pathway in the photoinduced structural phase transition of vanadium dioxide. Results from bulk crystals and single-crystalline thin-films reveal a common, stepwise mechanism: First, there is a femtosecond V−V bond dilation within 300 fs, second, an intracell adjustment in picoseconds and, third, a nanoscale shear motion within tens of picoseconds. Experiments at different ambient temperatures and pump laser fluences reveal a temperature-dependent excitation threshold required to trigger the transitional reaction path of the atomic motions.

MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments

International Nuclear Information System (INIS)

Gabadinho, José; Beteva, Antonia; Guijarro, Matias; Rey-Bakaikoa, Vicente; Spruce, Darren

2010-01-01

MxCuBE is a beamline control environment optimized for the needs of macromolecular crystallography. This paper describes the design of the software and the features that MxCuBE currently provides. The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1

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

Czech Academy of Sciences Publication Activity Database

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

2012-01-01

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

Shallow surface depth profiling with atomic resolution

International Nuclear Information System (INIS)

Xi, J.; Dastoor, P.C.; King, B.V.; O'Connor, D.J.

1999-01-01

It is possible to derive atomic layer-by-layer composition depth profiles from popular electron spectroscopic techniques, such as X-ray photoelectron spectroscopy (XPS) or Auger electron spectroscopy (AES). When ion sputtering assisted AES or XPS is used, the changes that occur during the establishment of the steady state in the sputtering process make these techniques increasingly inaccurate for depths less than 3nm. Therefore non-destructive techniques of angle-resolved XPS (ARXPS) or AES (ARAES) have to be used in this case. In this paper several data processing algorithms have been used to extract the atomic resolved depth profiles of a shallow surface (down to 1nm) from ARXPS and ARAES data

A beamline for macromolecular crystallography at the Advanced Light Source

International Nuclear Information System (INIS)

Padmore, H.A.; Earnest, T.; Kim, S.H.; Thompson, A.C.; Robinson, A.L.

1994-08-01

A beamline for macromolecular crystallography has been designed for the ALS. The source will be a 37-pole wiggler with a, 2-T on-axis peak field. The wiggler will illuminate three beamlines, each accepting 3 mrad of horizontal aperture. The central beamline will primarily be used for multiple-wavelength anomalous dispersion measurements in the wavelength range from 4 to 0.9 angstrom. The beamline optics will comprise a double-crystal monochromator with a collimating pre-mirror and a double-focusing mirror after the monochromator. The two side stations will be used for fixed-wavelength experiments within the wavelength range from 1.5 to 0.95 angstrom. The optics will consist of a conventional vertically focusing cylindrical mirror followed by an asymmetrically cut curved-crystal monochromator. This paper presents details of the optimization of the wiggler source for crystallography, gives a description of the beamline configuration, and discusses the reasons for the choices made

10 years of protein crystallography at AR-NW12A beamline

Science.gov (United States)

Chavas, L. M. G.; Yamada, Y.; Hiraki, M.; Igarashi, N.; Matsugaki, N.; Wakatsuki, S.

2013-03-01

The exponential growth of protein crystallography can be observed in the continuously increasing demand for synchrotron beam time, both from academic and industrial users. Nowadays, the screening of a profusion of sample crystals for more and more projects is being implemented by taking advantage of fully automated procedures at every level of the experiments. The insertion device AR-NW12A beamline is one of the five macromolecular crystallography (MX) beamlines at the Photon Factory (PF). Currently the oldest MX beamline operational at the High Energy Accelerator Research Organization (KEK), the end-station was launched in 2001 as part of an upgrade of the PF Advanced Ring. Since its commissioning, AR-NW12A has been operating as a high-throughput beamline, slowly evolving to a multipurpose end-station for MX experiments. The development of the beamline took place about a decade ago, in parallel with a drastic development of protein crystallography and more general synchrotron technology. To keep the beamline up-to-date and competitive with other MX stations in Japan and worldwide, new features have been constantly added, with the goal of user friendliness of the various beamline optics and other instruments. Here we describe the evolution of AR-NW12A for its tenth anniversary. We also discuss the plans for upgrades for AR-NW12A, the future objectives in terms of the beamline developments, and especially the strong desire to open the beamline to a larger user community.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

International Nuclear Information System (INIS)

Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

2013-01-01

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully

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.

Automation of specimen selection and data acquisition for protein electron crystallography

NARCIS (Netherlands)

Oostergetel, G.T.; Keegstra, W.; Brisson, A.D R

A system is presented for semi-automatic specimen selection and data acquisition for protein electron crystallography, based on a slow-scan CCD camera connected to a transmission electron microscope and control from an external computer. Areas of interest on the specimen are localised at low

Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.

Science.gov (United States)

Aguda, Adeleke H; Lavallee, Vincent; Cheng, Ping; Bott, Tina M; Meimetis, Labros G; Law, Simon; Nguyen, Nham T; Williams, David E; Kaleta, Jadwiga; Villanueva, Ivan; Davies, Julian; Andersen, Raymond J; Brayer, Gary D; Brömme, Dieter

2016-08-26

Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.

Structure of catalase determined by MicroED

Science.gov (United States)

Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

2014-01-01

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

Atomic inner-shell physics

International Nuclear Information System (INIS)

Crasemann, B.

1985-01-01

This book discusses: relativistic and quantum electrodynamic effects on atomic inner shells; relativistic calculation of atomic transition probabilities; many-body effects in energetic atomic transitions; Auger Electron spectrometry of core levels of atoms; experimental evaluation of inner-vacancy level energies for comparison with theory; mechanisms for energy shifts of atomic K-X rays; atomic physics research with synchrotron radiation; investigations of inner-shell states by the electron energy-loss technique at high resolution; coherence effects in electron emission by atoms; inelastic X-ray scattering including resonance phenomena; Rayleigh scattering: elastic photon scattering by bound electrons; electron-atom bremsstrahlung; X-ray and bremsstrahlung production in nuclear reactions; positron production in heavy-ion collisions, and X-ray processes in heavy-ion collisions

Accounting for partiality in serial crystallography using ray-tracing principles

International Nuclear Information System (INIS)

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

2015-01-01

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

Accounting for partiality in serial crystallography using ray-tracing principles

Energy Technology Data Exchange (ETDEWEB)

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

2015-08-25

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

High-resolution X-ray spectroscopy of hollow atoms created in plasma heated by subpicosecond laser radiation

International Nuclear Information System (INIS)

Faenov, A.Ya.; Magunov, A.I.; Pikuz, T.A.

1997-01-01

The investigations of ultrashort (0.4-0.6 ps) laser pulse radiation interaction with solid targets have been carried out. The Trident subpicosecond laser system was used for plasma creation. The X-ray plasma emission was investigated with the help of high-resolution spectrographs with spherically bent mica crystals. It is shown that when high contrast ultrashort laser pulses were used for plasma heating its emission spectra could not be explained in terms of commonly used theoretical models, and transitions in so called hollow atoms must be taken into account for adequate description of plasma radiation

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1.

Directory of Open Access Journals (Sweden)

Matthew C Clifton

Full Text Available Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.

[Determination of sulfur in plant using a high-resolution continuum source atomic absorption spectrometer].

Science.gov (United States)

Wang, Yu; Li, Jia-xi

2009-05-01

A method for the analysis of sulfur (S) in plant by molecular absorption of carbon monosulfide (CS) using a high-resolution continuum source atomic absorption spectrometer (CS AAS) with a fuel-rich air/acetylene flame has been devised. The strong CS absorption band was found around 258 nm. The half-widths of some absorption bands were of the order of picometers, the same as the common atomic absorption lines. The experimental procedure in this study provided optimized instrumental conditions (the ratio of acetylene to air, the burner height) and parameters, and researched the spectral interferences and chemical interferences. The influence of the organic solvents on the CS absorption signals and the different digestion procedures for the determination of sulfur were also investigated. The limit of detection achieved for sulfur was 14 mg x L(-1), using the CS wavelength of 257. 961 nm and a measurement time of 3 s. The accuracy and precision were verified by analysis of two plant standard reference materials. The major applications of this method have been used for the determination of sulfur in plant materials, such as leaves. Compared to the others, this method for the analysis of sulfur is rapid, easy and simple for sulfur determination in plant.

Probing the Surface Charge on the Basal Planes of Kaolinite Particles with High-Resolution Atomic Force Microscopy.

Science.gov (United States)

Kumar, N; Andersson, M P; van den Ende, D; Mugele, F; Siretanu, I

2017-12-19

High-resolution atomic force microscopy is used to map the surface charge on the basal planes of kaolinite nanoparticles in an ambient solution of variable pH and NaCl or CaCl 2 concentration. Using DLVO theory with charge regulation, we determine from the measured force-distance curves the surface charge distribution on both the silica-like and the gibbsite-like basal plane of the kaolinite particles. We observe that both basal planes do carry charge that varies with pH and salt concentration. The silica facet was found to be negatively charged at pH 4 and above, whereas the gibbsite facet is positively charged at pH below 7 and negatively charged at pH above 7. Investigations in CaCl 2 at pH 6 show that the surface charge on the gibbsite facet increases for concentration up to 10 mM CaCl 2 and starts to decrease upon further increasing the salt concentration to 50 mM. The increase of surface charge at low concentration is explained by Ca 2+ ion adsorption, while Cl - adsorption at higher CaCl 2 concentrations partially neutralizes the surface charge. Atomic resolution imaging and density functional theory calculations corroborate these observations. They show that hydrated Ca 2+ ions can spontaneously adsorb on the gibbsite facet of the kaolinite particle and form ordered surface structures, while at higher concentrations Cl - ions will co-adsorb, thereby changing the observed ordered surface structure.

Protein energy landscapes determined by five-dimensional crystallography

International Nuclear Information System (INIS)

Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

2013-01-01

Barriers of activation within the photocycle of a photoactive protein were extracted from comprehensive time courses of time resolved crystallographic data collected at multiple temperature settings. Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012 ▶), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001 ▶), Chem. Rev.101, 1569–1581; Schmidt et al. (2005 ▶), Methods Mol. Biol.305, 115–154; Schmidt (2008 ▶), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallography, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010 ▶), Acta Cryst. A66, 198–206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallographic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes

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

Czech Academy of Sciences Publication Activity Database

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

2015-01-01

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

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

International Nuclear Information System (INIS)

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

2004-01-01

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

Atom localization via controlled spontaneous emission in a five-level atomic system

International Nuclear Information System (INIS)

Wang Zhiping; Yu Benli; Zhu Jun; Cao Zhigang; Zhen Shenglai; Wu Xuqiang; Xu Feng

2012-01-01

We investigate the one- and two-dimensional atom localization behaviors via spontaneous emission in a coherently driven five-level atomic system by means of a radio-frequency field driving a hyperfine transition. It is found that the detecting probability and precision of atom localization behaviors can be significantly improved via adjusting the system parameters. More importantly, the two-dimensional atom localization patterns reveal that the maximal probability of finding an atom within the sub-wavelength domain of the standing waves can reach unity when the corresponding conditions are satisfied. As a result, our scheme may be helpful in laser cooling or the atom nano-lithography via atom localization. - Highlights: ► One- and two-dimensional atom localization behaviors via spontaneous emission in five-level atoms are investigated. ► An assisting radio-frequency field is used to control the atom localization behaviors. ► High-precision and high-resolution two-dimensional atom localization can be realized in this scheme.

Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse

Directory of Open Access Journals (Sweden)

L. Galli

2015-07-01

Full Text Available Current hard X-ray free-electron laser (XFEL sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.

Investigation of artifacts caused by deuterium background correction in the determination of phosphorus by electrothermal atomization using high-resolution continuum source atomic absorption spectrometry

International Nuclear Information System (INIS)

Dessuy, Morgana B.; Vale, Maria Goreti R.; Lepri, Fabio G.; Borges, Daniel L.G.; Welz, Bernhard; Silva, Marcia M.; Heitmann, Uwe

2008-01-01

The artifacts created in the measurement of phosphorus at the 213.6-nm non-resonance line by electrothermal atomic absorption spectrometry using line source atomic absorption spectrometry (LS AAS) and deuterium lamp background correction (D 2 BC) have been investigated using high-resolution continuum source atomic absorption spectrometry (HR-CS AAS). The absorbance signals and the analytical curves obtained by LS AAS without and with D 2 BC, and with HR-CS AAS without and with automatic correction for continuous background absorption, and also with least-squares background correction for molecular absorption with rotational fine structure were compared. The molecular absorption due to the suboxide PO that exhibits pronounced fine structure could not be corrected by the D 2 BC system, causing significant overcorrection. Among the investigated chemical modifiers, NaF, La, Pd and Pd + Ca, the Pd modifier resulted in the best agreement of the results obtained with LS AAS and HR-CS AAS. However, a 15% to 100% higher sensitivity, expressed as slope of the analytical curve, was obtained for LS AAS compared to HR-CS AAS, depending on the modifier. Although no final proof could be found, the most likely explanation is that this artifact is caused by a yet unidentified phosphorus species that causes a spectrally continuous absorption, which is corrected without problems by HR-CS AAS, but which is not recognized and corrected by the D 2 BC system of LS AAS

Electron crystallography with the EIGER detector

Directory of Open Access Journals (Sweden)

Gemma Tinti

2018-03-01

Full Text Available Electron crystallography is a discipline that currently attracts much attention as method for inorganic, organic and macromolecular structure solution. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 µm2, frame rates up to 23 kHz and a dead time between frames as low as 3 µs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure determination of a SAPO-34 zeotype from electron diffraction data.

X-ray holography: atoms in 3D

International Nuclear Information System (INIS)

Tegze, M.; Faigel, G.; Bortel, G.; Marchesini, S.; Belakhovsky, M.; Simionovici, A.

2004-01-01

X-ray holography is a novel method for the investigation of local atomic arrangements in solids. In conventional diffraction experiments only the intensity of the scattered radiation is measured, its phase is lost. This loss of information makes difficult to reconstruct the atomic arrangements. In holography both the intensity and the phase information is recorded. Using one of the atoms of the solid as source or detector of the x-radiation, atomic resolution can be reached. A three-dimensional picture of the atoms surrounding the source/detector atom can be easily reconstructed from the measured hologram. While in principle the measurement is very simple, in practice the weak signal-to-background ratio (∼ 10-3) makes it difficult. Using high intensity synchrotron radiation the measurement time can be reduced and high quality holograms can be recorded. In this talk we review the principles and experimental techniques of atomic resolution x-ray holography and present a few examples of its application. (author)

Yeast-expressed human membrane protein aquaporin-1 yields excellent resolution of solid-state MAS NMR spectra

International Nuclear Information System (INIS)

Emami, Sanaz; Fan Ying; Munro, Rachel; Ladizhansky, Vladimir; Brown, Leonid S.

