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.
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TL;DR: The results suggest that the formation of disulfide radicals in protein crystals owing to X-ray irradiation can be observed experimentally, both by structural means and by absorption spectroscopy.
Abstract: Irradiation of proteins with intense X-ray radiation produced by third-generation synchrotron sources generates specific structural and chemical alterations, including breakage of disulfide bonds and decarboxylation. In this paper, disulfide bond lengths in irradiated crystals of the enzyme Torpedo californica acetylcholinesterase are examined based on quantum simulations and on experimental data published previously. The experimental data suggest that one disulfide bond elongates by approximately 0.7 A upon X-ray irradiation as seen in a series of nine data sets collected on a single crystal. Simulation of the same bond suggests elongation by a similar value if a disulfide-radical anion is formed by trapping an electron. The absorption spectrum of a crystal irradiated under similar conditions shows a peak at approximately 400 nm, which in aqueous solution has been attributed to disulfide radicals. The results suggest that the formation of disulfide radicals in protein crystals owing to X-ray irradiation can be observed experimentally, both by structural means and by absorption spectroscopy.
67 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...All isolated disul®des were fully optimized using large basis sets (6±31+G*) at the MP2 level (Head-Gordon et al., 1988) using the program GAUSSIAN98 (Frisch et al., 1998)....
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...The crystal was then plunged into liquid nitrogen and mounted in the cryostream of a cooling device (600 series, Oxford Cryosystems, operating at 100 K) on an of¯ine microspectrophotometer operating with a deuterium light source (Bourgeois et al., 2002)....
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01 Mar 2017
TL;DR: A high-throughput method is described for crystal soaking using acoustic droplet ejection, and its effectiveness is demonstrated.
Abstract: The steady expansion in the capacity of modern beamlines for high-throughput data collection, enabled by increasing X-ray brightness, capacity of robotics and detector speeds, has pushed the bottleneck upstream towards sample preparation. Even in ligand-binding studies using crystal soaking, the experiment best able to exploit beamline capacity, a primary limitation is the need for gentle and nontrivial soaking regimens such as stepwise concentration increases, even for robust and well characterized crystals. Here, the use of acoustic droplet ejection for the soaking of protein crystals with small molecules is described, and it is shown that it is both gentle on crystals and allows very high throughput, with 1000 unique soaks easily performed in under 10 min. In addition to having very low compound consumption (tens of nanolitres per sample), the positional precision of acoustic droplet ejection enables the targeted placement of the compound/solvent away from crystals and towards drop edges, allowing gradual diffusion of solvent across the drop. This ensures both an improvement in the reproducibility of X-ray diffraction and increased solvent tolerance of the crystals, thus enabling higher effective compound-soaking concentrations. The technique is detailed here with examples from the protein target JMJD2D, a histone lysine demethylase with roles in cancer and the focus of active structure-based drug-design efforts.
67 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...X-ray diffraction data were collected on beamline I04-1 at Diamond Light Source and were processed using the Diamond autoprocessing pipeline, which utilizes xia2 (Winter, 2010), DIALS (Waterman et al., 2016), XDS (Kabsch, 2010), POINTLESS (Evans, 2006) and CCP4 (Winn et al., 2011)....
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TL;DR: Single-crystal high-pressure X-ray diffraction studies on the protein crystals of orthorhombic and tetragonal hen egg-white lysozyme polymorphs were carried out using a Merrill-Bassett diamond-anvil cell, image-plate detector and synchrotron radiation.
Abstract: Single-crystal high-pressure X-ray diffraction studies on the protein crystals of orthorhombic and tetragonal hen egg-white lysozyme polymorphs were carried out using a Merrill-Bassett diamond-anvil cell, image-plate detector and synchrotron radiation. The orthorhombic crystal has been squeezed to 85.5% of its ambient pressure volume at about 1.0 GPa; the crystal compresses anisotropically, and neither a glass transition or denaturation was observed. The tetragonal polymorph of lysozyme undergoes amorphization at pressures about 0.2 GPa.
66 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Kundrot & Richards (1986) designed especially for diffractometric studies of protein crystal a pressure cell withstanding about 200 MPa,t attached to an external pressure generator....
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TL;DR: The standard settings of (3 + d)-dimensional superspace groups are determined for a series of modulated compounds, especially concentrating on d = 2 and 3.
Abstract: An algorithm is presented which determines the equivalence of two settings of a (3 + d)-dimensional superspace group (d = 1, 2, 3). The algorithm has been implemented as a web tool {\tt findssg} on {\tt SSG(3+d)D}, providing the transformation of any user-given superspace group to the standard setting of this superspace group in {\tt SSG(3+d)D}. It is shown how the standard setting of a superspace group can be directly obtained by an appropriate transformation of the external-space lattice vectors (the basic structure unit cell) and a transformation of the internal-space lattice vectors (new modulation wavevectors are linear combinations of old modulation wavevectors plus a three-dimensional reciprocal-lattice vector). The need for non-standard settings in some cases and the desirability of employing standard settings of superspace groups in other cases are illustrated by an analysis of the symmetries of a series of compounds, comparing published and standard settings and the transformations between them. A compilation is provided of standard settings of compounds with two- and three-dimensional modulations. The problem of settings of superspace groups is discussed for incommensurate composite crystals and for chiral superspace groups.
66 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...They are of particular importance in the life sciences, because all proteins and nucleotides are molecules of this type (Lovelace et al., 2008)....
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TL;DR: A method has been developed that combines fast inverse-kinematics algorithms with a real-space torsion-angle refinement procedure in a two-stage approach to fit missing main-chain fragments into the electron density between two anchor points.
Abstract: Rapid protein-structure determination relies greatly on software that can automatically build a protein model into an experimental electron-density map. In favorable circumstances, various software systems are capable of building over 90% of the final model. However, completeness falls off rapidly with the resolution of the diffraction data. Manual completion of these partial models is usually feasible, but is time-consuming and prone to subjective interpretation. Except for the N- and C-termini of the chain, the end points of each missing fragment are known from the initial model. Hence, fitting fragments reduces to an inverse-kinematics problem. A method has been developed that combines fast inverse-kinematics algorithms with a real-space torsion-angle refinement procedure in a two-stage approach to fit missing main-chain fragments into the electron density between two anchor points. The first stage samples a large number of closing conformations, guided by the electron density. These candidates are ranked according to density fit. In a subsequent refinement stage, optimization steps are projected onto a carefully chosen subspace of conformation space to preserve rigid geometry and closure. Experimental results show that fitted fragments are in excellent agreement with the final refined structure for lengths of up to 12-15 residues in areas of weak or ambiguous electron density, even at medium to low resolution.
66 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...…vdbedem@slac.stanford.edu, adeacon@slac.stanford.edu # 2005 International Union of Crystallography Printed in Denmark ± all rights reserved Rapid protein-structure determination relies greatly on software that can automatically build a protein model into an experimental electron-density map....
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...Various third-generation synchrotrons now feature highly automated protein crystallography beamlines and allow collection of a complete X-ray diffraction data set in a matter of minutes (Walsh et al., 1999; Cohen et al., 2002; van den Bedem et al., 2003)....
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References
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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
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
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
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
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