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Journal of Applied Crystallography

Kathryn L Shelley, Thomas P E Dixon, Jonathan C Brooks-Bartlett, Elspeth F Garman
Radiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures...
April 1, 2018: Journal of Applied Crystallography
Martha G Pamato, Ian G Wood, David P Dobson, Simon A Hunt, Lidunka Vočadlo
On the basis of ab initio computer simulations, pre-melting phenomena have been suggested to occur in the elastic properties of hexagonal close-packed iron under the conditions of the Earth's inner core just before melting. The extent to which these pre-melting effects might also occur in the physical properties of face-centred cubic metals has been investigated here under more experimentally accessible conditions for gold, allowing for comparison with future computer simulations of this material. The thermal expansion of gold has been determined by X-ray powder diffraction from 40 K up to the melting point (1337 K)...
April 1, 2018: Journal of Applied Crystallography
M Raventós, E H Lehmann, M Boin, M Morgano, J Hovind, R Harti, J Valsecchi, A Kaestner, C Carminati, P Boillat, P Trtik, F Schmid, M Siegwart, D Mannes, M Strobl, C Grünzweig
The development of neutron imaging from a qualitative inspection tool towards a quantitative technique in materials science has increased the requirements for accuracy significantly. Quantifying the thickness or the density of polycrystalline samples with high accuracy using neutron imaging has two main problems: (i) the scattering from the sample creates artefacts on the image and (ii) there is a lack of specific reference attenuation coefficients. This work presents experimental and simulation results to explain and approach these problems...
April 1, 2018: Journal of Applied Crystallography
Judith Elizabeth Houston, Georg Brandl, Matthias Drochner, Günter Kemmerling, Ralf Engels, Aristeidis Papagiannopoulos, Mona Sarter, Andreas Stadler, Aurel Radulescu
A new detection system based on an array of 3 He tubes and innovative fast detection electronics has been installed on the high-intensity small-angle neutron scattering (SANS) diffractometer KWS-2 operated by the Jülich Centre for Neutron Science (JCNS) at the Heinz Meier-Leibnitz Zentrum in Garching, Germany. The new detection system is composed of 18 eight-pack modules of 3 He tubes that work independently of one another (each unit has its own processor and electronics). To improve the read-out characteristics and reduce the noise, the detection electronics are mounted in a closed case on the rear of the 3 He tubes' frame...
April 1, 2018: Journal of Applied Crystallography
Feng Ye, Yaohua Liu, Ross Whitfield, Ray Osborn, Stephan Rosenkranz
The CORELLI instrument at Oak Ridge National Laboratory is a statistical chopper spectrometer designed and optimized to probe complex disorder in crystalline materials through diffuse scattering experiments. On CORELLI, the high efficiency of white-beam Laue diffraction combined with elastic discrimination have enabled an unprecedented data collection rate to obtain both the total and the elastic-only scattering over a large volume of reciprocal space from a single measurement. To achieve this, CORELLI is equipped with a statistical chopper to modulate the incoming neutron beam quasi-randomly, and then the cross-correlation method is applied to reconstruct the elastic component from the scattering data...
April 1, 2018: Journal of Applied Crystallography
Ken Holst Andersen, Mads Bertelsen, Luca Zanini, Esben Bryndt Klinkby, Troels Schönfeldt, Phillip Martin Bentley, Jan Saroun
A global approach coupling the moderator to the beam extraction system has been applied for the design optimization of the thermal and cold moderators of the European Spallation Source (ESS), which will be the brightest neutron source in the world for condensed-matter studies. The design is based on the recently developed high-brightness low-dimensional moderator concepts. Para -hydrogen is used for the cold neutron source, while thermal neutrons are provided by moderation in water. The overall moderation configuration was chosen in order to satisfy a range of requirements on bispectral extraction, beamport configuration and instrument performance...
April 1, 2018: Journal of Applied Crystallography
Ti-Yen Lan, Jennifer L Wierman, Mark W Tate, Hugh T Philipp, Veit Elser, Sol M Gruner
[This corrects the article DOI: 10.1107/S1600576717006537.].
February 1, 2018: Journal of Applied Crystallography
Natalie T Johnson, Holger Ott, Michael R Probert
The rigorous analysis of crystallographic models, refined through the use of least-squares minimization, is founded on the expectation that the data provided have a normal distribution of residuals. Processed single-crystal diffraction data rarely exhibit this feature without a weighting scheme being applied. These schemes are designed to reflect the precision and accuracy of the measurement of observed reflection intensities. While many programs have the ability to calculate optimal parameters for applied weighting schemes, there are still programs that do not contain this functionality, particularly when moving beyond the spherical atom model...