2013-01-01

One of the biggest challenges in solid-state NMR studies of membrane proteins is to obtain a homogeneous natively folded sample giving high spectral resolution sufficient for structural studies. Eukaryotic membrane proteins are especially difficult and expensive targets in this respect. Methylotrophic yeast Pichia pastoris is a reliable producer of eukaryotic membrane proteins for crystallography and a promising economical source of isotopically labeled proteins for NMR. We show that eukaryotic membrane protein human aquaporin 1 can be doubly ( 13 C/ 15 N) isotopically labeled in this system and functionally reconstituted into phospholipids, giving excellent resolution of solid-state magic angle spinning NMR spectra.

On absolute scaling in protein crystallography using sums of low-resolution intensities and Wilson statistics at low resolution

International Nuclear Information System (INIS)

Roth, M.

1986-01-01

A method of absolute scaling of diffraction data is proposed, based on the calculation of the sum of the intensity diffracted at low resolution (Bragg d spacing > 15 A). This sum is proportional to the mean-square deviation of the scattering-length density in the unit cell, and this property is used to determine the scale factor. The method is applied to the case of neutron diffraction using contrast variation experiments with biological molecules, and it is used to check the validity of some assumptions concerning the system under study, such as the global rate of H/D exchange or the uniformity of scattering-length density in the molecules. The use of this method requires an asymptotic correction of the sum of intensity. This correction is based on Porod's law, whose application to diffraction experiments is discussed, in particular for contrast variation experiments. An analysis of the spherical average of the diffracted intensity as a function of the scattering vector, compared to isotropic solution scattering, allows the conditions of applicability of Wilson statistics to be specified at low and medium resolution, i.e. the random statistical model underlying the Wilson statistics in this scattering range to be defined. (orig.)

High-resolution inner-shell spectroscopies of free atoms and molecules using soft-x-ray beamlines at the third-generation synchrotron radiation sources

International Nuclear Information System (INIS)

Ueda, Kiyoshi

2003-01-01

This article reviews the current status of inner-shell spectroscopies of free atoms and molecules using high-resolution soft-x-ray monochromators installed in the soft-x-ray beamlines at the third-generation synchrotron radiation facilities. Beamlines and endstations devoted to atomic and molecular inner-shell spectroscopies and various types of experimental techniques, such as ion yield spectroscopy, resonant photoemission spectroscopy and multiple-coincidence momentum imaging, are described. Experimental results for K-shell excitation of Ne, O K-shell excitation of H 2 O and CO 2 , C K-shell excitation and ionization of CO 2 and B K-shell excitation of BF 3 , obtained at beamline 27SU of SPring-8 in Japan, are discussed as examples of atomic and molecular inner-shell spectroscopies using the third-generation synchrotron radiation sources. (topical review)

Atomic-resolution environmental TEM for quantitative in-situ microscopy in materials science.

Science.gov (United States)

Takeda, Seiji; Yoshida, Hideto

2013-02-01

We have compiled our recent in-situ quantitative environmental transmission electron microscopy (ETEM) studies on typical gold nanoparticulate catalysts for the low-temperature oxidation of CO to describe the issues surrounding the application of ETEM, with a special regard to catalyst chemistry. Thanks to the recent development of high-resolution environmental transmission electron microscopes that can work robustly to accumulate observation data in controlled environments, we can deal with the electron irradiation effects and heterogeneity of real catalysts. We established a structural evolution diagram that summarizes the structure of catalysts under electron irradiation as a function of the electron current density ϕ and the electron dose, D. By extrapolating to ϕ = 0, D = 0, we could deduce the intrinsic catalysis structure (without electron irradiation) in various environments, including reaction environments. By numerically and statistically analyzing a substantial number of ETEM images of gold nanoparticles, we established a morphology phase diagram that summarizes how the majority of gold nanoparticles change their morphology systematically as a function of the partial pressures of CO and O(2). Similar diagrams will be helpful in elucidating the phenomena that directly correlate with the catalytic activity determined from ETEM observations. Using these quantitative analyses, we could analyze Cs-corrected ETEM images of the catalysts. The surfaces of gold nanoparticles were structurally reconstructed under reaction conditions, via interactions with CO molecules. CO molecules were observed on the surfaces of catalysts under reaction conditions using high-resolution ETEM. Finally, we discuss the potential of environmental transmission electron microscopy for quantitative in-situ microscopy at the atomic scale.

Atom chips: mesoscopic physics with cold atoms

International Nuclear Information System (INIS)

Krueger, P.; Wildermuth, S.; Hofferberth, S.; Haller, E.; GAllego Garcia, D.; Schmiedmayer, J.

2005-01-01

Full text: Cold neutral atoms can be controlled and manipulated in microscopic potentials near surfaces of atom chips. These integrated micro-devices combine the known techniques of atom optics with the capabilities of well established micro- and nanofabrication technology. In analogy to electronic microchips and integrated fiber optics, the concept of atom chips is suitable to explore the domain of mesoscopic physics with matter waves. We use current and charge carrying structures to form complex potentials with high spatial resolution only microns from the surface. In particular, atoms can be confined to an essentially one-dimensional motion. In this talk, we will give an overview of our experiments studying the manipulation of both thermal atoms and BECs on atom chips. First experiments in the quasi one-dimensional regime will be presented. These experiments profit from strongly reduced residual disorder potentials caused by imperfections of the chip fabrication with respect to previously published experiments. This is due to our purely lithographic fabrication technique that proves to be advantageous over electroplating. We have used one dimensionally confined BECs as an ultra-sensitive probe to characterize these potentials. These smooth potentials allow us to explore various aspects of the physics of degenerate quantum gases in low dimensions. (author)

X-ray crystallography facility for the international space station

International Nuclear Information System (INIS)

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

High-precision atom localization via controllable spontaneous emission in a cycle-configuration atomic system.

Science.gov (United States)

Ding, Chunling; Li, Jiahua; Yu, Rong; Hao, Xiangying; Wu, Ying

2012-03-26

A scheme for realizing two-dimensional (2D) atom localization is proposed based on controllable spontaneous emission in a coherently driven cycle-configuration atomic system. As the spatial-position-dependent atom-field interaction, the frequency of the spontaneously emitted photon carries the information about the position of the atom. Therefore, by detecting the emitted photon one could obtain the position information available, and then we demonstrate high-precision and high-resolution 2D atom localization induced by the quantum interference between the multiple spontaneous decay channels. Moreover, we can achieve 100% probability of finding the atom at an expected position by choosing appropriate system parameters under certain conditions.

Atomic-Resolution Transmission Electron Microscopic Movies for Study of Organic Molecules, Assemblies, and Reactions: The First 10 Years of Development.

Science.gov (United States)

Nakamura, Eiichi

2017-06-20

A molecule is a quantum mechanical entity. "Watching motions and reactions of a molecule with our eyes" has therefore been a dream of chemists for a century. This dream has come true with the aid of the movies of atomic-resolution transmission electron microscopic (AR-TEM) molecular images through real-time observation of dynamic motions of single organic molecules (denoted hereafter as single-molecule atomic-resolution real-time (SMART) TEM imaging). Since 2007, we have reported movies of a variety of single organic molecules, organometallic molecules, and their assemblies, which are rotating, stretching, and reacting. Like movies in the theater, the atomic-resolution molecular movies provide us information on the 3-D structures of the molecules and also their time evolution. The success of the SMART-TEM imaging crucially depends on the development of "chemical fishhooks" with which fish (organic molecules) in solution can be captured on a single-walled carbon nanotube (CNT, serving as a "fishing rod"). The captured molecules are connected to a slowly vibrating CNT, and their motions are displayed on a monitor in real time. A "fishing line" connecting the fish and the rod may be a σ-bond, a van der Waals force, or other weak connections. Here, the molecule/CNT system behaves as a coupled oscillator, where the low-frequency anisotropic vibration of the CNT is transmitted to the molecules via the weak chemical connections that act as an energy filter. Interpretation of the observed motions of the molecules at atomic resolution needs us to consider the quantum mechanical nature of electrons as well as bond rotation, letting us deviate from the conventional statistical world of chemistry. What new horizons can we explore? We have so far carried out conformational studies of individual molecules, assigning anti or gauche conformations to each C-C bond in conformers that we saw. We can also determine the structures of van der Waals assemblies of organic molecules

Protein Crystallography: A 'Must' Technology for Drug Design

International Nuclear Information System (INIS)

Matsuzaki, Takao

2004-01-01

The history of drug-related protein crystallography and drug design is reviewed to show that 'Lead Generation' is high-lighted in the pharmaceutical industry nowadays. A new drug design method has been developed. The method gave very high success rate; 10-60 % gave < 100 μM, 90 % gave < 10 mM. The crystal structures of drug-protein complexes have become even more important to give solid experimental bases for e.g. 1,000 designed structures and to find the new mechanisms of drug action

Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic-Resolution Electron Microscopy and Field Evaporation Simulation.

Science.gov (United States)

Devaraj, Arun; Colby, Robert; Vurpillot, François; Thevuthasan, Suntharampillai

2014-04-17

Oxide-supported metal nanoparticles are widely used in heterogeneous catalysis. The increasingly detailed design of such catalysts necessitates three-dimensional characterization with high spatial resolution and elemental selectivity. Laser-assisted atom probe tomography (APT) is uniquely suited to the task but faces challenges with the evaporation of metal/insulator systems. Correlation of APT with aberration-corrected scanning transmission electron microscopy (STEM), for Au nanoparticles embedded in MgO, reveals preferential evaporation of the MgO and an inaccurate assessment of nanoparticle composition. Finite element field evaporation modeling is used to illustrate the evolution of the evaporation front. Nanoparticle composition is most accurately predicted when the MgO is treated as having a locally variable evaporation field, indicating the importance of considering laser-oxide interactions and the evaporation of various molecular oxide ions. These results demonstrate the viability of APT for analysis of oxide-supported metal nanoparticles, highlighting the need for developing a theoretical framework for the evaporation of heterogeneous materials.

Optimizing 1-μs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope.

Science.gov (United States)

Edwards, Devin T; Faulk, Jaevyn K; Sanders, Aric W; Bull, Matthew S; Walder, Robert; LeBlanc, Marc-Andre; Sousa, Marcelo C; Perkins, Thomas T

2015-10-14

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is widely used to mechanically measure the folding and unfolding of proteins. However, the temporal resolution of a standard commercial cantilever is 50-1000 μs, masking rapid transitions and short-lived intermediates. Recently, SMFS with 0.7-μs temporal resolution was achieved using an ultrashort (L = 9 μm) cantilever on a custom-built, high-speed AFM. By micromachining such cantilevers with a focused ion beam, we optimized them for SMFS rather than tapping-mode imaging. To enhance usability and throughput, we detected the modified cantilevers on a commercial AFM retrofitted with a detection laser system featuring a 3-μm circular spot size. Moreover, individual cantilevers were reused over multiple days. The improved capabilities of the modified cantilevers for SMFS were showcased by unfolding a polyprotein, a popular biophysical assay. Specifically, these cantilevers maintained a 1-μs response time while eliminating cantilever ringing (Q ≅ 0.5). We therefore expect such cantilevers, along with the instrumentational improvements to detect them on a commercial AFM, to accelerate high-precision AFM-based SMFS studies.

High-resolution spectroscopy of deeply-bound pionic atoms in heavy nuclei by pion-transfer reactions of inverse kinematics using the GSI cooler ring ESR

International Nuclear Information System (INIS)

Yamazaki, Toshimitsu.

1991-02-01

Many studies published in the past are reviewed first in relation to high-resolution spectroscopy of deeply-bound pionic atoms in heavy nuclei. The report then describes a procedure for applying the method of inverse kinematics to the case of (d, 3 He) reactions. The (d, 3 He) reaction in inverse kinematics is feasible from practical viewpoints. Thus a discussion is made of the inverse kinematics in which a heavy-ion beam ( 208 Pb for instance) with a projectile kinetic energy hits a deuteron target and ejected recoil 3 He nuclei are measured in the forward direction. The recoil momentum is calculated as a function of the Q value. Analysis shows that the recoil spectroscopy with inverse kinematics can be applied to the case of (d, 3 He) reaction, which will yield a very high mass resolution. The experimental setup for use in the first stage is then outlined, and a simple detector configuration free of magnetic field is discussed. These investigations demonstrate that the (d, 3 He) reaction in inverse kinematics provides a promising tool for obtaining high-resolution spectra of deeply-bound pionic atoms. (N.K.)

JBluIce-EPICS control system for macromolecular crystallography

International Nuclear Information System (INIS)

Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J.L.; Fischetti, R.F.

2011-01-01

The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

ISPyB: an information management system for synchrotron macromolecular crystallography.

Science.gov (United States)

Delagenière, Solange; Brenchereau, Patrice; Launer, Ludovic; Ashton, Alun W; Leal, Ricardo; Veyrier, Stéphanie; Gabadinho, José; Gordon, Elspeth J; Jones, Samuel D; Levik, Karl Erik; McSweeney, Seán M; Monaco, Stéphanie; Nanao, Max; Spruce, Darren; Svensson, Olof; Walsh, Martin A; Leonard, Gordon A

2011-11-15

Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.

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

Science.gov (United States)

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

2017-01-17

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

Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.

Science.gov (United States)

Hipp, Katharina; Grimm, Clemens; Jeske, Holger; Böttcher, Bettina

2017-08-01

African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved. Copyright © 2017 Elsevier Ltd. All rights reserved.

Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Berendzen, Joel

1999-01-01

The presence of distinct regions of high and low density variation in electron-density maps is found to be a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods. An automated examination of the native Fourier is tested as a means of evaluation of a heavy-atom solution in MAD and MIR methods for macromolecular crystallography. It is found that the presence of distinct regions of high and low density variation in electron-density maps is a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods. The method can be used to evaluate heavy-atom solutions during MAD and MIR structure solutions and to determine the handedness of the structure if anomalous data have been measured

Effect of laser power and specimen temperature on atom probe analyses of magnesium alloys

International Nuclear Information System (INIS)

Oh-ishi, K.; Mendis, C.L.; Ohkubo, T.; Hono, K.

2011-01-01

The influence of laser power, wave length, and specimen temperature on laser assisted atom probe analyses for Mg alloys was investigated. Higher laser power and lower specimen temperature led to improved mass and spatial resolutions. Background noise and mass resolutions were degraded with lower laser power and higher specimen temperature. By adjusting the conditions for laser assisted atom probe analyses, atom probe results with atomic layer resolutions were obtained from all the Mg alloys so far investigated. Laser assisted atom probe investigations revealed detailed chemical information on Guinier-Preston zones in Mg alloys. -- Research highlights: → We study performance of UV laser assisted atom probe analysis for Mg alloys. → There is an optimized range of laser power and specimen temperature. → Optimized UV laser enables atom probe data of Mg alloys with high special resolution.

Investigations of the dynamics and growth of insulator films by high resolution helium atom scattering. Final report, May 1, 1985--April 30, 1997

Energy Technology Data Exchange (ETDEWEB)

Safron, S.A.; Skofronick, J.G.

1997-07-01

Over the twelve years of this grant from the U.S. Department of Energy, DE-FG05-85ER45208, the over-reaching aims of this work have been to explore and to attempt to understand the fundamental physics and chemistry of surfaces and interfaces. The instrument we have employed m in this work is high-resolution helium atom scattering (HAS) which we have become even more convinced is an exceptionally powerful and useful tool for surface science. One can follow the evolution of the development and progress of the experiments that we have carried out by the evolution of the proposal titles for each of the four three-year periods. At first, m in 1985-1988, the main objective of this grant was to construct the HAS instrument so that we could begin work on the surface vibrational dynamics of crystalline materials; the title was {open_quotes}Helium Atom-Surface Scattering Apparatus for Studies of Crystalline Surface Dynamics{close_quotes}. Then, as we became more interested m in the growth of films and interfaces the title m in 1988-1991 became {open_quotes}Helium Atom Surface Spectroscopy: Surface Lattice Dynamics of Insulators, Metal and Metal Overlayers{close_quotes}. In 1991-1994, we headed even more m in this direction, and also recognized that we should focus more on insulator materials as very few techniques other than helium atom scattering could be applied to insulators without causing surface damage. Thus, the proposal title became {open_quotes}Helium Atom-Surface Scattering: Surface Dynamics of Insulators, Overlayers and Crystal Growth{close_quotes}. M in the final period of this grant the title ended up {open_quotes}Investigations of the Dynamics and Growth of Insulator Films by High Resolution Helium Atom Scattering{close_quotes} m in 1994-1997. The list of accomplishments briefly discussed in this report are: tests of the shell model; multiphoton scattering; physisorbed monolayer films; other surface phase transitions; and surface magnetic effects.

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

2015-01-01

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 Mg2+ 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 Mg2+ in GTPases. The Mg2+ 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. PMID:26272610

Distributed control of protein crystallography beamline 5.0 using CORBA

International Nuclear Information System (INIS)

Timossi, Chris

1999-01-01

The Protein Crystallography Beamline at Berkeley Lab's Advanced Light Source is a facility that is being used to solve the structure of proteins. The software that is being used to control this beamline uses Java for user interface applications which communicate via CORBA with workstations that control the beamline hardware. We describe the software architecture for the beamline and our experiences after two years of operation

Primed for Discovery: Atomic-Resolution Cryo-EM Structure of a Reovirus Entry Intermediate

Directory of Open Access Journals (Sweden)

Shane D. Trask

2010-06-01

Full Text Available A recently solved structure of the aquareovirus virion (Zhang, X; Jin, L.; Fang, Q; Hui, W.H.; Zhou Z.H. 3.3 Å Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry. Cell 2010, 141, 472-482 [1] provides new insights into the order of entry events, as well as confirming and refining several aspects of the entry mechanism, for aquareovirus and the related orthoreovirus. In particular, the structure provides evidence of a defined order for the progressive proteolytic cleavages of myristoylated penetration protein VP5 that prime the virion for membrane penetration. These observations reinforce the concept that, much like enveloped viruses, nonenveloped virions often undergo priming events that lead to a meta-stable state, preparing the virus for membrane penetration under the appropriate circumstances. In addition, this and other recent studies highlight the increasing power of electron cryomicroscopy to analyze large, geometrically regular structures, such as icosahedral viruses, at atomic resolution.

Investigating effects of sample pretreatment on protein stability using size-exclusion chromatography and high-resolution continuum source atomic absorption spectrometry.

Science.gov (United States)

Rakow, Tobias; El Deeb, Sami; Hahne, Thomas; El-Hady, Deia Abd; AlBishri, Hassan M; Wätzig, Hermann

2014-09-01

In this study, size-exclusion chromatography and high-resolution atomic absorption spectrometry methods have been developed and evaluated to test the stability of proteins during sample pretreatment. This especially includes different storage conditions but also adsorption before or even during the chromatographic process. For the development of the size exclusion method, a Biosep S3000 5 μm column was used for investigating a series of representative model proteins, namely bovine serum albumin, ovalbumin, monoclonal immunoglobulin G antibody, and myoglobin. Ambient temperature storage was found to be harmful to all model proteins, whereas short-term storage up to 14 days could be done in an ordinary refrigerator. Freezing the protein solutions was always complicated and had to be evaluated for each protein in the corresponding solvent. To keep the proteins in their native state a gentle freezing temperature should be chosen, hence liquid nitrogen should be avoided. Furthermore, a high-resolution continuum source atomic absorption spectrometry method was developed to observe the adsorption of proteins on container material and chromatographic columns. Adsorption to any container led to a sample loss and lowered the recovery rates. During the pretreatment and high-performance size-exclusion chromatography, adsorption caused sample losses of up to 33%. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein crystallography beamline (PX-BL21); its utilization and research highlights

International Nuclear Information System (INIS)

Kumar, Ashwani; Ghosh, Biplab; Singh, Rahul; Makde, Ravindra; Sharma, Surinder M.

2016-01-01

The protein crystallography beamline (PX-BL21) is sourced on 1.5 T bending magnet of 2.5 GeV Indus-2 synchrotron. This beamline has been designed to perform monochromatic and anomalous diffraction experiments on single crystals of biological macromolecules such as protein, DNA and their complexes. PX beamline also has a state-of-art ancillary biochemical laboratory to prepare single crystals of biological macromolecules. Since the commissioning of the beamline, it has been utilized by more than 70% of research groups working in the area of protein crystallography in India. About 30 crystal structures of proteins, determined using this beamline, have been deposited in Protein Data Bank (PDB). Some of these structures have been determined using experimental phasing, such as the single wavelength anomalous diffraction (SAD) experiments. The energy tunability of the synchrotron have been exploited to carry our various SAD experiments: Selenium-SAD, Zinc-SAD and Manganese-SAD and Sulphar-SAD. In the present talk, the key results from the PX-BL21 beamline will be discussed. (author)

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-07-27

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

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography.

Science.gov (United States)

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

2015-12-01

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

Microstructure evolution and crystallography of the phase-change material TiSbTe films annealed in situ

International Nuclear Information System (INIS)

Chen, Yong-Jin; Zhang, Bin; Ding, Qing-Qing; Deng, Qing-Song; Chen, Yan; Song, Zhi-Tang; Li, Ji-Xue; Zhang, Ze; Han, Xiao-Dong

2016-01-01

In this work, the morphology, crystallization process and crystal structure of the phase-change material TiSbTe (TST) alloy have been successfully established, which is essential for applying this alloy in phase-change memory. Specifically, atomic force microscopy (AFM) was employed to characterize the as-deposited and post-annealed thin films, and transmission electron microscopy (TEM) analyses of the films annealed in situ were used in combination with selected-area electron diffraction (SAED) and radial distribution function (RDF) analyses to investigate the structural evolution from the amorphous phase to the polycrystalline phase. Moreover, the presence of structures with medium-range order in amorphous TST, which is beneficial for high-speed crystallization, was indicated by the structure factors S(Q)s. The crystallization temperature was determined to be approximately 170 °C, and the grain size varied from several to dozens of nanometers. As the temperature increased, particularly above 200 °C, the first single peak of the rG(r) curves transformed into double shoulder peaks due to the increasing impact of the Ti−Te bonds. In general, the majority of Ti atoms were doped into the SbTe lattice and tended to form structural defects, whereas the remainder of the Ti atoms aggregated, leading to the appearance of TiTe 2 phase separation, as confirmed by the SAED patterns, high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) images and corresponding energy-dispersive X-ray (EDX) mappings. - Highlights: • TEM morphology, SAED and RDF were used to investigate the structural evolution. • The S(Q)s implied the existence of medium range order structure in a-TST. • The rG(r) implied the impact of the Ti−Te bonds in crystallization process. • The crystallography of c-TST was revealed through Cs-HAADF-STEM and EDX.

Microstructure evolution and crystallography of the phase-change material TiSbTe films annealed in situ

Energy Technology Data Exchange (ETDEWEB)

Chen, Yong-Jin; Zhang, Bin [Beijing Key Laboratory and Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China); Ding, Qing-Qing [Center of Electron Microscopy and State Key Laboratory of Silicon Materials, Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Deng, Qing-Song [Beijing Key Laboratory and Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China); Chen, Yan; Song, Zhi-Tang [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Micro-system and Information Technology, Chinese Academy of Sciences, Shanghai 200050 (China); Li, Ji-Xue [Center of Electron Microscopy and State Key Laboratory of Silicon Materials, Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Zhang, Ze [Beijing Key Laboratory and Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China); Center of Electron Microscopy and State Key Laboratory of Silicon Materials, Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Han, Xiao-Dong, E-mail: xdhan@bjut.edu.cn [Beijing Key Laboratory and Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China)

2016-09-05

In this work, the morphology, crystallization process and crystal structure of the phase-change material TiSbTe (TST) alloy have been successfully established, which is essential for applying this alloy in phase-change memory. Specifically, atomic force microscopy (AFM) was employed to characterize the as-deposited and post-annealed thin films, and transmission electron microscopy (TEM) analyses of the films annealed in situ were used in combination with selected-area electron diffraction (SAED) and radial distribution function (RDF) analyses to investigate the structural evolution from the amorphous phase to the polycrystalline phase. Moreover, the presence of structures with medium-range order in amorphous TST, which is beneficial for high-speed crystallization, was indicated by the structure factors S(Q)s. The crystallization temperature was determined to be approximately 170 °C, and the grain size varied from several to dozens of nanometers. As the temperature increased, particularly above 200 °C, the first single peak of the rG(r) curves transformed into double shoulder peaks due to the increasing impact of the Ti−Te bonds. In general, the majority of Ti atoms were doped into the SbTe lattice and tended to form structural defects, whereas the remainder of the Ti atoms aggregated, leading to the appearance of TiTe{sub 2} phase separation, as confirmed by the SAED patterns, high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) images and corresponding energy-dispersive X-ray (EDX) mappings. - Highlights: • TEM morphology, SAED and RDF were used to investigate the structural evolution. • The S(Q)s implied the existence of medium range order structure in a-TST. • The rG(r) implied the impact of the Ti−Te bonds in crystallization process. • The crystallography of c-TST was revealed through Cs-HAADF-STEM and EDX.

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

Energy Technology Data Exchange (ETDEWEB)

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

2013-11-01

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

Two-dimensional atom localization based on coherent field controlling in a five-level M-type atomic system.

Science.gov (United States)

Jiang, Xiangqian; Li, Jinjiang; Sun, Xiudong

2017-12-11

We study two-dimensional sub-wavelength atom localization based on the microwave coupling field controlling and spontaneously generated coherence (SGC) effect. For a five-level M-type atom, introducing a microwave coupling field between two upper levels and considering the quantum interference between two transitions from two upper levels to lower levels, the analytical expression of conditional position probability (CPP) distribution is obtained using the iterative method. The influence of the detuning of a spontaneously emitted photon, Rabi frequency of the microwave field, and the SGC effect on the CPP are discussed. The two-dimensional sub-half-wavelength atom localization with high-precision and high spatial resolution is achieved by adjusting the detuning and the Rabi frequency, where the atom can be localized in a region smaller thanλ/10×λ/10. The spatial resolution is improved significantly compared with the case without the microwave field.

In-vacuum long-wavelength macromolecular crystallography.

Science.gov (United States)

Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

2016-03-01

Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline.

Atom optics in the time domain

Science.gov (United States)

Arndt, M.; Szriftgiser, P.; Dalibard, J.; Steane, A. M.

1996-05-01

Atom-optics experiments are presented using a time-modulated evanescent light wave as an atomic mirror in the trampoline configuration, i.e., perpendicular to the direction of the atomic free fall. This modulated mirror is used to accelerate cesium atoms, to focus their trajectories, and to apply a ``multiple lens'' to separately focus different velocity classes of atoms originating from a point source. We form images of a simple two-slit object to show the resolution of the device. The experiments are modelled by a general treatment analogous to classical ray optics.

Viscous hydrophilic injection matrices for serial crystallography

Directory of Open Access Journals (Sweden)

Gabriela Kovácsová

2017-07-01

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

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

Science.gov (United States)

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

2010-11-21

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

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

Science.gov (United States)

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

2013-11-01

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

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. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

High-resolution continuum source electrothermal atomic absorption spectrometry: Linearization of the calibration curves within a broad concentration range

Energy Technology Data Exchange (ETDEWEB)

Katskov, Dmitri, E-mail: katskovda@tut.ac.za [Tshwane University of Technology, Chemistry Department, Pretoria 0001 (South Africa); Hlongwane, Miranda [Tshwane University of Technology, Chemistry Department, Pretoria 0001 (South Africa); Heitmann, Uwe [German Aerospace Center, Rose-Luxemburg Str. 2, 10178 Berlin (Germany); Florek, Stefan [ISAS-Leibniz-Institut fuer Analytische Wissenschaften e.V., Albert-Einstein-Str. 9,12489 Berlin (Germany)

2012-05-15

The calculation algorithm suggested provides linearization of the calibration curves in high-resolution continuum source electrothermal atomic absorption spectrometry. The algorithm is based on the modification of the function wavelength-integrated absorbance vs. concentration of analyte vapor in the absorption volume. According to the suggested approach, the absorption line is represented by a triangle for low and trapezium for high analyte vapor concentration in the absorption volume. The respective semi-empirical formulas include two linearization parameters, which depend on properties of the absorption line and characteristics of the atomizer and spectrometer. The parameters can be approximately evaluated from the theory and determined in practice from the original broad-range calibration curve. The parameters were found and the proposed calculation algorithm verified in the experiments on direct determination of Ag, Cd, Cu, Fe, Mn and Pb in the solutions within a concentration ranges from 0.15 to 625 {mu}g{center_dot}L{sup -1} using tube, platform tube and filter furnace atomizers. The use of various atomizers, lines, elements and atomization temperatures made possible the simulation of various practical analytical conditions. It was found that the algorithm and optimal linearization parameters made it possible to obtain for each line and atomizer linear approximations of the calibration curves within 3-4 orders of magnitude with correlation coefficients close to 0.999. The algorithm makes possible to employ a single line for the direct element determination over a broad concentration range. The sources of errors and the possibility of a priori theoretical evaluation of the linearization parameters are discussed. - Highlights: Black-Right-Pointing-Pointer New calculation algorithm for HR-CS ET AAS measurements was proposed and applied. Black-Right-Pointing-Pointer The suggested formulas include two parameters to be determined experimentally. Black

The influence of Mn on the crystallography and electrochemistry of nonstoichiometric AB5-type hydride-forming compounds

International Nuclear Information System (INIS)

Notten, P.H.L.; Latroche, M.; Percheron-Guegan, A.

1999-01-01

To design Co-free, low-pressure, hydride-forming compounds for application in rechargeable nickel metal hydride batteries, nonstoichiometric AB x materials were investigated. The influence of both the Mn content and the degree of nonstoichiometry on the crystallography, electrochemical cycling stability, and electrode morphology were studied. The investigated composition was in the range of La(Ni 1-z Mn z ) x with 5.0 le x le 6.0 and 0 le xz le 2.0. The annealing temperature was essential in preparing homogeneous compounds. In agreement with geometric considerations, both the a and c axis of the hexagonal unit cell increase with increasing Mn content. In contrast, the a axis decreases with increasing degree of nonstoichiometry. As proved by neutron-diffraction experiments, the introduction of dumbbell pairs of Ni or Mn atoms on the La positions in the crystal lattice is responsible for this behavior. The electrochemical cycling stability is found to be strongly dependent on both the chemical and nonstoichiometric composition. Electrochemically stable materials are characterized by the absence of a significant particle-size reduction upon electrode cycling, reducing the overall oxidation rate. Unstable materials suffer from severe mechanical cracking through which the oxidation rate is increased. The improved mechanical stability is attributed to the reduced discrete lattice expansion. The most stable compound has a partial hydrogen pressure of only 0.1 bar, which matches well with that desirable in practical NiMH batteries. Neutron-diffraction experiments confirmed the hypothesis that La atoms are replaced by dumbbell pairs of Ni, in the case of the binary LaNi 5.4 , and by Mn atoms in the case of the mn-containing nonstoichiometric compounds. Electron-probe microanalyses and density measurements support the dumbbell hypothesis

Phasing in crystallography a modern perspective

CERN Document Server

Giacovazzo, Carmelo

2014-01-01

Modern crystallographic methods originate from the synergy of two main research streams, the small-molecule and the macro-molecular streams. The first stream was able to definitively solve the phase problem for molecules up to 200 atoms in the asymmetric unit. The achievements obtained by the macromolecular stream are also impressive. A huge number of protein structures have been deposited in the Protein Data Bank. The solution of them is no longer reserved to an elite group of scientists, but may be attained in a large number of laboratories around the world, even by young scientists. New probabilistic approaches have been tailored to deal with larger structures, errors in the experimental data, and modest data resolution. Traditional phasing techniques like ab initio, molecular replacement, isomorphous replacement, and anomalous dispersion techniques have been revisited. The new approaches have been implemented in robust phasing programs, which have been organized in automatic pipelines usable even by non-e...

Atomic resolution observation of conversion-type anode RuO 2 during the first electrochemical lithiation

KAUST Repository

Mao, Minmin

2015-03-05

Transition metal oxides have attracted great interest as alternative anode materials for rechargeable lithium-ion batteries. Among them, ruthenium dioxide is considered to be a prototype material that reacts with the Li ions in the conversion type. In situ transmission electron microscopy reveals a two-step process during the initial lithiation of the RuO2 nanowire anode at atomic resolution. The first step is characterized by the formation of the intermediate phase LixRuO2 due to the Li-ion intercalation. The following step is manifested by the solid-state amorphization reaction driven by advancing the reaction front. The crystalline/amorphous interface is consisted of {011} atomic terraces, revealing the orientation-dependent mobility. In the crystalline matrix, lattice disturbance and dislocation are identified to be two major stress-induced distortions. The latter can be effective diffusion channels, facilitating transportation of the Li ions inside the bulk RuO2 crystal and further resulting in non-uniform Li-ion distribution. It is expected that the local enrichment of the Li ions may account for the homogeneous nucleation of dislocations in the bulk RuO2 crystal and the special island-like structures. These results elucidate the structural evolution and the phase transformation during electrochemical cycling, which sheds light on engineering RuO2 anode materials.

Raman Spectroscopy Adds Complementary Detail to the High-Resolution X-Ray Crystal Structure of Photosynthetic PsbP from Spinacia oleracea

Czech Academy of Sciences Publication Activity Database

Kopecký, V. Jr.; Kohoutová, Jaroslava; Lapkouski, Mikalai; Hofbauerová, Kateřina; Sovová, Žofie; Ettrichová, Olga; Gonzalez-Perez, S.; Dulebo, A.; Kaftan, D.; Kutá-Smatanová, Ivana; Reveuelta, J. L.; Arellano, J. B.; Carey, J.; Ettrich, Rüdiger

2012-01-01

Roč. 7, č. 10 (2012), s. 46694-46694 E-ISSN 1932-6203 Institutional research plan: CEZ:AV0Z60870520; CEZ:AV0Z50200510 Keywords : secondary-structure-analysis * oxygen-evolving complexO * plant photosystem-II * moleculars-dynamics * assisted crystallography * angstrom resolution * protein-structure * amide-I * conformation * biomolecules Subject RIV: BO - Biophysics; EE - Microbiology, Virology (MBU-M) Impact factor: 3.730, year: 2012

High-resolution inelastic X-ray scattering to study the high-frequency atomic dynamics of disordered systems

International Nuclear Information System (INIS)

Monaco, G.

2008-01-01

The use of momentum-resolved inelastic X-ray scattering with meV energy resolution to study the high-frequency atomic dynamics in disordered systems is here reviewed. The typical realization of this experiment is described together with some common models used to interpret the measured spectra and to extract parameters of interest for the investigation of disordered systems. With the help of some selected examples, the present status of the field is discussed. Particular attention is given to those results which are still open for discussion or controversial, and which will require further development of the technique to be fully solved. Such an instrumental development seems nowadays possible at the light of recently proposed schemes for advanced inelastic X-ray scattering spectrometers. (author)

Seeing the atoms more clearly: STEM imaging from the Crewe era to today

International Nuclear Information System (INIS)

Pennycook, S.J.

2012-01-01

This review covers the development of scanning transmission electron microscopy from the innovations of Albert Crewe to the two-dimensional spectrum imaging in the era of aberration correction. It traces the key events along the path, the first atomic resolution Z-contrast imaging of individual atoms, the realization of incoherent imaging in crystals and the role of dynamical diffraction, simultaneous, atomic resolution electron energy loss spectroscopy, and finally the tremendous impact of the successful correction of lens aberrations, not just in terms of resolution but also in single atom sensitivity. -- Highlights: ► We review the development of scanning transmission electron microscopy. ► We discuss the innovations of Albert Crewe in the first field emission STEM. ► We discuss use of the high angle annular detector for materials science. ► We discuss atomic resolution Z-contrast imaging and EELS. ► We discuss the benefits of aberration correction.

A comparison of single knock-on and complete bubble destruction models of the fission induced re-solution of gas atoms from bubbles

International Nuclear Information System (INIS)

Wood, M.H.

1978-03-01

In previous theoretical studies of the behaviour of the fission gases in nuclear fuel, the Nelson single knock-on model of the fission induced re-solution of gas atoms from fission gas bubbles has been employed. In the present investigation, predictions from this model are compared with those from a complete bubble destruction model of the re-solution process. The main conclusions of the study are that the complete bubble destruction model predicts more gas release after a particular irradiation time than the single knock-on model, for the same choice of the model parameters, and that parameter sets chosen to give the same gas release predict significantly different bubble size distribution functions. (author)

Room-temperature macromolecular serial crystallography using synchrotron radiation

Directory of Open Access Journals (Sweden)

Francesco Stellato

2014-07-01

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

X-ray powder crystallography with vertex instrumentation

International Nuclear Information System (INIS)

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

1998-01-01

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

Accelerated Oxygen Atom Transfer and C-H Bond Oxygenation by Remote Redox Changes in Fe3 Mn-Iodosobenzene Adducts.

Science.gov (United States)

de Ruiter, Graham; Carsch, Kurtis M; Gul, Sheraz; Chatterjee, Ruchira; Thompson, Niklas B; Takase, Michael K; Yano, Junko; Agapie, Theodor

2017-04-18

We report the synthesis, characterization, and reactivity of [LFe 3 (PhPz) 3 OMn( s PhIO)][OTf] x (3: x=2; 4: x=3), where 4 is one of very few examples of iodosobenzene-metal adducts characterized by X-ray crystallography. Access to these rare heterometallic clusters enabled differentiation of the metal centers involved in oxygen atom transfer (Mn) or redox modulation (Fe). Specifically, 57 Fe Mössbauer and X-ray absorption spectroscopy provided unique insights into how changes in oxidation state (Fe III 2 Fe II Mn II vs. Fe III 3 Mn II ) influence oxygen atom transfer in tetranuclear Fe 3 Mn clusters. In particular, a one-electron redox change at a distal metal site leads to a change in oxygen atom transfer reactivity by ca. two orders of magnitude. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atom-probe field-ion-microscope mass spectrometer

International Nuclear Information System (INIS)

Nishikawa, Osamu

1983-01-01

The titled analyzer, called simply atom-probe, has been developed by combining a field ion microscope (FIM) and a mass spectrometer, and is divided into the time-of-flight type, magnetic sector type, and quadrupole type depending on the types of mass spectrometers. In this paper, the author first describes on the principle and construction of a high resolution, time-of-flight atom-probe developed and fabricated in his laboratory. The feature of the atom-probe lies in the analysis of atoms and molecules in hyper-fine structure region one by one utilizing the high resolution of FIM. It also has the advantages of directly determining the composition by a ratio of the numbers of respective ions because of a constant detection sensitivity regardless of mass numbers, of the resolution as high as single atom layer in depth direction, and of detecting the positional relationship among detected ions by the order of detection in a sample. To determine the composition in a hyperfine structure region, the limited small number of atoms and molecules in the region must be identified distinctly one by one. In the analyzed result of Ni-silicide formed by heating Si evaporated on a Ni tip at 1000 K for 5 minutes, each isotope was not only clearly separated, but also their abundance ratio was very close to the natural abundance ratio. The second half of the paper reports on the analysis of TiC promising for a cold cathode material, adsorption of CO and alcohol, and the composition and structure of silicides, as a few application examples. (Wakatsuki, Y.)

Radical Chemistry and Charge Manipulation with an Atomic Force Microscope

Science.gov (United States)

Gross, Leo

The fuctionalization of tips by atomic manipulation dramatically increased the resolution of atomic force microscopy (AFM). The combination of high-resolution AFM with atomic manipulation now offers the unprecedented possibility to custom-design individual molecules by making and breaking bonds with the tip of the microscope and directly characterizing the products on the atomic scale. We recently applied this technique to generate and study reaction intermediates and to investigate chemical reactions trigged by atomic manipulation. We formed diradicals by dissociating halogen atoms and then reversibly triggered ring-opening and -closing reactions via atomic manipulation, allowing us to switch and control the molecule's reactivity, magnetic and optical properties. Additional information about charge states and charge distributions can be obtained by Kelvin probe force spectroscopy. On multilayer insulating films we investigated single-electron attachment, detachment and transfer between individual molecules. EU ERC AMSEL (682144), EU project PAMS (610446).

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

International Nuclear Information System (INIS)

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

2013-01-01

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

Highly charged atomic physics at HIRFL-CSR

International Nuclear Information System (INIS)

Ma Xinwen; Wang Youde; Hou Mingdong; Jin Gengmin

1996-01-01

HIRFL-CSR is a proposed electron cooling storage ring optimized to accelerate and store beams of highly charged heavy ions. Several possibilities for advanced atomic physics studies are discussed, such as studies of electron-ion, ion-atoms, photon-ion-electron interactions and high resolution spectroscopy

Interfacial force measurements using atomic force microscopy

NARCIS (Netherlands)

Chu, L.

2018-01-01

Atomic Force Microscopy (AFM) can not only image the topography of surfaces at atomic resolution, but can also measure accurately the different interaction forces, like repulsive, adhesive and lateral existing between an AFM tip and the sample surface. Based on AFM, various extended techniques have

Atomic Force Microscope

Energy Technology Data Exchange (ETDEWEB)

Day, R.D.; Russell, P.E.

1988-12-01

The Atomic Force Microscope (AFM) is a recently developed instrument that has achieved atomic resolution imaging of both conducting and non- conducting surfaces. Because the AFM is in the early stages of development, and because of the difficulty of building the instrument, it is currently in use in fewer than ten laboratories worldwide. It promises to be a valuable tool for obtaining information about engineering surfaces and aiding the .study of precision fabrication processes. This paper gives an overview of AFM technology and presents plans to build an instrument designed to look at engineering surfaces.

Atomic collisions involving pulsed positrons

DEFF Research Database (Denmark)

Merrison, J. P.; Bluhme, H.; Field, D.

2000-01-01

Conventional slow positron beams have been widely and profitably used to study atomic collisions and have been instrumental in understanding the dynamics of ionization. The next generation of positron atomic collision studies are possible with the use of charged particle traps. Not only can large...... instantaneous intensities be achieved with in-beam accumulation, but more importantly many orders of magnitude improvement in energy and spatial resolution can be achieved using positron cooling. Atomic collisions can be studied on a new energy scale with unprecedented precion and control. The use...

"XANSONS for COD": a new small BOINC project in crystallography

Science.gov (United States)

Neverov, Vladislav S.; Khrapov, Nikolay P.

2018-04-01

"XANSONS for COD" (http://xansons4cod.com) is a new BOINC project aimed at creating the open-access database of simulated x-ray and neutron powder diffraction patterns for nanocrystalline phase of materials from the collection of the Crystallography Open Database (COD). The project uses original open-source software XaNSoNS to simulate diffraction patterns on CPU and GPU. This paper describes the scientific problem this project solves, the project's internal structure, its operation principles and organization of the final database.

Atom and Bond Fukui Functions and Matrices: A Hirshfeld-I Atoms-in-Molecule Approach.

Science.gov (United States)

Oña, Ofelia B; De Clercq, Olivier; Alcoba, Diego R; Torre, Alicia; Lain, Luis; Van Neck, Dimitri; Bultinck, Patrick

2016-09-19

The Fukui function is often used in its atom-condensed form by isolating it from the molecular Fukui function using a chosen weight function for the atom in the molecule. Recently, Fukui functions and matrices for both atoms and bonds separately were introduced for semiempirical and ab initio levels of theory using Hückel and Mulliken atoms-in-molecule models. In this work, a double partitioning method of the Fukui matrix is proposed within the Hirshfeld-I atoms-in-molecule framework. Diagonalizing the resulting atomic and bond matrices gives eigenvalues and eigenvectors (Fukui orbitals) describing the reactivity of atoms and bonds. The Fukui function is the diagonal element of the Fukui matrix and may be resolved in atom and bond contributions. The extra information contained in the atom and bond resolution of the Fukui matrices and functions is highlighted. The effect of the choice of weight function arising from the Hirshfeld-I approach to obtain atom- and bond-condensed Fukui functions is studied. A comparison of the results with those generated by using the Mulliken atoms-in-molecule approach shows low correlation between the two partitioning schemes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vladimír Vand (1911-1968): Pioneer of computational methods in crystallography

Czech Academy of Sciences Publication Activity Database

Šolcová, A.; Křížek, Michal

2011-01-01

Roč. 33, č. 4 (2011), s. 38-44 ISSN 1058-6180 R&D Projects: GA AV ČR(CZ) IAA100190803 Institutional research plan: CEZ:AV0Z10190503 Keywords : history of computing * Vladimír Vand * crystallography Subject RIV: BA - General Mathematics Impact factor: 0.378, year: 2011 http://www.computer.org/portal/web/csdl/doi/10.1109/MAHC.2011.80

Spectroscopy of highly ionized atoms

International Nuclear Information System (INIS)

Livingston, A.E.

