J. Appl. Cryst.の発刊に際して
10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
Citations
More filters
TL;DR: In this article, X-ray diffraction intensities were measured from a BeO single crystal with wurtzite structure specially treated to reduce the extinction effects, and preliminary least squares refinement yielded experimental structure factors on an absolute scale, corrected for extinction and anomalous dispersion, and a reference model Be 2+ O 2− with the position parameter z = 0.3778 (4) and anisotropic Debye-Waller factors corresponding to atomic mean-square displacements with spherical average ⟨u 2 ⟩= 0.0045 (3
Abstract: X-ray diffraction intensities were measured from a BeO single crystal with wurtzite structure specially treated to reduce the extinction effects. Preliminary least-squares refinement yielded experimental structure factors on an absolute scale, corrected for extinction and anomalous dispersion, and a reference model Be 2+ O 2– with the position parameter z = 0.3778 (4) and anisotropic Debye-Waller factors corresponding to atomic mean-square displacements with spherical average ⟨u 2 ⟩ = 0.0045 (3) and 0.00353 (1) A 2 and prolateness ⟨u 3 2 ⟩ – ⟨u 2 ⟩ = 0.0008 (4) and 0.00005 (9) A 2 for Be 2+ and O 2– , respectively. The residual differences F o – F c (of these experimental structure factors and those of the reference model) were analysed in terms of sitesymmetrized multipole expansions. The phases of F o were refined iteratively to take into account the effect of the significant multipole components found. The contribution of the Be 2+ ion was subtracted to make possible a study of the oxygen lattice. Significant multipole components of third, fourth and sixth order indicate that the oxygen in BeO forms bonded hexagonal O 2– planes. They build up diffuse O–O bridges strongly bent towards the stabilizing Be 2+ ions above the plane. The Be 2+ ions exhibit a stretching quadrupole-like deformation suggesting some covalency of the bonding they build between the O 2– planes. There is some evidence of anharmonicity of atomic vibrations, particularly in the direction of the hexagonal axis.
37 citations
TL;DR: Comprehensive characterization of the morphology of single-core and multi-core magnetic nanoparticle systems for future use as reference materials for magnetic properties was performed using a combination of small-angle X-ray scattering and static light scattering.
Abstract: This article reports on the characterization of four superparamagnetic iron oxide nanoparticles stabilized with dimercaptosuccinic acid, which are suitable candidates for reference materials for magnetic properties. Particles p1 and p2 are single-core particles, while p3 and p4 are multi-core particles. Small-angle X-ray scattering analysis reveals a lognormal type of size distribution for the iron oxide cores of the particles. Their mean radii are 6.9 nm (p1), 10.6 nm (p2), 5.5 nm (p3) and 4.1 nm (p4), with narrow relative distribution widths of 0.08, 0.13, 0.08 and 0.12. The cores are arranged as a clustered network in the form of dense mass fractals with a fractal dimension of 2.9 in the multi-core particles p3 and p4, but the cores are well separated from each other by a protecting organic shell. The radii of gyration of the mass fractals are 48 and 44 nm, and each network contains 117 and 186 primary particles, respectively. The radius distributions of the primary particle were confirmed with transmission electron microscopy. All particles contain purely maghemite, as shown by X-ray absorption fine structure spectroscopy.
37 citations
TL;DR: On the basis of the continuum theory of micromagnetics, the correlation function of the spin-misalignment small-angle neutron scattering cross section of bulk ferromagnets is computed and discussed.
Abstract: On the basis of the continuum theory of micromagnetics, the correlation function of the spin-misalignment small-angle neutron scattering cross section of bulk ferromagnets (e.g. elemental polycrystalline ferromagnets, soft and hard magnetic nanocomposites, nanoporous ferromagnets, or magnetic steels) is computed. For such materials, the spin disorder which is related to spatial variations in the saturation magnetization and magnetic anisotropy field results in strong spin-misalignment scattering dΣM/dΩ along the forward direction. When the applied magnetic field is perpendicular to the incoming neutron beam, the characteristics of dΣM/dΩ (e.g. the angular anisotropy on a two-dimensional detector or the asymptotic power-law exponent) are determined by the ratio of magnetic anisotropy field strength Hp to the jump ΔM in the saturation magnetization at internal interfaces. Here, the corresponding one- and two-dimensional real-space correlations are analyzed as a function of applied magnetic field, the ratio Hp/ΔM, the single-particle form factor and the particle volume fraction. Finally, the theoretical results for the correlation function are compared with experimental data on nanocrystalline cobalt and nickel.
37 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...…means of the indirect Fourier transformation technique (Glatter, 1977; Hansen, 2000; Fritz & Glatter, 2006; Hansen, 2012), which has recently been extended to allow for the analysis of two-dimensional small-angle scattering patterns of oriented samples (Fritz-Popovski, 2013; FritzPopovski, 2015)....
[...]
...…1 Zþ1 1 d M d ðqy; qzÞ dqy dqz: ð37Þ Because d M=d ¼ ðd M=d Þðqy; qzÞ, the cðy; zÞ that is computed according to equation (37) represents a projection (average) of the three-dimensional correlation function cðx; y; zÞ along the direction of the incident neutron beam (Fritz-Popovski, 2013, 2015)....
[...]
TL;DR: A new biological small-angle X-ray scattering beamline (BioSAXS, BL19U2) at the Shanghai Synchrotron Radiation Facility (SSRF) is dedicated exclusively to small-angles scattering experiments from biological macromolecules in solution, the first in China to serve the rapidly increasing biology communities.
Abstract: The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained.
36 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing, showing that the BioSAXS facility of BL19U2 at the SSRF is already providing reasonable SAXS results....
[...]
...Data processing can be performed either manually in batch using the software package BioXTAS RAW (Nielsen et al., 2009) or automatically by running the EMBL (European Molecular Biology Laboratory), Hamburg, self-developed data analysis pipeline (SASFLOW; Franke et al., 2012)....
[...]
TL;DR: The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated.
Abstract: The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 A resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.
36 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling....
[...]
...In situ datacollection methodology (from crystals in crystallization plates) has matured to the point where the structure determination of viruses and other soluble proteins is now approaching routine (Axford et al., 2012; Heidari Khajepour et al., 2013; Wang et al., 2012)....
[...]
References
More filters
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
28,425 citations
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
27,505 citations
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
18,531 citations
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations