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Journal of Applied Crystallography

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https://www.readbyqxmd.com/read/27980519/contaminer-and-contabase-a-webserver-and-database-for-early-identification-of-unwantedly-crystallized-protein-contaminants
#1
Arnaud Hungler, Afaque Momin, Kay Diederichs, Stefan T Arold
Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980518/synchrotron-based-macromolecular-crystallography-module-for-an-undergraduate-biochemistry-laboratory-course
#2
Kyle M Stiers, Christopher B Lee, Jay C Nix, John J Tanner, Lesa J Beamer
This paper describes the introduction of synchrotron-based macromolecular crystallography (MX) into an undergraduate laboratory class. An introductory 2 week experimental module on MX, consisting of four laboratory sessions and two classroom lectures, was incorporated into a senior-level biochemistry class focused on a survey of biochemical techniques, including the experimental characterization of proteins. Students purified recombinant protein samples, set up crystallization plates and flash-cooled crystals for shipping to a synchrotron...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980517/combinatorial-refinement-of-thin-film-microstructure-properties-and-process-conditions-iterative-nanoscale-search-for-self-assembled-tialn-nanolamellae
#3
J Zalesak, J Todt, R Pitonak, A Köpf, R Weißenbacher, B Sartory, M Burghammer, R Daniel, J Keckes
Because of the tremendous variability of crystallite sizes and shapes in nano-materials, it is challenging to assess the corresponding size-property relationships and to identify microstructures with particular physical properties or even optimized functions. This task is especially difficult for nanomaterials formed by self-organization, where the spontaneous evolution of microstructure and properties is coupled. In this work, two compositionally graded TiAlN films were (i) grown using chemical vapour deposition by applying a varying ratio of reacting gases and (ii) subsequently analysed using cross-sectional synchrotron X-ray nanodiffraction, electron microscopy and nanoindentation in order to evaluate the microstructure and hardness depth gradients...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980516/use-of-small-angle-x-ray-scattering-to-resolve-intracellular-structure-changes-of-escherichia-coli-cells-induced-by-antibiotic-treatment
#4
A R von Gundlach, V M Garamus, T M Willey, J Ilavsky, K Hilpert, A Rosenhahn
The application of small-angle X-ray scattering (SAXS) to whole Escherichia coli cells is challenging owing to the variety of internal constituents. To resolve their contributions, the outer shape was captured by ultra-small-angle X-ray scattering and combined with the internal structure resolved by SAXS. Building on these data, a model for the major structural components of E. coli was developed. It was possible to deduce information on the occupied volume, occurrence and average size of the most important intracellular constituents: ribosomes, DNA and proteins...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980515/multiparameter-characterization-of-subnanometre-cr-sc-multilayers-based-on-complementary-measurements
#5
Anton Haase, Saša Bajt, Philipp Hönicke, Victor Soltwisch, Frank Scholze
Cr/Sc multilayer systems can be used as near-normal incidence mirrors for the water window spectral range. It is shown that a detailed characterization of these multilayer systems with 400 bilayers of Cr and Sc, each with individual layer thicknesses <1 nm, is attainable by the combination of several analytical techniques. EUV and X-ray reflectance measurements, resonant EUV reflectance across the Sc L edge, and X-ray standing wave fluorescence measurements were used. The parameters of the multilayer model were determined via a particle-swarm optimizer and validated using a Markov chain Monte Carlo maximum-likelihood approach...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980514/pushing-the-limits-of-crystallography
#6
Janusz Wolny, Ireneusz Buganski, Pawel Kuczera, Radoslaw Strzalka
A very serious concern of scientists dealing with crystal structure refinement, including theoretical research, pertains to the characteristic bias in calculated versus measured diffraction intensities, observed particularly in the weak reflection regime. This bias is here attributed to corrective factors for phonons and, even more distinctly, phasons, and credible proof supporting this assumption is given. The lack of a consistent theory of phasons in quasicrystals significantly contributes to this characteristic bias...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980513/the-use-of-haptic-interfaces-and-web-services-in-crystallography-an-application-for-a-screen-to-beam-interface
#7
Andrew E Bruno, Alexei S Soares, Robin L Owen, Edward H Snell
Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. The work presented here illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from 'point and click' to 'touch and share', where results can be selected, annotated and discussed collaboratively...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980512/small-angle-scattering-and-morphologies-of-ultra-flexible-microemulsions