1987-01-01

The atomic structure and decay characteristics of excited states in multiply ionized atoms represent a fertile testing ground for atomic calculations ranging from accurate ab initio theory for few-electron systems to practical semi-empirical approaches for many-electron species. Excitation of fast ions by thin foils generally produces the highest ionization stages for heavy ions in laboratory sources. The associated characteristics of spectroscopic purity and high time resolution provide unique capabilities for studying the atomic properties of highly-ionized atoms. This report is limited to a brief discussion of three classes of atomic systems that are experiencing current theoretical and experimental interest: precision structure of helium-like ions, fine structure of doubly-excited states, and lifetimes of metastable states. Specific measurements in each of these types of systems are mentioned, with emphasis on the relation to studies involving slow, highly-charged ions

Determination of silicon in biomass and products of pyrolysis process via high-resolution continuum source atomic absorption spectrometry.

Science.gov (United States)

Nakadi, Flávio V; Prodanov, Caroline; Boschetti, Wiliam; Vale, Maria Goreti R; Welz, Bernhard; de Andrade, Jailson B

2018-03-01

Thermochemical processes can convert the biomass into fuels, such as bio-oil. The biomass submitted to pyrolysis process, such as fibers, are generally rich in silicon, an element that can lead to damages in an engine when there is high concentration in a fuel. High-resolution continuum source atomic absorption spectrometry (HR-CS AAS) is an interesting alternative for Si determination in the products and byproducts of the pyrolysis process because, besides the flame (F) and graphite furnace (GF) atomizers, it has enhanced the application of direct analysis of solid samples (SS) within GF. This study aimed the development of methods to determine Si in biomass samples, their products and byproducts using HR-CS AAS. A high-resolution continuum source atomic absorption spectrometer contrAA 700 equipped with F and GF atomizers was used throughout the study. HR-CS F AAS (λ = 251.611nm, 1 detection pixel, N 2 O/C 2 H 2 flame) was used to evaluate Si content in biomass and ash, after a microwave-assisted acid digestion with HNO 3 and HF. HR-CS GF AAS (T pyr = 1400°C, T atom = 2650°C) has evaluated Si in pyrolysis water and bio-oil at 251.611nm, and in peach pit biomass and ash at 221.174nm using SS, both wavelengths with 1 detection pixel. Rhodium (300μg) was applied as permanent modifier and 10μgPd + 6μg Mg were pipetted onto the standards/samples at each analysis. Three different biomass samples were studied: palm tree fiber, coconut fiber and peach pit, and three certified reference materials (CRM) were used to verify the accuracy of the methods. The figures of merit were LOD 0.09-20mgkg -1 , and LOQ 0.3-20mgkg -1 , considering all the methods. There were no significant differences between the CRM certified values and the determined ones, using a Student t-test with a confidence interval of 95% (n = 5). Si concentration ranged from 0.11-0.92% mm -1 , 1.1-1.7mgkg -1 , 3.3-13mgkg -1 , and 0.41-1.4%mm -1 , in biomass, bio-oil, pyrolysis water and ash, respectively

StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images

Energy Technology Data Exchange (ETDEWEB)

De Backer, A.; Bos, K.H.W. van den [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Van den Broek, W. [AG Strukturforschung/Elektronenmikroskopie, Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Sijbers, J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium)

2016-12-15

An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. - Highlights: • An efficient model-based method for quantitative electron microscopy is introduced. • Images are modelled as a superposition of 2D Gaussian peaks. • Overlap between neighbouring columns is taken into account. • Structure parameters can be obtained with the highest precision and accuracy. • StatSTEM, auser friendly program (GNU public license) is developed.

A new approach for the determination of sulphur in food samples by high-resolution continuum source flame atomic absorption spectrometer.

Science.gov (United States)

Ozbek, N; Baysal, A

2015-02-01

The new approach for the determination of sulphur in foods was developed, and the sulphur concentrations of various fresh and dried food samples determined using a high-resolution continuum source flame atomic absorption spectrometer with an air/acetylene flame. The proposed method was optimised and the validated using standard reference materials, and certified values were found to be within the 95% confidence interval. The sulphur content of foods ranged from less than the LOD to 1.5mgg(-1). The method is accurate, fast, simple and sensitive. Copyright © 2014 Elsevier Ltd. All rights reserved.

An Ultrahigh Resolution Structure of TEM-1 β-Lactamase Suggests a Role for Glu166 as the General Base in Acylation

International Nuclear Information System (INIS)

Minasov, George; Wang, Xiaojun; Shoichet, Brian K.

2002-01-01

Although TEM-1 β-lactamase is among the best studied enzymes, its acylation mechanism remains controversial. To investigate this problem, the structure of TEM-1 in complex with an acylation transition-state analogue was determined at ultrahigh resolution (0.85 (angstrom)) by X-ray crystallography. The quality of the data was such as to allow for refinement to an R-factor of 9.1% and an R free of 11.2%. In the resulting structure, the electron density features were clear enough to differentiate between single and double bonds in carboxylate groups, to identify multiple conformations that are occupied by residues and loops, and to assign 70% of the protons in the protein. Unexpectedly, even at pH 8.0 where the protein was crystallized, the active site residue Glu166 is clearly protonated. This supports the hypothesis that Glu166 is the general base in the acylation half of the reaction cycle. This structure suggests that Glu166 acts through the catalytic water to activate Ser70 for nucleophilic attack on the β-lactam ring of the substrate. The hydrolytic mechanism of class A β-lactamases, such as TEM-1, appears to be symmetrical, as are the serine proteases. Apart from its mechanistic implications, this atomic resolution structure affords an unusually detailed view of the structure, dynamics, and hydrogen-bonding networks of TEM-1, which may be useful for the design of inhibitors against this key antibiotic resistance target.

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

International Nuclear Information System (INIS)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So; Evans, Gwyndaf

2013-01-01

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Aller, Pierre [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz; Cameron, Alex [Imperial College, London SW7 2AZ (United Kingdom); Axford, Danny; Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Armour, Wes [Oxford e-Research Centre (OeRC), Keble Road, Oxford OX1 3QG (United Kingdom); Waterman, David G. [Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

2013-08-01

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-09-01

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

The crystallographic information file (CIF): A new standard archive file for crystallography

International Nuclear Information System (INIS)

Hall, S.R.; Allen, F.H.; Brown, I.D.

1991-01-01

The specification of a new standard Crystallographic Information File (CIF) is described. Its development is based on the Self-Defining Text Archieve and Retrieval (STAR) procedure. The CIF is a general, flexible and easily extensible free-format archive file; it is human and machine readable and can be edited by a simple editor. The CIF is designed for the electronic transmission of crystallographic data between individual laboratories, journals and databases: It has been adopted by the International Union of Crystallography as the recommended medium for this purpose. The file consists of data names and data items, together with a loop facility for repeated items. The data names, constructed hierarchically so as to form data categories, are self-descriptive within a 32-character limit. The sorted list of data names, together with their precise definitions, constitutes the CIF dictionary (core version 1991). The CIF core dictionary is presented in full and covers the fundamental and most commonly used data items relevant to crystal structure analysis. The dictionary is also available as an electronic file suitable for CIF computer applications. Future extensions to the dictionary will include data items used in more specialized areas of crystallography. (orig.)

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.

The $\\mu$TPC Method: Improving the Position Resolution of Neutron Detectors Based on MPGDs

CERN Document Server

Pfeiffer, Dorothea; Birch, Jens; Hall-Wilton, Richard; Höglund, Carina; Hultman, Lars; Iakovidis, George; Oliveri, Eraldo; Oksanen, Esko; Ropelewski, Leszek; Thuiner, Patrik

2015-01-01

Due to the Helium-3 crisis, alternatives to the standard neutron detection techniques are becoming urgent. In addition, the instruments of the European Spallation Source (ESS) require advances in the state of the art of neutron detection. The instruments need detectors with excellent neutron detection efficiency, high-rate capabilities and unprecedented spatial resolution. The Macromolecular Crystallography instrument (NMX) requires a position resolution in the order of 200 um over a wide angular range of incoming neutrons. Solid converters in combination with Micro Pattern Gaseous Detectors (MPGDs) are proposed to meet the new requirements. Charged particles rising from the neutron capture have usually ranges larger than several millimetres in gas. This is apparently in contrast with the requirements for the position resolution. In this paper, we present an analysis technique, new in the field of neutron detection, based on the Time Projection Chamber (TPC) concept. Using a standard Single-GEM with the catho...

Large-angle illumination STEM: Toward three-dimensional atom-by-atom imaging

Energy Technology Data Exchange (ETDEWEB)

Ishikawa, Ryo, E-mail: ishikawa@sigma.t.u-tokyo.ac.jp [Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656 (Japan); Lupini, Andrew R. [Materials Science & Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Hinuma, Yoyo [Department of Materials Science and Engineering, Kyoto University, Kyoto 606-8501 (Japan); Pennycook, Stephen J. [Department of Materials Science and Engineering, The University of Tennessee, 328 Ferris Hall, Knoxville, TN 37996 (United States)

2015-04-15

To fully understand and control materials and their properties, it is of critical importance to determine their atomic structures in all three dimensions. Recent revolutionary advances in electron optics – the inventions of geometric and chromatic aberration correctors as well as electron source monochromators – have provided fertile ground for performing optical depth sectioning at atomic-scale dimensions. In this study we theoretically demonstrate the imaging of top/sub-surface atomic structures and identify the depth of single dopants, single vacancies and the other point defects within materials by large-angle illumination scanning transmission electron microscopy (LAI-STEM). The proposed method also allows us to measure specimen properties such as thickness or three-dimensional surface morphology using observations from a single crystallographic orientation. - Highlights: • We theoretically demonstrate 3D near-atomic depth resolution imaging by large-angle illumination STEM. • This method can be useful to identify the depth of single dopants, single vacancies within materials. • This method can be useful to determine reconstructed surface atomic structures.

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

NARCIS (Netherlands)

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

2007-01-01

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

Atomic column resolved electron energy-loss spectroscopy

International Nuclear Information System (INIS)

Duscher, G.; Pennycook, S.J.; Browning, N.D.

1998-01-01

Spatially resolved electron energy-loss spectroscopy (EELS) is rapidly developing into a unique and powerful tool to characterize internal interfaces. Because atomic column resolved Z-contrast imaging can be performed simultaneously with EELS in the scanning transmission electron microscope, this combination allows the atomic structure to be correlated with the electronic structure, and thus the local properties of interfaces or defects can be determined directly. However, the ability to characterize interfaces and defects at that level requires not only high spatial resolution but also the exact knowledge of the beam location, from where the spectrum is obtained. Here we discuss several examples progressing from cases where the limitation in spatial resolution is given by the microscopes or the nature of the sample, to one example of impurity atoms at a grain boundary, which show intensity and fine structure changes from atomic column to atomic column. Such data can be interpreted as changes in valence of the impurity, depending on its exact site in the boundary plane. Analysis ofthis nature is a valuable first step in understanding the microscopic structural, optical and electronic properties of materials. (orig.)

Direct determination of a radiation-damage profile with atomic resolution in ion-irradiated platinum. MSC report No. 5030

International Nuclear Information System (INIS)

Pramanik, D.; Seidman, D.N.

1983-05-01

The field-ion microscope (FIM) technique has been employed to determine directly a radiation damage profile, with atomic resolution, in a platinum specimen which had been irradiated at 80 0 K with 20-keV Kr + ions to a fluence of 5 x 10 12 cm - 2 . It is shown that the microscopic spatial-vacancy distribution (radiation-damage profile) is directly related to the elastically-deposited-energy profile. The experimentally constructed radiation-damage profile is compared with a theoretical damage profile - calculated employing the TRIM Monte Carlo code - and excellent agreement is obtained between the two, thus demonstrating that it is possible to go directly from a microscopic spatial distribution of vacancies to a continuous radiation-damage profile

US Atomic Energy Law

International Nuclear Information System (INIS)

1981-01-01

This is a new volume follows in the series supplementing the volumes 11 and 12 published in 1965 and 1966, updating the collection of Federal Acts and Executive Orders of the President of the United States of America relating to atomic energy legislation. Since the publication of volumes 11 and 12, the US Atomic Energy Act of 1954 alone has been amended 25 times, mainly as a consequence of by the Nuclear Non-Proliferation Act and the Uranium Mill Tailings Radiation Control Act, both of 1978. The Atomic Energy Act of 1954 is supplemented by a selection of the most important Federal Acts, Executive Orders of the President and Resolutions of the Congress. (orig./HSCH) [de

Nanometer-scale isotope analysis of bulk diamond by atom probe tomography

NARCIS (Netherlands)

Schirhagl, R.; Raatz, N.; Meijer, J.; Markham, M.; Gerstl, S. S. A.; Degen, C. L.

2015-01-01

Atom-probe tomography (APT) combines field emission of atoms with mass spectrometry to reconstruct three-dimensional tomograms of materials with atomic resolution and isotope specificity. Despite significant recent progress in APT technology, application to wide-bandgap materials with strong

High-resolution electron microscopy

CERN Document Server

Spence, John C H

2013-01-01

This new fourth edition of the standard text on atomic-resolution transmission electron microscopy (TEM) retains previous material on the fundamentals of electron optics and aberration correction, linear imaging theory (including wave aberrations to fifth order) with partial coherence, and multiple-scattering theory. Also preserved are updated earlier sections on practical methods, with detailed step-by-step accounts of the procedures needed to obtain the highest quality images of atoms and molecules using a modern TEM or STEM electron microscope. Applications sections have been updated - these include the semiconductor industry, superconductor research, solid state chemistry and nanoscience, and metallurgy, mineralogy, condensed matter physics, materials science and material on cryo-electron microscopy for structural biology. New or expanded sections have been added on electron holography, aberration correction, field-emission guns, imaging filters, super-resolution methods, Ptychography, Ronchigrams, tomogr...

An acoustic on-chip goniometer for room temperature macromolecular crystallography.

