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Journal of Applied Crystallography

Tara M Michels-Clark, Andrei T Savici, Vickie E Lynch, Xiaoping Wang, Michal Chodkiewicz, Thomas Weber, Hans-Beat Bürgi, Christina M Hoffmann
[This corrects the article DOI: 10.1107/S1600576716001369.].
October 1, 2017: Journal of Applied Crystallography
Jesse Bennett Hopkins, Richard E Gillilan, Soren Skou
BioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes...
October 1, 2017: Journal of Applied Crystallography
Ruben A Dilanian, Victor Streltsov, Hannah D Coughlan, Harry M Quiney, Andrew V Martin, Nectarios Klonis, Con Dogovski, Sébastien Boutet, Marc Messerschmidt, Garth J Williams, Sophie Williams, Nicholas W Phillips, Keith A Nugent, Leann Tilley, Brian Abbey
The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage...
October 1, 2017: Journal of Applied Crystallography
Roland Morak, Stephan Braxmeier, Lukas Ludescher, Florian Putz, Sebastian Busch, Nicola Hüsing, Gudrung Reichenauer, Oskar Paris
A new in situ setup combining small-angle neutron scattering (SANS) and dilatometry was used to measure water-adsorption-induced deformation of a monolithic silica sample with hierarchical porosity. The sample exhibits a disordered framework consisting of macropores and struts containing two-dimensional hexagonally ordered cylindrical mesopores. The use of an H2O/D2O water mixture with zero scattering length density as an adsorptive allows a quantitative determination of the pore lattice strain from the shift of the corresponding diffraction peak...
October 1, 2017: Journal of Applied Crystallography
Lukas Karge, Ralph Gilles, Sebastian Busch
An improved data-reduction procedure is proposed and demonstrated for small-angle neutron scattering (SANS) measurements. Its main feature is the correction of geometry- and wavelength-dependent intensity variations on the detector in a separate step from the different pixel sensitivities: the geometric and wavelength effects can be corrected analytically, while pixel sensitivities have to be calibrated to a reference measurement. The geometric effects are treated for position-sensitive (3)He proportional counter tubes, where they are anisotropic owing to the cylindrical geometry of the gas tubes...
October 1, 2017: Journal of Applied Crystallography
Jose H Pereira, Ryan P McAndrew, Giovani P Tomaleri, Paul D Adams
Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing...
October 1, 2017: Journal of Applied Crystallography
Brian R Pauw, Claudia Kästner, Andreas F Thünemann
This paper presents the first worldwide inter-laboratory comparison of small-angle X-ray scattering (SAXS) for nanoparticle sizing. The measurands in this comparison are the mean particle radius, the width of the size distribution and the particle concentration. The investigated sample consists of dispersed silver nanoparticles, surrounded by a stabilizing polymeric shell of poly(acrylic acid). The silver cores dominate the X-ray scattering pattern, leading to the determination of their radius size distribution using (i) the generalized indirect Fourier transformation method, (ii) classical model fitting using SASfit and (iii) a Monte Carlo fitting approach using McSAS...
October 1, 2017: Journal of Applied Crystallography
Ahmed Abass, James S Bell, Martin T Spang, Sally Hayes, Keith M Meek, Craig Boote
This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions...
August 1, 2017: Journal of Applied Crystallography
D Franke, M V Petoukhov, P V Konarev, A Panjkovich, A Tuukkanen, H D T Mertens, A G Kikhney, N R Hajizadeh, J M Franklin, C M Jeffries, D I Svergun
ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data...
August 1, 2017: Journal of Applied Crystallography
Jason Porta, Jeff Lovelace, Gloria E O Borgstahl
Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved...
August 1, 2017: Journal of Applied Crystallography
Leighton Coates, Lee Robertson
Visualizing hydrogen atoms in biological materials is one of the biggest remaining challenges in biophysical analysis. While X-ray techniques have unrivaled capacity for high-throughput structure determination, neutron diffraction is uniquely sensitive to hydrogen atom positions in crystals of biological materials and can provide a more complete picture of the atomic and electronic structures of biological macromolecules. This information can be essential in providing predictive understanding and engineering control of key biological processes, for example, in catalysis, ligand binding and light harvesting, and to guide bioengineering of enzymes and drug design...
August 1, 2017: Journal of Applied Crystallography
Alexander T Martin, Shane M Nichols, Sichao Li, Melissa Tan, Bart Kahr
Circular birefringence (CB) is generally responsible for only a small perturbation to the state of light polarization in crystals that also exhibit linear birefringence (LB). As such, the magnetoelectric tensor of gyration, which gives rise to CB and optical activity, is less well determined than the electric permittivity tensor in optical models of the Mueller matrix. To visualize the effect of the magnetoelectric tensor on polarimetric measurements, reported here are experimental mappings of the Mueller matrix and of the CB in a new chiral crystal with accidental null LB at an accessible optical frequency...
