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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: Averaged kick maps are the sum of a series of individual kick maps, where each map is calculated from atomic coordinates modified by random shifts, and offer the possibility of an improved and less model-biased map interpretation.
Abstract: Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map-calculation methods. AK maps are the sum of a series of kick maps, where each kick map is calculated from atomic coordinates modified by random shifts. As such, they are a numerical analogue of maximum-likelihood maps. AK maps can be unweighted or maximum-likelihood (σA) weighted. Analysis shows that they are comparable and correspond better to the final model than σA and simulated-annealing maps. The AK maps were challenged by a difficult structure-validation case, in which they were able to clarify the problematic region in the density without the need for model rebuilding. The conclusion is that AK maps can be useful throughout the entire progress of crystal structure determination, offering the possibility of improved map interpretation.

63 citations


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

  • ...…AK map approach is yet another contribution to the series of map calculations dealing with model-bias removal such as OMIT, SA OMIT maps, composite OMIT maps (Bhat & Cohen, 1984; Bhat, 1988; Hodel et al., 1992; Brünger et al., 1998) and the prime-and-switch phasing approach (Terwilliger, 2004)....

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Journal ArticleDOI
TL;DR: Reaction between a β-diketiminato magnesium hydride and carbon monoxide results in the isolation of a dimeric cis-enediolate species through the reductive coupling of two CO molecules.
Abstract: Reaction between a β-diketiminato magnesium hydride and carbon monoxide results in the isolation of a dimeric cis-enediolate species through the reductive coupling of two CO molecules. Under catalytic conditions with PhSiH3, an observable magnesium formyl species may be intercepted for the mild reductive cleavage of the CO triple bond.

63 citations

Journal ArticleDOI
TL;DR: A high-density sample mount has been developed for efficient goniometer-based sample delivery at synchrotron and XFEL sources.
Abstract: Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice/DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.

63 citations


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

  • ...Proof of principle LCP crystallization experiments were performed on grids using an adaptation of a protocol for the growth of lysozyme in LCP (Aherne et al., 2012)....

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  • ...A rapidly advancing tool for diffraction experiments is the use of LCP injectors both at XFEL and synchrotron sources (Nogly et al., 2015)....

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  • ...The grid is therefore a complementary technique to the LCP injector as it can be used both for direct data collection and for screening LCP conditions....

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  • ...LCP crystallization experiments may also be performed on grids with the use of a specialized tray, eliminating the need to cut open a glass sandwich plate and manually harvest crystals for data collection....

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  • ...The grid LCP tray assembly consists of two siliconized glass slides, 1 mm thick double-sided tape and a tray with a support for a magnetic base and glass slides....

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Journal ArticleDOI
TL;DR: In this paper, the average thicknesses of the lamellae, the average period and the corresponding variances were determined using both the stacking model and the lattice model, and the width of the domain boundary and the preferred orientation were determined.
Abstract: Oriented lamellar nanocomposites formed of alternating organic and inorganic layers were prepared by evaporation-induced self-assembly and studied by small-angle X-ray scattering in symmetrical and asymmetrical reflection. Analytical expressions were used for a quantitative fit of the experimental data. The fitting procedure leads to a comprehensive characterization of the lamellar two-phase system in terms of the average thicknesses of the lamellae, the average period and the corresponding variances, using both the stacking model and the lattice model. Furthermore, the width of the domain boundary and the preferred orientation were determined. No significant differences could be found between the parameters obtained for the two models, but the lattice model leads to a better curve fitting. The effects of finite stack height and of instrumental broadening were found to be indistinguishable.

63 citations


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

  • ...An analytical expression for Il can be obtained using the relationship Il s F Pl r (Warren & Averbach, 1950), where the Fourier transform Pl of the line pro®le Il is composed of various factors (see e.g. Ruland & Smarsly, 2002)....

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Journal ArticleDOI
TL;DR: Using the MPCS, diffraction-ready crystals were grown in the plastic MPCS CrystalCard and were used to solve the structure of methionine-R-sulfoxide reductase.
Abstract: The Microcapillary Protein Crystallization System (MPCS) embodies a new semi-automated plug-based crystallization technology which enables nanolitre-volume screening of crystallization conditions in a plasticware format that allows crystals to be easily removed for traditional cryoprotection and X-ray diffraction data collection. Protein crystals grown in these plastic devices can be directly subjected to in situ X-ray diffraction studies. The MPCS integrates the formulation of crystallization cocktails with the preparation of the crystallization experiments. Within microfluidic Teflon tubing or the microfluidic circuitry of a plastic CrystalCard, ∼10–20 nl volume droplets are generated, each representing a microbatch-style crystallization experiment with a different chemical composition. The entire protein sample is utilized in crystallization experiments. Sparse-matrix screening and chemical gradient screening can be combined in one com­prehensive `hybrid' crystallization trial. The technology lends itself well to optimization by high-granularity gradient screening using optimization reagents such as precipitation agents, ligands or cryoprotectants.

62 citations


Additional excerpts

  • ...This allows the crystallographer to assess the quality of the crystals grown before alteration by the cryoprotection process (Luft et al., 1999; McPherson, 2000; Ng et al., 2003; Yadav et al., 2005; Lunde et al., 2008) and to collect data for structure determination from robust crystals....

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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

Journal ArticleDOI
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