Science.gov (United States)

Burton, C G; Axford, D; Edwards, A M J; Gildea, R J; Morris, R H; Newton, M I; Orville, A M; Prince, M; Topham, P D; Docker, P T

2017-12-05

This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

Protein crystal growth studies at the Center for Macromolecular Crystallography

International Nuclear Information System (INIS)

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

2000-01-01

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

Automated sample mounting and technical advance alignment system for biological crystallography at a synchrotron source

International Nuclear Information System (INIS)

Snell, Gyorgy; Cork, Carl; Nordmeyer, Robert; Cornell, Earl; Meigs, George; Yegian, Derek; Jaklevic, Joseph; Jin, Jian; Stevens, Raymond C.; Earnest, Thomas

2004-01-01

High-throughput data collection for macromolecular crystallography requires an automated sample mounting system for cryo-protected crystals that functions reliably when integrated into protein-crystallography beamlines at synchrotrons. Rapid mounting and dismounting of the samples increases the efficiency of the crystal screening and data collection processes, where many crystals can be tested for the quality of diffraction. The sample-mounting subsystem has random access to 112 samples, stored under liquid nitrogen. Results of extensive tests regarding the performance and reliability of the system are presented. To further increase throughput, we have also developed a sample transport/storage system based on 'puck-shaped' cassettes, which can hold sixteen samples each. Seven cassettes fit into a standard dry shipping Dewar. The capabilities of a robotic crystal mounting and alignment system with instrumentation control software and a relational database allows for automated screening and data collection to be developed

Radiation Re-solution Calculation in Uranium-Silicide Fuels

International Nuclear Information System (INIS)

Matthews, Christopher; Andersson, Anders David Ragnar; Unal, Cetin

2017-01-01

The release of fission gas from nuclear fuels is of primary concern for safe operation of nuclear power plants. Although the production of fission gas atoms can be easily calculated from the fission rate in the fuel and the average yield of fission gas, the actual diffusion, behavior, and ultimate escape of fission gas from nuclear fuel depends on many other variables. As fission gas diffuses through the fuel grain, it tends to collect into intra-granular bubbles, as portrayed in Figure 1.1. These bubbles continue to grow due to absorption of single gas atoms. Simultaneously, passing fission fragments can cause collisions in the bubble that result in gas atoms being knocked back into the grain. This so called ''re-solution'' event results in a transient equilibrium of single gas atoms within the grain. As single gas atoms progress through the grain, they will eventually collect along grain boundaries, creating inter-granular bubbles. As the inter-granular bubbles grow over time, they will interconnect with other grain-face bubbles until a pathway is created to the outside of the fuel surface, at which point the highly pressurized inter-granular bubbles will expel their contents into the fuel plenum. This last process is the primary cause of fission gas release. From the simple description above, it is clear there are several parameters that ultimately affect fission gas release, including the diffusivity of single gas atoms, the absorption and knockout rate of single gas atoms in intra-granular bubbles, and the growth and interlinkage of intergranular bubbles. Of these, the knockout, or re-solution rate has an particularly important role in determining the transient concentration of single gas atoms in the grain. The re-solution rate will be explored in the following sections with regards to uranium-silicide fuels in order to support future models of fission gas bubble behavior.

Supersonic pulsed free-jet of atoms and molecules of refractory metals: laser induced fluorescence spectroscopic studies on zirconium atoms and zirconium oxide molecules

International Nuclear Information System (INIS)

Nakhale, S.G.

2004-11-01

The experimental setup for generating supersonic pulsed free-jet containing atoms and molecules of refractory nature has been built. The technique of laser vaporization in conjunction with supersonic cooling is used to generate these species. The cooled atoms and molecules in supersonic free-jet are probed by laser induced fluorescence spectroscopy. In particular, the technique has been used to perform low-resolution laser induced fluorescence spectroscopy, limited by laser linewidth, on cold Zr atoms and ZrO molecules. The translational temperatures of ∼ 26.5 K and the rotational temperatures of ∼ 81 K have been achieved. It is possible to achieve the Doppler width of few tens of MHz allowing it to perform high-resolution spectroscopy on these atomic and molecular species. Also because of low rotational temperature of molecules the spectral congestion is greatly reduced. In general, this technique can be applied to perform spectroscopy on atoms and molecules of refractory nature. (author)

Atomic resolution ultrafast scanning tunneling microscope with scan rate breaking the resonant frequency of a quartz tuning fork resonator.

Science.gov (United States)

Li, Quanfeng; Lu, Qingyou

2011-05-01

We present an ultra-fast scanning tunneling microscope with atomic resolution at 26 kHz scan rate which surpasses the resonant frequency of the quartz tuning fork resonator used as the fast scan actuator. The main improvements employed in achieving this new record are (1) fully low voltage design (2) independent scan control and data acquisition, where the tuning fork (carrying a tip) is blindly driven to scan by a function generator with the scan voltage and tunneling current (I(T)) being measured as image data (this is unlike the traditional point-by-point move and measure method where data acquisition and scan control are switched many times).

Crystallography of lath martensite and stabilization of retained austenite

International Nuclear Information System (INIS)

Sarikaya, M.

1982-10-01

TEM was used to study the morphology and crystallography of lath martensite in low and medium carbon steels in the as-quenched and 200 0 C tempered conditions. The steels have microduplex structures of dislocated lath martensite and continuous thin films of retained austenite at the lath interfaces. Stacks of laths form the packets which are derived from different [111] variants of the same austenite grain. The residual parent austenite enables microdiffraction experiments with small electron beam spot sizes for the orientation relationships (OR) between austenite and martensite. All three most commonly observed ORs, namely Kurdjumov-Sachs, Nishiyama-Wassermann, and Greninger-Troiano, operate within the same sample

Crystallography of lath martensite and stabilization of retained austenite

Energy Technology Data Exchange (ETDEWEB)

Sarikaya. M.

1982-10-01

TEM was used to study the morphology and crystallography of lath martensite in low and medium carbon steels in the as-quenched and 200/sup 0/C tempered conditions. The steels have microduplex structures of dislocated lath martensite and continuous thin films of retained austenite at the lath interfaces. Stacks of laths form the packets which are derived from different (111) variants of the same austenite grain. The residual parent austenite enables microdiffraction experiments with small electron beam spot sizes for the orientation relationships (OR) between austenite and martensite. All three most commonly observed ORs, namely Kurdjumov-Sachs, Nishiyama-Wassermann, and Greninger-Troiano, operate within the same sample.

Templated Atom-Precise Galvanic Synthesis and Structure Elucidation of a [Ag 24 Au(SR) 18 ] − Nanocluster

KAUST Repository

Bootharaju, Megalamane Siddaramappa

2015-11-27

Synthesis of atom-precise alloy nanoclusters with uniform composition is challenging when the alloying atoms are similar in size (for example, Ag and Au). A galvanic exchange strategy has been devised to produce a compositionally uniform [Ag24Au(SR)18]- cluster (SR: thiolate) using a pure [Ag25(SR)18]- cluster as a template. Conversely, the direct synthesis of Ag24Au cluster leads to a mixture of [Ag25-xAux(SR)18]-, x=1-8. Mass spectrometry and crystallography of [Ag24Au(SR)18]- reveal the presence of the Au heteroatom at the Ag25 center, forming Ag24Au. The successful exchange of the central Ag of Ag25 with Au causes perturbations in the Ag25 crystal structure, which are reflected in the absorption, luminescence, and ambient stability of the particle. These properties are compared with those of Ag25 and Ag24Pd clusters with same ligand and structural framework, providing new insights into the modulation of cluster properties with dopants at the single-atom level.

Cationic and Anionic Disorder in CZTSSe Kesterite Compounds: A Chemical Crystallography Study.

Science.gov (United States)

Bais, Pierre; Caldes, Maria Teresa; Paris, Michaël; Guillot-Deudon, Catherine; Fertey, Pierre; Domengès, Bernadette; Lafond, Alain

2017-10-02

The cationic and anionic disorder in the Cu 2 ZnSnSe 4 -Cu 2 ZnSnS 4 (CZTSe-CZTS) system has been investigated through a chemical crystallography approach including X-ray diffraction (in conventional and resonant setup), 119 Sn and 77 Se NMR spectroscopy, and high-resolution transmission electron microscopy (HRTEM) techniques. Single-crystal XRD analysis demonstrates that the studied compounds behave as a solid solution with the kesterite crystal structure in the whole S/(S + Se) composition range. As previously reported for pure sulfide and pure selenide compounds, the 119 Sn NMR spectroscopy study gives clear evidence that the level of Cu/Zn disorder in mixed S/Se compounds depends on the thermal history of the samples (slow cooled or quenched). This conclusion is also supported by the investigation of the 77 Se NMR spectra. The resonant single-crystal XRD technique shows that regardless of the duration of annealing step below the order-disorder critical temperature the ordering is not a long-range phenomenon. Finally, for the very first time, HREM images of pure selenide and mixed S/Se crystals clearly show that these compounds have different microstructures. Indeed, only the mixed S/Se compound exhibits a mosaic-type contrast which could be the sign of short-range anionic order. Calculated images corroborate that HRTEM contrast is highly dependent on the nature of the anion as well as on the local anionic order.

Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor.

Science.gov (United States)

Dziedzic, Pawel; Cisneros, José A; Robertson, Michael J; Hare, Alissa A; Danford, Nadia E; Baxter, Richard H G; Jorgensen, William L

2015-03-04

Optimization is reported for biaryltriazoles as inhibitors of the tautomerase activity of human macrophage migration inhibitory factor (MIF), a proinflammatory cytokine associated with numerous inflammatory diseases and cancer. A combined approach was taken featuring organic synthesis, enzymatic assaying, crystallography, and modeling including free-energy perturbation (FEP) calculations. X-ray crystal structures for 3a and 3b bound to MIF are reported and provided a basis for the modeling efforts. The accommodation of the inhibitors in the binding site is striking with multiple hydrogen bonds and aryl-aryl interactions. Additional modeling encouraged pursuit of 5-phenoxyquinolinyl analogues, which led to the very potent compound 3s. Activity was further enhanced by addition of a fluorine atom adjacent to the phenolic hydroxyl group as in 3w, 3z, 3aa, and 3bb to strengthen a key hydrogen bond. It is also shown that physical properties of the compounds can be modulated by variation of solvent-exposed substituents. Several of the compounds are likely the most potent known MIF tautomerase inhibitors; the most active ones are more than 1000-fold more active than the well-studied (R)-ISO-1 and more than 200-fold more active than the chromen-4-one Orita-13.

Stitching Grid-wise Atomic Force Microscope Images

DEFF Research Database (Denmark)

Vestergaard, Mathias Zacho; Bengtson, Stefan Hein; Pedersen, Malte

2016-01-01

Atomic Force Microscopes (AFM) are able to capture images with a resolution in the nano metre scale. Due to this high resolution, the covered area per image is relatively small, which can be problematic when surveying a sample. A system able to stitch AFM images has been developed to solve this p...

A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source

International Nuclear Information System (INIS)

Owen, Robin L.; Pearson, Arwen R.; Meents, Alke; Boehler, Pirmin; Thominet, Vincent; Schulze-Briese, Clemens

2009-01-01

Complementary techniques greatly aid the interpretation of macromolecule structures to yield functional information, and can also help to track radiation-induced changes. A new on-axis spectrometer being integrated into the macromolecular crystallography beamlines of the Swiss Light Source is presented. X-ray crystallography at third-generation synchrotron sources permits tremendous insight into the three-dimensional structure of macromolecules. Additional information is, however, often required to aid the transition from structure to function. In situ spectroscopic methods such as UV–Vis absorption and (resonance) Raman can provide this, and can also provide a means of detecting X-ray-induced changes. Here, preliminary results are introduced from an on-axis UV–Vis absorption and Raman multimode spectrometer currently being integrated into the beamline environment at X10SA of the Swiss Light Source. The continuing development of the spectrometer is also outlined

Micro-sampling method based on high-resolution continuum source graphite furnace atomic absorption spectrometry for calcium determination in blood and mitochondrial suspensions.

Science.gov (United States)

Gómez-Nieto, Beatriz; Gismera, Mª Jesús; Sevilla, Mª Teresa; Satrústegui, Jorgina; Procopio, Jesús R

2017-08-01

A micro-sampling and straightforward method based on high resolution continuum source atomic absorption spectrometry (HR-CS AAS) was developed to determine extracellular and intracellular Ca in samples of interest in clinical and biomedical analysis. Solid sampling platforms were used to introduce the micro-samples into the graphite furnace atomizer. The secondary absorption line for Ca, located at 239.856nm, was selected to carry out the measurements. Experimental parameters such as pyrolysis and atomization temperatures and the amount of sample introduced for the measurements were optimized. Calibration was performed using aqueous standards and the approach to measure at the wings of the absorption lines was employed for the expansion of the linear response range. The limit of detection was of 0.02mgL -1 Ca (0.39ng Ca) and the upper limit of linear range was increased up to 8.0mgL -1 Ca (160ng Ca). The proposed method was used to determine Ca in mitochondrial suspensions and whole blood samples with successful results. Adequate recoveries (within 91-107%) were obtained in the tests performed for validation purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

Focusing of atoms with spatially localized light pulses

International Nuclear Information System (INIS)

Helseth, Lars Egil

2002-01-01

We theoretically study the focusing of atoms using strongly localized light pulses. It is shown that when inhomogenously polarized light is focused at high angular apertures, one may obtain useful potentials for atom focusing. Here we analyze the case of pulsed light potentials for red- and blue-detuned focusings of atoms. In particular, we show that the atomic beam aperture must be stopped considerably down in order to reduce the sidelobes of the atomic density, which is similar to the situation often encountered in conventional optics. It is suggested that an annular aperture in front of the atomic beam could be useful for increasing the resolution, at the cost of a lower atomic density

Mechanisms and energetics of surface atomic processes

International Nuclear Information System (INIS)

Tsong, T.T.

1991-01-01

The energies involved in various surface atomic processes such as surface diffusion, the binding of small atomic clusters on the surface, the interaction between two adsorbed atoms, the dissociation of an atom from a small cluster or from a surface layer, the binding of kink size atoms or atoms at different adsorption sites to the surface etc., can be derived from an analysis of atomically resolved field ion microscope images and a kinetic energy measurement of low temperature field desorbed ions using the time-of-flight atom-probe field ion microscope. These energies can be used to compare with theories and to understand the transport of atoms on the surface in atomic reconstructions, epitaxial growth of surface layers and crystal growth, adsorption layer superstructure formation, and also why an atomic ordering or atomic reconstruction at the surface is energetically favored. Mechanisms of some of the surface atomic processes are also clarified from these quantitative, atomic resolution studies. In this paper work in this area is bris briefly reviewed

Determination of silicon and aluminum in silicon carbide nanocrystals by high-resolution continuum source graphite furnace atomic absorption spectrometry.