August 1, 2017: Journal of Applied Crystallography
Henry N Chapman, Oleksandr M Yefanov, Kartik Ayyer, Thomas A White, Anton Barty, Andrew Morgan, Valerio Mariani, Dominik Oberthuer, Kanupriya Pande
The intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg peaks). Ensembles of molecules in several orientations, but uncorrelated in position, give rise to the incoherent sum of the diffraction from those objects, modifying the statistics in a similar way as crystal twinning modifies the distribution of Bragg intensities...
August 1, 2017: Journal of Applied Crystallography
Kenneth R Beyerlein, Thomas A White, Oleksandr Yefanov, Cornelius Gati, Ivan G Kazantsev, Nicolai Fog-Gade Nielsen, Peter M Larsen, Henry N Chapman, Søren Schmidt
A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues-Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals...
August 1, 2017: Journal of Applied Crystallography
Shirin Nouhi, Maja S Hellsing, Vassilios Kapaklis, Adrian R Rennie
Changes of scattering are observed as the grazing angle of incidence of an incoming beam increases and probes different depths in samples. A model has been developed to describe the observed intensity in grazing-incidence small-angle neutron scattering (GISANS) experiments. This includes the significant effects of instrument resolution, the sample transmission, which depends on both absorption and scattering, and the sample structure. The calculations are tested with self-organized structures of two colloidal samples with different size particles that were measured on two different instruments...
August 1, 2017: Journal of Applied Crystallography
Ti-Yen Lan, Jennifer L Wierman, Mark W Tate, Hugh T Philipp, Veit Elser, Sol M Gruner
Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such 'sparse' frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source...
August 1, 2017: Journal of Applied Crystallography
J Filik, A W Ashton, P C Y Chang, P A Chater, S J Day, M Drakopoulos, M W Gerring, M L Hart, O V Magdysyuk, S Michalik, A Smith, C C Tang, N J Terrill, M T Wharmby, H Wilhelm
A software package for the calibration and processing of powder X-ray diffraction and small-angle X-ray scattering data is presented. It provides a multitude of data processing and visualization tools as well as a command-line scripting interface for on-the-fly processing and the incorporation of complex data treatment tasks. Customizable processing chains permit the execution of many data processing steps to convert a single image or a batch of raw two-dimensional data into meaningful data and one-dimensional diffractograms...
June 1, 2017: Journal of Applied Crystallography
A Abboud, C Kirchlechner, J Keckes, T Conka Nurdan, S Send, J S Micha, O Ulrich, R Hartmann, L Strüder, U Pietsch
The full strain and stress tensor determination in a triaxially stressed single crystal using X-ray diffraction requires a series of lattice spacing measurements at different crystal orientations. This can be achieved using a tunable X-ray source. This article reports on a novel experimental procedure for single-shot full strain tensor determination using polychromatic synchrotron radiation with an energy range from 5 to 23 keV. Microbeam X-ray Laue diffraction patterns were collected from a copper micro-bending beam along the central axis (centroid of the cross section)...
June 1, 2017: Journal of Applied Crystallography
Philipp Jacobs, Andreas Houben, Werner Schweika, Andrei L Tchougréeff, Richard Dronskowski
The method of angular- and wavelength-dispersive (e.g. two-dimensional) Rietveld refinement is a new and emerging tool for the analysis of neutron diffraction data measured at time-of-flight instruments with large area detectors. Following the approach for one-dimensional refinements (using either scattering angle or time of flight), the first step at each beam time cycle is the calibration of the instrument including the determination of instrumental contributions to the peak shape variation to be expected for diffraction patterns measured by the users...
June 1, 2017: Journal of Applied Crystallography
Jiangkun Fan, Jinshan Li, Yudong Zhang, Hongchao Kou, Jaafar Ghanbaja, Weimin Gan, Lionel Germain, Claude Esling
For the β phase of Ti-5553-type metastable β-Ti alloys, striations in transmission electron microscopy (TEM) bright- and dark-field images have been frequently observed but their origin has not been sufficiently investigated. In the present work, this phenomenon is studied in depth from the macroscopic scale by neutron diffraction to the atomic scale by high-resolution TEM. The results reveal that the β phase contains homogeneously distributed modulated structures, intermediate between that of the β phase (cubic) and that of the α phase or the ω phase (hexagonal), giving rise to the appearance of additional diffraction spots at 1/2, 1/3 and 2/3 β diffraction positions...
June 1, 2017: Journal of Applied Crystallography
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