#8
Sylvain Prevost, Tobias Lopian, Maximilian Pleines, Olivier Diat, Thomas Zemb
The phase diagrams of ternary mixtures of partly miscible solvents containing a hydrotropic co-solvent exhibit a variable miscibility gap and one critical point. This work investigates the entire monophasic region far from and near to the miscibility gap in octan-1-ol/ethanol/water, for which ultra-flexible micro-emulsions (UFMEs) are observed by small-angle scattering techniques. SWAXS (combined small- and wide-angle X-ray scattering) allows the elucidation of these types of structure. Three distinct areas can be identified in the phase diagram, with scattering data resembling those from direct, bicontinuous and reverse local structures...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980511/structure-beyond-pair-correlations-x-ray-cross-correlation-from-colloidal-crystals
#9
Felix Lehmkühler, Birgit Fischer, Leonard Müller, Beatrice Ruta, Gerhard Grübel
The results of an X-ray cross-correlation analysis (XCCA) study on hard-sphere colloidal crystals and glasses are presented. The article shows that cross-correlation functions can be used to extract structural information beyond the static structure factor in such systems. In particular, the powder average can be overcome by accessing the crystals' unit-cell structure. In this case, the results suggest that the crystal is of face-centered cubic type. It is demonstrated that XCCA is a valuable tool for X-ray crystallography, in particular for studies on colloidal systems...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980510/contrast-variation-by-dynamic-nuclear-polarization-and-time-of-flight-small-angle-neutron-scattering-i-application-to-industrial-multi-component-nanocomposites
#10
Yohei Noda, Satoshi Koizumi, Tomomi Masui, Ryo Mashita, Hiroyuki Kishimoto, Daisuke Yamaguchi, Takayuki Kumada, Shin-Ichi Takata, Kazuki Ohishi, Jun-Ichi Suzuki
Dynamic nuclear polarization (DNP) at low temperature (1.2 K) and high magnetic field (3.3 T) was applied to a contrast variation study in small-angle neutron scattering (SANS) focusing on industrial rubber materials. By varying the scattering contrast by DNP, time-of-flight SANS profiles were obtained at the pulsed neutron source of the Japan Proton Accelerator Research Complex (J-PARC). The concentration of a small organic molecule, (2,2,6,6-tetramethylpiperidine-1-yl)oxy (TEMPO), was carefully controlled by a doping method using vapour sorption into the rubber specimens...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980509/sec-sans-size-exclusion-chromatography-combined-in-situ-with-small-angle-neutron-scattering
#11
Ashley Jordan, Mark Jacques, Catherine Merrick, Juliette Devos, V Trevor Forsyth, Lionel Porcar, Anne Martel
The first implementation and use of an in situ size exclusion chromatography (SEC) system on a small-angle neutron scattering instrument (SANS) is described. The possibility of deploying such a system for biological solution scattering at the Institut Laue-Langevin (ILL) has arisen from the fact that current day SANS instruments at ILL now allow datasets to be acquired using small sample volumes with exposure times that are often shorter than a minute. This capability is of particular importance for the study of unstable biological macromolecules where aggregation or denaturation issues are a major problem...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980508/robust-background-modelling-in-dials
#12
James M Parkhurst, Graeme Winter, David G Waterman, Luis Fuentes-Montero, Richard J Gildea, Garib N Murshudov, Gwyndaf Evans
A method for estimating the background under each reflection during integration that is robust in the presence of pixel outliers is presented. The method uses a generalized linear model approach that is more appropriate for use with Poisson distributed data than traditional approaches to pixel outlier handling in integration programs. The algorithm is most applicable to data with a very low background level where assumptions of a normal distribution are no longer valid as an approximation to the Poisson distribution...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980507/a-synchrotron-x-ray-diffraction-deconvolution-method-for-the-measurement-of-residual-stress-in-thermal-barrier-coatings-as-a-function-of-depth
#13
C Li, S D M Jacques, Y Chen, D Daisenberger, P Xiao, N Markocsan, P Nylen, R J Cernik
The average residual stress distribution as a function of depth in an air plasma-sprayed yttria stabilized zirconia top coat used in thermal barrier coating (TBC) systems was measured using synchrotron radiation X-ray diffraction in reflection geometry on station I15 at Diamond Light Source, UK, employing a series of incidence angles. The stress values were calculated from data deconvoluted from diffraction patterns collected at increasing depths. The stress was found to be compressive through the thickness of the TBC and a fluctuation in the trend of the stress profile was indicated in some samples...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980506/atomistic-modelling-of-scattering-data-in-the-collaborative-computational-project-for-small-angle-scattering-ccp-sas
#14