Science.gov (United States)

Dravecz, Gabriella; Bencs, László; Beke, Dávid; Gali, Adam

2016-01-15

The determination of Al contaminant and the main component Si in silicon carbide (SiC) nanocrystals with the size-distribution of 1-8nm dispersed in an aqueous solution was developed using high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS-GFAAS). The vaporization/atomization processes were investigated in a transversally heated graphite atomizer by evaporating solution samples of Al and Si preserved in various media (HCl, HNO3). For Si, the best results were obtained by applying a mixture of 5µg Pd plus 5µg Mg, whereas for Al, 10µg Mg (each as nitrate solution) was dispensed with the samples, but the results obtained without modifier were found to be better. This way a maximum pyrolysis temperature of 1200°C for Si and 1300°C for Al could be used, and the optimum (compromise) atomization temperature was 2400°C for both analytes. The Si and Al contents of different sized SiC nanocrystals, dispersed in aqueous solutions, were determined against aqueous (external) calibration standards. The correlation coefficients (R values) of the calibrations were found to be 0.9963 for Si and 0.9991 for Al. The upper limit of the linear calibration range was 2mg/l Si and 0.25mg/l Al. The limit of detection was 3µg/l for Si and 0.5µg/l for Al. The characteristic mass (m0) was calculated to be 389pg Si and 6.4pg Al. The Si and Al content in the solution samples were found to be in the range of 1.0-1.7mg/l and 0.1-0.25mg/l, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

Crystallographic and dynamic aspects of solid-state NMR calibration compounds: towards ab initio NMR crystallography

DEFF Research Database (Denmark)

Li, Xiaozhou; Tapmeyer, Lukas; Bolte, Michael

2016-01-01

The excellent results of dispersion-corrected density functional theory (DFT-D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT-D calculations is a target, especially for the field of molecular NMR crystallography. Four 13C ss...

Ghost imaging with atoms

Science.gov (United States)

Khakimov, R. I.; Henson, B. M.; Shin, D. K.; Hodgman, S. S.; Dall, R. G.; Baldwin, K. G. H.; Truscott, A. G.

2016-12-01

Ghost imaging is a counter-intuitive phenomenon—first realized in quantum optics—that enables the image of a two-dimensional object (mask) to be reconstructed using the spatio-temporal properties of a beam of particles with which it never interacts. Typically, two beams of correlated photons are used: one passes through the mask to a single-pixel (bucket) detector while the spatial profile of the other is measured by a high-resolution (multi-pixel) detector. The second beam never interacts with the mask. Neither detector can reconstruct the mask independently, but temporal cross-correlation between the two beams can be used to recover a ‘ghost’ image. Here we report the realization of ghost imaging using massive particles instead of photons. In our experiment, the two beams are formed by correlated pairs of ultracold, metastable helium atoms, which originate from s-wave scattering of two colliding Bose-Einstein condensates. We use higher-order Kapitza-Dirac scattering to generate a large number of correlated atom pairs, enabling the creation of a clear ghost image with submillimetre resolution. Future extensions of our technique could lead to the realization of ghost interference, and enable tests of Einstein-Podolsky-Rosen entanglement and Bell’s inequalities with atoms.

Proposal for efficient two-dimensional atom localization using probe absorption in a microwave-driven four-level atomic system

International Nuclear Information System (INIS)

Ding Chunling; Li Jiahua; Yang Xiaoxue; Xiong Hao; Zhang Duo

2011-01-01

The behavior of two-dimensional (2D) atom localization is explored by monitoring the probe absorption in a microwave-driven four-level atomic medium under the action of two orthogonal standing-wave fields. Because of the position-dependent atom-field interaction, the information about the position of the atom can be obtained via the absorption measurement of the weak probe field. It is found that the localization behavior is significantly improved due to the joint quantum interference induced by the standing-wave and microwave-driven fields. Most importantly, the atom can be localized at a particular position and the maximal probability of finding the atom in one period of the standing-wave fields reaches unity by properly adjusting the system parameters. The proposed scheme may provide a promising way to achieve high-precision and high-resolution 2D atom localization.

Some Aspects of Crystal Centering During X-ray High-throughput Protein Crystallography Experiment

Science.gov (United States)

Gaponov, Yu. A.; Matsugaki, N.; Sasajima, K.; Igarashi, N.; Wakatsuki, S.

A set of algorithms and procedures of a crystal loop centering during X-ray high-throughput protein crystallography experiment has been designed and developed. A simple algorithm of the crystal loop detection and preliminary recognition has been designed and developed. The crystal loop detection algorithm is based on finding out the crystal loop ending point (opposite to the crystal loop pin) using image cross section (digital image column) profile analysis. The crystal loop preliminary recognition procedure is based on finding out the crystal loop sizes and position using image cross section profile analysis. The crystal loop fine recognition procedure based on Hooke-Jeeves pattern search method with an ellipse as a fitting pattern has been designed and developed. The procedure of restoring missing coordinate of the crystal loop is described. Based on developed algorithms and procedures the optimal auto-centering procedure has been designed and developed. A procedure of optimal manual crystal centering (Two Clicks Procedure) has been designed and developed. Developed procedures have been integrated into control software system PCCS installed at crystallography beamlines Photon Factory BL5A and PF-AR NW12, KEK.

High resolution UV spectroscopy and laser-focused nanofabrication

NARCIS (Netherlands)

Myszkiewicz, G.

2005-01-01

This thesis combines two at first glance different techniques: High Resolution Laser Induced Fluorescence Spectroscopy (LIF) of small aromatic molecules and Laser Focusing of atoms for Nanofabrication. The thesis starts with the introduction to the high resolution LIF technique of small aromatic

Stopping atoms with diode lasers

International Nuclear Information System (INIS)

Watts, R.N.; Wieman, C.E.

1986-01-01

The use of light pressure to cool and stop neutral atoms has been an area of considerable interest recently. Cooled neutral atoms are needed for a variety of interesting experiments involving neutral atom traps and ultrahigh-resolution spectroscopy. Laser cooling of sodium has previously been demonstrated using elegant but quite elaborate apparatus. These techniques employed stabilized dye lasers and a variety of additional sophisticated hardware. The authors have demonstrated that a frequency chirp technique can be implemented using inexpensive diode lasers and simple electronics. In this technique the atoms in an atomic beam scatter resonant photons from a counterpropagating laser beam. The momentum transfer from the photons slows the atoms. The primary difficulty is that as the atoms slow their Doppler shift changes, and so they are no longer in resonance with the incident photons. In the frequency chirp technique this is solved by rapidly changing the laser frequency so that the atoms remain in resonance. To achieve the necessary frequency sweep with a dye laser one must use an extremely sophisticated high-speed electrooptic modulator. With a diode laser, however, the frequency can be smoothly and rapidly varied over many gigahertz simply by changing the injection current

Self-corrected sensors based on atomic absorption spectroscopy for atom flux measurements in molecular beam epitaxy

International Nuclear Information System (INIS)

Du, Y.; Liyu, A. V.; Droubay, T. C.; Chambers, S. A.; Li, G.

2014-01-01

A high sensitivity atom flux sensor based on atomic absorption spectroscopy has been designed and implemented to control electron beam evaporators and effusion cells in a molecular beam epitaxy system. Using a high-resolution spectrometer and a two-dimensional charge coupled device detector in a double-beam configuration, we employ either a non-resonant line or a resonant line with low cross section from the same hollow cathode lamp as the reference for nearly perfect background correction and baseline drift removal. This setup also significantly shortens the warm-up time needed compared to other sensor technologies and drastically reduces the noise coming from the surrounding environment. In addition, the high-resolution spectrometer allows the most sensitive resonant line to be isolated and used to provide excellent signal-to-noise ratio

Auger electron and X-ray spectroscopy of hollow atoms

NARCIS (Netherlands)

Morgenstern, R; Johnson, RL; Schmidtbocking, H; Sonntag, BF

1997-01-01

Hollow atoms as formed during collisions of multiply charged ions on metallic, semiconducting and insulating surfaces have in recent years successfully been investigated by various spectroscopic methods: low- and high-resolution X-ray spectroscopy as well as high resolution Auger electron

Validation of an analytical method based on the high-resolution continuum source flame atomic absorption spectrometry for the fast-sequential determination of several hazardous/priority hazardous metals in soil.

Science.gov (United States)

Frentiu, Tiberiu; Ponta, Michaela; Hategan, Raluca

2013-03-01

The aim of this paper was the validation of a new analytical method based on the high-resolution continuum source flame atomic absorption spectrometry for the fast-sequential determination of several hazardous/priority hazardous metals (Ag, Cd, Co, Cr, Cu, Ni, Pb and Zn) in soil after microwave assisted digestion in aqua regia. Determinations were performed on the ContrAA 300 (Analytik Jena) air-acetylene flame spectrometer equipped with xenon short-arc lamp as a continuum radiation source for all elements, double monochromator consisting of a prism pre-monocromator and an echelle grating monochromator, and charge coupled device as detector. For validation a method-performance study was conducted involving the establishment of the analytical performance of the new method (limits of detection and quantification, precision and accuracy). Moreover, the Bland and Altman statistical method was used in analyzing the agreement between the proposed assay and inductively coupled plasma optical emission spectrometry as standardized method for the multielemental determination in soil. The limits of detection in soil sample (3σ criterion) in the high-resolution continuum source flame atomic absorption spectrometry method were (mg/kg): 0.18 (Ag), 0.14 (Cd), 0.36 (Co), 0.25 (Cr), 0.09 (Cu), 1.0 (Ni), 1.4 (Pb) and 0.18 (Zn), close to those in inductively coupled plasma optical emission spectrometry: 0.12 (Ag), 0.05 (Cd), 0.15 (Co), 1.4 (Cr), 0.15 (Cu), 2.5 (Ni), 2.5 (Pb) and 0.04 (Zn). Accuracy was checked by analyzing 4 certified reference materials and a good agreement for 95% confidence interval was found in both methods, with recoveries in the range of 94-106% in atomic absorption and 97-103% in optical emission. Repeatability found by analyzing real soil samples was in the range 1.6-5.2% in atomic absorption, similar with that of 1.9-6.1% in optical emission spectrometry. The Bland and Altman method showed no statistical significant difference between the two spectrometric

Magnetic dichroism in photoemission: a new element-specific magnetometer with atomic-layer resolution

International Nuclear Information System (INIS)

Starke, K.; Arenholz, E.; Kaindl, G.

1998-01-01

Full text: Magnetic coupling in layered metallic structures has become a key issue in thin-film magnetism since the observation of oscillatory exchange coupling across non-ferromagnetic spacer layers. Although this phenomenon was discovered in rare earths (RE) superlattices, mostly transition-metal systems have been studied and are now applied in data-storage industry. An understanding of the coupling mechanisms has been reached after a fabrication of high-quality interfaces became possible. It allowed, in particular, the experimental finding of induced ferromagnetic order in 'nonmagnetic' atomic layers near an interface, using element-specific probes such as magnetic circular dichroism in x-ray absorption. - In layered RE systems, by contrast, the well known intermiscibility has prevented a preparation of atomically sharp interfaces, and all RE superlattices studied so far showed interdiffusion zones of several atomic layers. In the present overview, we report the first fabrication of atomically flat heteromagnetic RE interfaces, their structural characterization and their magnetic analysis using magnetic dichroism in photoemission (MDPE). This new tool gives access to the magnetization of individual atomic layers near interfaces in favourite cases. Merits of MDPE as a magnetometer are demonstrated at the example of Eu/Gd(0001), where chemical shifts of core-level photoemission lines allow to spectroscopically separate up to four different atomic layers. The high surface sensitivity of MDPE, together with the well known dependence of the core-level binding energies on the coordination number of the photo emitting atom, opens the door to future site-specific studies of magnetism in sub-monolayer systems such as 'nanowires'

Optimum aberration coefficients for recording high-resolution off-axis holograms in a Cs-corrected TEM

Energy Technology Data Exchange (ETDEWEB)

Linck, Martin, E-mail: linck@ceos-gmbh.de [CEOS GmbH, Englerstr. 28, D-69126 Heidelberg (Germany)

2013-01-15

Amongst the impressive improvements in high-resolution electron microscopy, the Cs-corrector also has significantly enhanced the capabilities of off-axis electron holography. Recently, it has been shown that the signal above noise in the reconstructable phase can be significantly improved by combining holography and hardware aberration correction. Additionally, with a spherical aberration close to zero, the traditional optimum focus for recording high-resolution holograms ('Lichte's defocus') has become less stringent and both, defocus and spherical aberration, can be selected freely within a certain range. This new degree of freedom can be used to improve the signal resolution in the holographically reconstructed object wave locally, e.g. at the atomic positions. A brute force simulation study for an aberration corrected 200 kV TEM is performed to determine optimum values for defocus and spherical aberration for best possible signal to noise in the reconstructed atomic phase signals. Compared to the optimum aberrations for conventional phase contrast imaging (NCSI), which produce 'bright atoms' in the image intensity, the resulting optimum values of defocus and spherical aberration for off-axis holography enable 'black atom contrast' in the hologram. However, they can significantly enhance the local signal resolution at the atomic positions. At the same time, the benefits of hardware aberration correction for high-resolution off-axis holography are preserved. It turns out that the optimum is depending on the object and its thickness and therefore not universal. -- Highlights: Black-Right-Pointing-Pointer Optimized aberration parameters for high-resolution off-axis holography. Black-Right-Pointing-Pointer Simulation and analysis of noise in high-resolution off-axis holograms. Black-Right-Pointing-Pointer Improving signal resolution in the holographically reconstructed phase shift. Black-Right-Pointing-Pointer Comparison of &apos

High resolution gamma-ray spectroscopy and the fascinating angular momentum realm of the atomic nucleus

International Nuclear Information System (INIS)

Riley, M A; Simpson, J; Paul, E S

2016-01-01

In 1974 Aage Bohr and Ben Mottelson predicted the different ‘phases’ that may be expected in deformed nuclei as a function of increasing angular momentum and excitation energy all the way up to the fission limit. While admitting their picture was highly conjectural they confidently stated ‘...with the ingenious experimental approaches that are being developed, we may look forward with excitement to the detailed spectroscopic studies that will illuminate the behaviour of the spinning quantised nucleus’ . High resolution gamma-ray spectroscopy has indeed been a major tool in studying the structure of atomic nuclei and has witnessed numerous significant advances over the last four decades. This article will select highlights from investigations at the Niels Bohr Institute, Denmark, and Daresbury Laboratory, UK, in the late 1970s and early 1980s, some of which have continued at other national laboratories in Europe and the USA to the present day. These studies illustrate the remarkable diversity of phenomena and symmetries exhibited by nuclei in the angular momentum–excitation energy plane that continue to surprise and fascinate scientists. (invited comment)

High resolution gamma-ray spectroscopy and the fascinating angular momentum realm of the atomic nucleus

Science.gov (United States)

Riley, M. A.; Simpson, J.; Paul, E. S.

2016-12-01

In 1974 Aage Bohr and Ben Mottelson predicted the different ‘phases’ that may be expected in deformed nuclei as a function of increasing angular momentum and excitation energy all the way up to the fission limit. While admitting their picture was highly conjectural they confidently stated ‘...with the ingenious experimental approaches that are being developed, we may look forward with excitement to the detailed spectroscopic studies that will illuminate the behaviour of the spinning quantised nucleus’. High resolution gamma-ray spectroscopy has indeed been a major tool in studying the structure of atomic nuclei and has witnessed numerous significant advances over the last four decades. This article will select highlights from investigations at the Niels Bohr Institute, Denmark, and Daresbury Laboratory, UK, in the late 1970s and early 1980s, some of which have continued at other national laboratories in Europe and the USA to the present day. These studies illustrate the remarkable diversity of phenomena and symmetries exhibited by nuclei in the angular momentum-excitation energy plane that continue to surprise and fascinate scientists.

