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Journal ArticleDOI

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
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Journal ArticleDOI
TL;DR: A comprehensive, statistically improved data analysis approach to correct and scale the complete volume of reciprocal space data in one step is described.
Abstract: Evidence is mounting that potentially exploitable properties of technologically and chemically interesting crystalline materials are often attributable to local structure effects, which can be observed as modulated diffuse scattering (mDS) next to Bragg diffraction (BD). BD forms a regular sparse grid of intense discrete points in reciprocal space. Traditionally, the intensity of each Bragg peak is extracted by integration of each individual reflection first, followed by application of the required corrections. In contrast, mDS is weak and covers expansive volumes of reciprocal space close to, or between, Bragg reflections. For a representative measurement of the diffuse scattering, multiple sample orientations are generally required, where many points in reciprocal space are measured multiple times and the resulting data are combined. The common post-integration data reduction method is not optimal with regard to counting statistics. A general and inclusive data processing method is needed. In this contribution, a comprehensive data analysis approach is introduced to correct and merge the full volume of scattering data in a single step, while correctly accounting for the statistical weight of the individual measurements. Development of this new approach required the exploration of a data treatment and correction protocol that includes the entire collected reciprocal space volume, using neutron time-of-flight or wavelength-resolved data collected at TOPAZ at the Spallation Neutron Source at Oak Ridge National Laboratory.

46 citations


Cites background or methods from "J. Appl. Cryst.の発刊に際して"

  • ...…from diffuse diffraction data (including measurement and appropriate application of corrections in order to prepare the data for integration) and computational modeling are much more complex (Weber & Bürgi, 2002; Bürgi et al., 2005; Michels-Clark et al., 2013; Welberry & Goossens, 2008)....

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  • ...…e-mail: choffmann@ornl.gov Evidence is mounting that potentially exploitable properties of technologically and chemically interesting crystalline materials are often attributable to local structure effects, which can be observed as modulated diffuse scattering (mDS) next to Bragg diffraction (BD)....

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  • ...In principle, a much smaller step size may be needed to extract the diffuse intensities and their associated standard uncertainties for quantitative computational modeling (Michels-Clark et al., 2013) as the grid definition is not restricted by the necessity of integer HKL values....

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Journal ArticleDOI
TL;DR: The heterodimeric structure of the MST1 and RASSF5 SARAH domains is presented and a comparison of homodimerics and heterodermic interactions provides a structural basis for the preferential association of the SARAH heterodrimer.
Abstract: Despite recent progress in research on the Hippo signalling pathway, the structural information available in this area is extremely limited. Intriguingly, the homodimeric and heterodimeric interactions of mammalian sterile 20-like (MST) kinases through the so-called `SARAH' (SAV/RASSF/HPO) domains play a critical role in cellular homeostasis, dictating the fate of the cell regarding cell proliferation or apoptosis. To understand the mechanism of the heterodimerization of SARAH domains, the three-dimensional structures of an MST1–RASSF5 SARAH heterodimer and an MST2 SARAH homodimer were determined by X-ray crystallography and were analysed together with that previously determined for the MST1 SARAH homodimer. While the structure of the MST2 homodimer resembled that of the MST1 homodimer, the MST1–RASSF5 heterodimer showed distinct structural features. Firstly, the six N-terminal residues (Asp432–Lys437), which correspond to the short N-terminal 310-helix h1 kinked from the h2 helix in the MST1 homodimer, were disordered. Furthermore, the MST1 SARAH domain in the MST1–RASSF5 complex showed a longer helical structure (Ser438–Lys480) than that in the MST1 homodimer (Val441–Lys480). Moreover, extensive polar and nonpolar contacts in the MST1–RASSF5 SARAH domain were identified which strengthen the interactions in the heterodimer in comparison to the interactions in the homodimer. Denaturation experiments performed using urea also indicated that the MST–RASSF heterodimers are substantially more stable than the MST homodimers. These findings provide structural insights into the role of the MST1–RASSF5 SARAH domain in apoptosis signalling.