Stephen J Perkins, David W Wright, Hailiang Zhang, Emre H Brookes, Jianhan Chen, Thomas C Irving, Susan Krueger, David J Barlow, Karen J Edler, David J Scott, Nicholas J Terrill, Stephen M King, Paul D Butler, Joseph E Curtis
The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27980505/introduction-to-the-special-issue-on-small-angle-scattering
#15
EDITORIAL
Michael Gradzielski, Andrew J Allen
This open-access collection of 11 selected articles covers a small but quite diverse and interesting part of the much wider range of scientific topics presented at the 16th International Conference on Small-Angle Scattering (SAS2015) in Berlin. The topics contained here describe the particular directions in which small-angle scattering is developing at the current moment and which will become increasingly important in the future. The virtual special issue is available at http://journals.iucr.org/special_issues/2016/sas2015/...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27738419/us-somo-hplc-saxs-module-dealing-with-capillary-fouling-and-extraction-of-pure-component-patterns-from-poorly-resolved-sec-saxs-data
#16
Emre Brookes, Patrice Vachette, Mattia Rocco, Javier Pérez
Size-exclusion chromatography coupled with SAXS (small-angle X-ray scattering), often performed using a flow-through capillary, should allow direct collection of monodisperse sample data. However, capillary fouling issues and non-baseline-resolved peaks can hamper its efficacy. The UltraScan solution modeler (US-SOMO) HPLC-SAXS (high-performance liquid chromatography coupled with SAXS) module provides a comprehensive framework to analyze such data, starting with a simple linear baseline correction and symmetrical Gaussian decomposition tools [Brookes, Pérez, Cardinali, Profumo, Vachette & Rocco (2013 ▸)...
October 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27738418/pore-shape-and-sorption-behaviour-in-mesoporous-ordered-silica-films
#17
Gerhard Fritz-Popovski, Roland Morak, Parvin Sharifi, Heinz Amenitsch, Oskar Paris
Mesoporous silica films templated by pluronic P123 were prepared using spin and dip coating. The ordered cylindrical structure within the films deforms due to shrinkage during calcination. Grazing-incidence small-angle X-ray scattering (GISAXS) measurements reveal that both the unit cell and the cross section of the pores decrease in size, mainly normal to the surface of the substrate, leading to elliptical cross sections of the pores with axis ratios of about 1:2. Water take-up by the pores upon changing the relative humidity can be monitored quantitatively by the shift in the critical angle of X-ray reflection as seen by the Yoneda peak...
October 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27738417/formation-of-swift-heavy-ion-tracks-on-a-rutile-tio2-001-surface
#18
Marko Karlušić, Sigrid Bernstorff, Zdravko Siketić, Branko Šantić, Ivančica Bogdanović-Radović, Milko Jakšić, Marika Schleberger, Maja Buljan
Nanostructuring of surfaces and two-dimensional materials using swift heavy ions offers some unique possibilities owing to the deposition of a large amount of energy localized within a nanoscale volume surrounding the ion trajectory. To fully exploit this feature, the morphology of nanostructures formed after ion impact has to be known in detail. In the present work the response of a rutile TiO2 (001) surface to grazing-incidence swift heavy ion irradiation is investigated. Surface ion tracks with the well known intermittent inner structure were successfully produced using 23 MeV I ions...
October 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27738416/magnetic-scattering-in-the-simultaneous-measurement-of-small-angle-neutron-scattering-and-bragg-edge-transmission-from-steel
#19
Yojiro Oba, Satoshi Morooka, Kazuki Ohishi, Nobuhiro Sato, Rintaro Inoue, Nozomu Adachi, Jun-Ichi Suzuki, Toshihiro Tsuchiyama, Elliot Paul Gilbert, Masaaki Sugiyama
Pulsed neutron sources enable the simultaneous measurement of small-angle neutron scattering (SANS) and Bragg edge transmission. This simultaneous measurement is useful for microstructural characterization in steel. Since most steels are ferromagnetic, magnetic scattering contributions should be considered in both SANS and Bragg edge transmission analyses. An expression for the magnetic scattering contribution to Bragg edge transmission analysis has been derived. The analysis using this expression was applied to Cu steel...
October 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27738415/phase-targeted-x-ray-diffraction
#20
G M Hansford
A powder X-ray diffraction (XRD) method to enhance the signal of a specific crystalline phase within a mixture is presented for the first time. Specificity to the targeted phase relies on finding coincidences in the ratios of crystal d spacings and the ratios of elemental characteristic X-ray energies. Such coincidences can be exploited so that the two crystal planes diffract through the same scattering angle at two different X-ray energies. An energy-resolving detector placed at the appropriate scattering angle will detect a significantly enhanced signal at these energies if the target mineral or phase is present in the sample...
October 1, 2016: Journal of Applied Crystallography
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