1,3-Oxazole-based selective picomolar inhibitors of cytosolic human carbonic anhydrase II alleviate ocular hypertension in rabbits: Potency is supported by X-ray crystallography of two leads.

Science.gov (United States)

Ferraroni, Marta; Lucarini, Laura; Masini, Emanuela; Korsakov, Mikhail; Scozzafava, Andrea; Supuran, Claudiu T; Krasavin, Mikhail

2017-09-01

Two lead 1,3-oxazole-based carbonic anhydrase inhibitors (CAIs) earlier identified as selective, picomolar inhibitors of hCA II (a cytosolic target for treatment of glaucoma) have been investigated further. Firstly, they were found to be conveniently synthesized on multigram scale, which enables further development. These compounds were found to be comparable in efficacy to dorzolamide eye drops when applied in the eye drop form as well. Finally, the reasons for unusually high potency of these compounds became understood from their high-resolution X-ray crystallography structures. These data significantly expand our understanding of heterocycle-based primary sulfonamides, many of which have recently emerged from our labs - particularly, from the corneal permeability standpoint. Copyright © 2017 Elsevier Ltd. All rights reserved.

A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF

International Nuclear Information System (INIS)

McCarthy, Andrew A.; Brockhauser, Sandor; Nurizzo, Didier; Theveneau, Pascal; Mairs, Trevor; Spruce, Darren; Guijarro, Matias; Lesourd, Marc; Ravelli, Raimond B. G.; McSweeney, Sean

2009-01-01

The improvement of the X-ray beam quality achieved on ID14-4 by the installation of new X-ray optical elements is described. ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade

Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry.

Science.gov (United States)

Bax, Ben; Chung, Chun Wa; Edge, Colin

2017-02-01

There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.

Structure-Based Design: Synthesis, X-ray Crystallography, and Biological Evaluation of N-Substituted-4-Hydroxy-2-Quinolone-3-Carboxamides as Potential Cytotoxic Agents.

Science.gov (United States)

Sabbah, Dima A; Hishmah, Bayan; Sweidan, Kamal; Bardaweel, Sanaa; AlDamen, Murad; Zhong, Haizhen A; Abu Khalaf, Reema; Hasan Ibrahim, Ameerah; Al-Qirim, Tariq; Abu Sheikha, Ghassan; Mubarak, Mohammad S

2018-01-01

Oncogenic potential of phosphatidylinositol 3-kinase (PI3Kα) has been highlighted as a therapeutic target for anticancer drug design. Target compounds were designed to address the effect of different substitution patterns at the N atom of the carboxamide moiety on the bioactivity of this series. Synthesis of the targeted compounds, crystallography, biological evaluation tests against human colon carcinoma (HCT-116), and Glide docking studies. A new series of N-substituted- 4-hydroxy-2-quinolone-3-carboxamides was prepared and characterized by means of FT-IR, 1H and 13C NMR, and elemental analysis. In addition, the identity of the core nucleus 5 was successfully characterized with the aid of X-ray crystallography. Biological activity of prepared compounds was investigated in vitro against human colon carcinoma (HCT-116) cell line. Results revealed that these compounds inhibit cell proliferation and induce apoptosis through an increase in caspase-3 activity and a decrease in DNA cellular content. Compounds 7, 14, and 17 which have H-bond acceptor moiety on p-position displayed promising PI3Kα inhibitory activity. On the other hand, derivatives tailored with bulky and hydrophobic motifs (16 and 18) on o- and m-positions exhibited moderate activity. Molecular docking studies against PI3Kα and caspase-3 showed an agreement between the predicted binding affinity (ΔGobsd) and IC50 values of the derivatives for the caspase-3 model. Furthermore, Glide docking studies against PI3Kα demonstrated that the newly synthesized compounds accommodate PI3Kα kinase catalytic domain and form H-bonding with key binding residues. The series exhibited a potential PI3Kα inhibitory activity in HCT-116 cell line. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

NATO Advanced Study Institute on Evolving Methods for Macromolecular Gystallography

CERN Document Server

Read, Randy J

2007-01-01

X-ray crystallography is the pre-eminent technique for visualizing the structures of macromolecules at atomic resolution. These structures are central to understanding the detailed mechanisms of biological processes, and to discovering novel therapeutics using a structure-based approach. As yet, structures are known for only a small fraction of the proteins encoded by human and pathogenic genomes. To counter the myriad modern threats of disease, there is an urgent need to determine the structures of the thousands of proteins whose structure and function remain unknown. This volume draws on the expertise of leaders in the field of macromolecular crystallography to illuminate the dramatic developments that are accelerating progress in structural biology. Their contributions span the range of techniques from crystallization through data collection, structure solution and analysis, and show how modern high-throughput methods are contributing to a deeper understanding of medical problems.

MicroED data collection and processing

Energy Technology Data Exchange (ETDEWEB)

Hattne, Johan; Reyes, Francis E.; Nannenga, Brent L.; Shi, Dan; Cruz, M. Jason de la [Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 (United States); Leslie, Andrew G. W. [Medical Research Council Laboratory of Molecular Biology, Cambridge (United Kingdom); Gonen, Tamir, E-mail: gonent@janelia.hhmi.org [Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 (United States)

2015-07-01

The collection and processing of MicroED data are presented. MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.

Visualization of arrangements of carbon atoms in graphene layers by Raman mapping and atomic-resolution TEM

KAUST Repository

Cong, Chunxiao; Li, Kun; Zhang, Xixiang; Yu, Ting

2013-01-01

In-plane and out-of-plane arrangements of carbon atoms in graphene layers play critical roles in the fundamental physics and practical applications of these novel two-dimensional materials. Here, we report initial results on the edge

Protein crystallography with a micrometre-sized synchrotron-radiation beam

International Nuclear Information System (INIS)

Moukhametzianov, Rouslan; Burghammer, Manfred; Edwards, Patricia C.; Petitdemange, Sebastien; Popov, Dimitri; Fransen, Maikel; McMullan, Gregory; Schertler, Gebhard F. X.; Riekel, Christian

2008-01-01

For the first time, protein microcrystallography has been performed with a focused synchrotron-radiation beam of 1 µm using a goniometer with a sub-micrometre sphere of confusion. The crystal structure of xylanase II has been determined with a flux density of about 3 × 10 10 photons s −1 µm −2 at the sample. For the first time, protein microcrystallography has been performed with a focused synchrotron-radiation beam of 1 µm using a goniometer with a sub-micrometre sphere of confusion. The crystal structure of xylanase II has been determined with a flux density of about 3 × 10 10 photons s −1 µm −2 at the sample. Two sets of diffraction images collected from different sized crystals were shown to comprise data of good quality, which allowed a 1.5 Å resolution xylanase II structure to be obtained. The main conclusion of this experiment is that a high-resolution diffraction pattern can be obtained from 20 µm 3 crystal volume, corresponding to about 2 × 10 8 unit cells. Despite the high irradiation dose in this case, it was possible to obtain an excellent high-resolution map and it could be concluded from the individual atomic B-factor patterns that there was no evidence of significant radiation damage. The photoelectron escape from a narrow diffraction channel is a possible reason for reduced radiation damage as indicated by Monte Carlo simulations. These results open many new opportunities in scanning protein microcrystallography and make random data collection from microcrystals a real possibility, therefore enabling structures to be solved from much smaller crystals than previously anticipated as long as the crystallites are well ordered

Atomic-resolution characterization of the effects of CdCl2 treatment on poly-crystalline CdTe thin films

Science.gov (United States)

Paulauskas, T.; Buurma, C.; Colegrove, E.; Guo, Z.; Sivananthan, S.; Chan, M. K. Y.; Klie, R. F.

2014-08-01

Poly-crystalline CdTe thin films on glass are used in commercial solar-cell superstrate devices. It is well known that post-deposition annealing of the CdTe thin films in a CdCl2 environment significantly increases the device performance, but a fundamental understanding of the effects of such annealing has not been achieved. In this Letter, we report a change in the stoichiometry across twin boundaries in CdTe and propose that native point defects alone cannot account for this variation. Upon annealing in CdCl2, we find that the stoichiometry is restored. Our experimental measurements using atomic-resolution high-angle annular dark field imaging, electron energy-loss spectroscopy, and energy dispersive X-ray spectroscopy in a scanning transmission electron microscope are supported by first-principles density functional theory calculations.

Theory of a Quantum Scanning Microscope for Cold Atoms.

Science.gov (United States)

Yang, D; Laflamme, C; Vasilyev, D V; Baranov, M A; Zoller, P

2018-03-30

We propose and analyze a scanning microscope to monitor "live" the quantum dynamics of cold atoms in a cavity QED setup. The microscope measures the atomic density with subwavelength resolution via dispersive couplings to a cavity and homodyne detection within the framework of continuous measurement theory. We analyze two modes of operation. First, for a fixed focal point the microscope records the wave packet dynamics of atoms with time resolution set by the cavity lifetime. Second, a spatial scan of the microscope acts to map out the spatial density of stationary quantum states. Remarkably, in the latter case, for a good cavity limit, the microscope becomes an effective quantum nondemolition device, such that the spatial distribution of motional eigenstates can be measured backaction free in single scans, as an emergent quantum nondemolition measurement.

Polycapillary x-ray optics for macromolecular crystallography

International Nuclear Information System (INIS)

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

1996-01-01

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

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

International Nuclear Information System (INIS)

Roedig, Philip

2017-07-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Roedig, Philip

2017-07-15

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

Laser ionization installation for measurement of atomic beam parameters

CERN Document Server

Tukhlibaev, O; Khalilov, E E; Alimov, U Z

2002-01-01

The design of the laser ionization installation for determination of the atomic beam intensity, density and spatial structure is described. The method of the atoms laser resonance staged photoionization is applied in the installation. The above installation consists of two lasers on the dyestuffs, the atomizer, the ionization system and the ion signals registration system. The results of studies on the spatial structure of the In atoms beam are presented. The proposed method provides for the spatial resolution at the level of 10-100 mu m

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

Science.gov (United States)

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

2015-09-01

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

A Transportable Gravity Gradiometer Based on Atom Interferometry

Science.gov (United States)

Yu, Nan; Thompson, Robert J.; Kellogg, James R.; Aveline, David C.; Maleki, Lute; Kohel, James M.

2010-01-01

A transportable atom interferometer-based gravity gradiometer has been developed at JPL to carry out measurements of Earth's gravity field at ever finer spatial resolutions, and to facilitate high-resolution monitoring of temporal variations in the gravity field from ground- and flight-based platforms. Existing satellite-based gravity missions such as CHAMP and GRACE measure the gravity field via precise monitoring of the motion of the satellites; i.e. the satellites themselves function as test masses. JPL's quantum gravity gradiometer employs a quantum phase measurement technique, similar to that employed in atomic clocks, made possible by recent advances in laser cooling and manipulation of atoms. This measurement technique is based on atomwave interferometry, and individual laser-cooled atoms are used as drag-free test masses. The quantum gravity gradiometer employs two identical atom interferometers as precision accelerometers to measure the difference in gravitational acceleration between two points (Figure 1). By using the same lasers for the manipulation of atoms in both interferometers, the accelerometers have a common reference frame and non-inertial accelerations are effectively rejected as common mode noise in the differential measurement of the gravity gradient. As a result, the dual atom interferometer-based gravity gradiometer allows gravity measurements on a moving platform, while achieving the same long-term stability of the best atomic clocks. In the laboratory-based prototype (Figure 2), the cesium atoms used in each atom interferometer are initially collected and cooled in two separate magneto-optic traps (MOTs). Each MOT, consisting of three orthogonal pairs of counter-propagating laser beams centered on a quadrupole magnetic field, collects up to 10(exp 9) atoms. These atoms are then launched vertically as in an atom fountain by switching off the magnetic field and introducing a slight frequency shift between pairs of lasers to create a moving

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Science.gov (United States)

Keedy, Daniel A; Hill, Zachary B; Biel, Justin T; Kang, Emily; Rettenmaier, T Justin; Brandao-Neto, Jose; Pearce, Nicholas M; von Delft, Frank; Wells, James A; Fraser, James S

2018-06-07

Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. © 2018, Keedy et al.

Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.

Science.gov (United States)

Jamsen, Joonas A; Beard, William A; Pedersen, Lars C; Shock, David D; Moon, Andrea F; Krahn, Juno M; Bebenek, Katarzyna; Kunkel, Thomas A; Wilson, Samuel H

2017-08-15

DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PP i . The product metal is not observed during DNA synthesis in the presence of magnesium. Kinetic analyses indicate that manganese increases the rate constant for deoxynucleoside 5'-triphosphate insertion compared to magnesium. The likely product stabilization role of the manganese product metal in pol μ is discussed. These observations provide insight on structural attributes of this X-family double-strand break repair polymerase that impact its biological function in genome maintenance.DNA polymerase (pol) μ functions in DNA double-strand break repair. Here the authors use time-lapse X-ray crystallography to capture the states of pol µ during the conversion from pre-catalytic to product complex and observe a third transiently bound metal ion in the product state.

Atomic clocks for geodesy

Science.gov (United States)

Mehlstäubler, Tanja E.; Grosche, Gesine; Lisdat, Christian; Schmidt, Piet O.; Denker, Heiner

2018-06-01

We review experimental progress on optical atomic clocks and frequency transfer, and consider the prospects of using these technologies for geodetic measurements. Today, optical atomic frequency standards have reached relative frequency inaccuracies below 10‑17, opening new fields of fundamental and applied research. The dependence of atomic frequencies on the gravitational potential makes atomic clocks ideal candidates for the search for deviations in the predictions of Einstein’s general relativity, tests of modern unifying theories and the development of new gravity field sensors. In this review, we introduce the concepts of optical atomic clocks and present the status of international clock development and comparison. Besides further improvement in stability and accuracy of today’s best clocks, a large effort is put into increasing the reliability and technological readiness for applications outside of specialized laboratories with compact, portable devices. With relative frequency uncertainties of 10‑18, comparisons of optical frequency standards are foreseen to contribute together with satellite and terrestrial data to the precise determination of fundamental height reference systems in geodesy with a resolution at the cm-level. The long-term stability of atomic standards will deliver excellent long-term height references for geodetic measurements and for the modelling and understanding of our Earth.

Atom-by-atom engineering of voltage-gated ion channels: Magnified insights into function and pharmacology

DEFF Research Database (Denmark)

Pless, Stephan Alexander; Kim, Robin Y; Ahern, Christopher A

2015-01-01

Unnatural amino acid incorporation into ion channels has proven to be a valuable approach to interrogate detailed hypotheses arising from atomic resolution structures. In this short review, we provide a brief overview of some of the basic principles and methods for incorporation of unnatural amino...