February 1, 2018: Journal of Applied Crystallography
Michał L Chodkiewicz, Szymon Migacz, Witold Rudnicki, Anna Makal, Jarosław A Kalinowski, Nigel W Moriarty, Ralf W Grosse-Kunstleve, Pavel V Afonine, Paul D Adams, Paulina Maria Dominiak
It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed...
February 1, 2018: Journal of Applied Crystallography
Wen Hu, Xiaojing Huang, Hanfei Yan
This article reports a theoretical study on the reconstruction artefacts in Bragg coherent diffractive imaging caused by dynamical diffraction effects. It is shown that, unlike the absorption and refraction effects that can be corrected after reconstruction, dynamical diffraction effects have profound impacts on both the amplitude and the phase of the reconstructed complex object, causing strong artefacts. At the dynamical diffraction limit, the reconstructed shape is no longer correct, as a result of the strong extinction effect...
February 1, 2018: Journal of Applied Crystallography
Vito Graziano, Lisa Miller, Lin Yang
The structural information contained in solution scattering data from empty lipid nanodiscs is examined in the context of a multi-component geometric model. X-ray scattering data were collected on nanodiscs of different compositions at scattering vector magnitudes up to 2.0 Å-1 . Through the calculation of the partial form factor for each of the nanodisc components before the isotropic average, structural parameters in the model were correlated to the features observed in the X-ray scattering data and to the corresponding distance distribution function...
February 1, 2018: Journal of Applied Crystallography
Salah Awel, Richard A Kirian, Max O Wiedorn, Kenneth R Beyerlein, Nils Roth, Daniel A Horke, Dominik Oberthür, Juraj Knoska, Valerio Mariani, Andrew Morgan, Luigi Adriano, Alexandra Tolstikova, P Lourdu Xavier, Oleksandr Yefanov, Andrew Aquila, Anton Barty, Shatabdi Roy-Chowdhury, Mark S Hunter, Daniel James, Joseph S Robinson, Uwe Weierstall, Andrei V Rode, Saša Bajt, Jochen Küpper, Henry N Chapman
High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid...
February 1, 2018: Journal of Applied Crystallography
Gianluca Santoni, Ulrich Zander, Christoph Mueller-Dieckmann, Gordon Leonard, Alexander Popov
This article describes ccCluster , a software providing an intuitive graphical user interface (GUI) and multiple functions to perform hierarchical cluster analysis on multiple crystallographic datasets. The program makes it easier for users to choose, in the case of multi-crystal data collection, those datasets that will be merged together to give good final statistics. It provides a simple GUI to analyse the dendrogram and various options for automated clustering and data merging.
December 1, 2017: Journal of Applied Crystallography
B R Pauw, A J Smith, T Snow, N J Terrill, A F Thünemann
Data correction is probably the least favourite activity amongst users experimenting with small-angle X-ray scattering: if it is not done sufficiently well, this may become evident only during the data analysis stage, necessitating the repetition of the data corrections from scratch. A recommended comprehensive sequence of elementary data correction steps is presented here to alleviate the difficulties associated with data correction, both in the laboratory and at the synchrotron. When applied in the proposed order to the raw signals, the resulting absolute scattering cross section will provide a high degree of accuracy for a very wide range of samples, with its values accompanied by uncertainty estimates...
December 1, 2017: Journal of Applied Crystallography
Annick P Baur, Cyril Cayron, Roland E Logé
A significant variant selection is reported in isothermal martensite formed on the surface of an Fe-30% Ni sample. The selection phenomenon is modelled using different descriptions of the martensitic phase transformation. In particular, matrices based on the phenomenological theory of martensite crystallography, the Jaswon and Wheeler distortion, and the continuous face centred cubic-body centred cubic distortion are compared. All descriptions allow good predictions of the variant selection. However, the Jaswon and Wheeler distortion and the continuous distortion better account for other features of the surface martensite, such as the {225}γ habit plane and the accommodation mechanism by twin-related variant pairing...
December 1, 2017: Journal of Applied Crystallography
Christian B Hübschle, Sander van Smaalen
A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method...
December 1, 2017: Journal of Applied Crystallography
Masato Anada, Yoshinori Nakanishi-Ohno, Masato Okada, Tsuyoshi Kimura, Yusuke Wakabayashi
Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes' theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories...
December 1, 2017: 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
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