46 citations


Cites methods from "J. Appl. Cryst.の発刊に際して"

  • ...All final models were validated by PROCHECK (Laskowski et al., 1993)....

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Journal ArticleDOI
TL;DR: Realistic defects in face-centred cubic nanocrystals are studied numerically, revealing various signatures in diffraction patterns depending on the Miller indices and providing an identification method.
Abstract: Crystal defects induce strong distortions in diffraction patterns. A single defect alone can yield strong and fine features that are observed in high-resolution diffraction experiments such as coherent X-ray diffraction. The case of face-centred cubic nanocrystals is studied numerically and the signatures of typical defects close to Bragg positions are identified. Crystals of a few tens of nanometres are modelled with realistic atomic potentials and `relaxed' after introduction of well defined defects such as pure screw or edge dislocations, or Frank or prismatic loops. Diffraction patterns calculated in the kinematic approximation reveal various signatures of the defects depending on the Miller indices. They are strongly modified by the dissociation of the dislocations. Selection rules on the Miller indices are provided, to observe the maximum effect of given crystal defects in the initial and relaxed configurations. The effect of several physical and geometrical parameters such as stacking fault energy, crystal shape and defect position are discussed. The method is illustrated on a complex structure resulting from the simulated nanoindentation of a gold nanocrystal.

46 citations


Cites background or methods from "J. Appl. Cryst.の発刊に際して"

  • ...However, the signature of defect cores, socalled Laue scattering (Larson & Schmatz, 1980) or structural diffuse scattering (Ehrhart et al., 1982), whose extent is limited in real space, is very diffuse in reciprocal space (Krivoglaz, 1969; Fultz & Howe, 2007) and orders of magnitude weaker than the…...

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  • ...…the perfect crystal lattice and has been successfully used to characterize elastic strain in isolated crystals (Beutier et al., 2012) and to show the presence of crystal defects such as stacking faults (Chamard et al., 2008; Favre-Nicolin et al., 2010) and dislocation loops (Jacques et al., 2011)....

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  • ...…their frequent occurrence in nanowires with low SFE (one-dimensional systems) has already motivated numerous studies of such materials using CXD (Chamard et al., 2008; Favre-Nicolin et al., 2010; Jacques et al., 2013): it has been used to evaluate the number of stacking faults in an InSb pillar…...

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  • ...In recent years, this limitation has been lifted by the introduction of ptychography, a scanning version of CDI: with scanning steps smaller than the beam size, sufficient redundancy is obtained in the data to allow the reconstruction of extended objects with the help of dedicated algorithms…...

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  • ...48, 621–644 (Chamard et al., 2008; Favre-Nicolin et al., 2010), and dislocations in charge and spin density waves (Le Bolloc’h et al., 2005; Jacques et al., 2009)....

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Journal ArticleDOI
01 Jul 2015-IUCrJ
TL;DR: Crucial ‘purification’ steps inherent to the ‘selection’ of particular molecular conformations and supramolecular synthons in solution leads to a successful synthetic strategy for ternary solids, and a parallel between such strategies and combinatorial chemistry is suggested.

46 citations


Cites background or methods from "J. Appl. Cryst.の発刊に際して"

  • ...Crystal structures were solved by direct methods and refined in the spherical-atom approximation using SHELXL2012 (Sheldrick, 2008) from the WinGX suite (Farrugia, 1999)....

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  • ...Which conformation and which synthon is preferred in any instance depend on the structure of the coformer, the presence of auxiliary molecules and other experimental variables....

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Journal ArticleDOI
TL;DR: A His‐tagged derivative of the multidrug efflux pump AcrB could be crystallized in three different space groups (R3, R32 and P321) and introduction of amino acids lacking in the 1iwg structure and deletion of a highly disordered region improved R free and average B factors in the 2.7 Å model.

46 citations


Cites methods from "J. Appl. Cryst.の発刊に際して"

  • ...The SeMet substructure of the SeMet derivative crystals was solved with SHELXD [17]....

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References
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Journal ArticleDOI
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

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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

Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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