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
More filters
TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Abstract: An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
81,116 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...These days such padding is less desirable and there are excellent programs such as enCIFer (Allen et al., 2004) for working with CIF files, so CIFTAB is now effectively redundant....
[...]
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
Cites methods from "J. Appl. Cryst.の発刊に際して"
...This dictionary contains among oth i ems descriptions of the solution components, the experime conditions, enumerated lists of the instruments used, as we information about structure refinement....
[...]
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
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Multithreading is achieved using OpenMP along the lines suggested by Diederichs (2000), and the program is particularly suitable for multiple-core processors....
[...]
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
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...…e-mail: emsley@ysbl.york.ac.uk # 2004 International Union of Crystallography Printed in Denmark ± all rights reserved 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…...
[...]
...The introduction of FRODO (Jones, 1978) and then O (Jones et al., 1991) to the ®eld of protein crystallography was in each case revolutionary, each in their time breaking new ground in demonstrating what was possible with the current hardware....
[...]
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
Cites methods from "J. Appl. Cryst.の発刊に際して"
...After ensuring that the diffraction data are sound and understood, the next critical necessity for solving a structure is the determination of phases using one of several strategies (Adams, Afonine et al., 2009)....
[...]
...Tools such as efficient rigid-body refinement (multiplezones algorithm; Afonine et al., 2009), simulated-annealing refinement (Brünger et al., 1987) in Cartesian or torsion-angle space (Grosse-Kunstleve et al., 2009), automatic NCS detection and its use as restraints in refinement are important at…...
[...]
References
More filters
TL;DR: The structure of ent-copalyl diphosphate synthase (CPS) reveals three α-helical domains (α, β, γ), as also observed in the related diterpene cyclase taxadiene synthase, but active sites are located at the interface of the βγ domains in CPS but exclusively in the α domain of taxadienes synthase.
Abstract: The structure of ent-copalyl diphosphate synthase reveals three α-helical domains (α, β and γ), as also observed in the related diterpene cyclase taxadiene synthase. However, active sites are located at the interface of the βγ domains in ent-copalyl diphosphate synthase but exclusively in the α domain of taxadiene synthase. Modular domain architecture in plant diterpene cyclases enables the evolution of alternative active sites and chemical strategies for catalyzing isoprenoid cyclization reactions.
143 citations
TL;DR: It is proposed that C-S-H of Ca/Si ratio ranging between ∼”0.6 and ∼ 1.7 can be described as nanocrystalline tobermorite affected by turbostratic disorder and arises from nanocrystalinity and possibly from an interstratification phenomenon.
Abstract: X-ray diffraction (XRD) patterns were calculated and compared to literature data with the aim of investigating the crystal structure of nanocrystalline calcium silicate hydrates (C-S-H), the main binding phase in hydrated Portland cement pastes. Published XRD patterns from C-S-H of Ca/Si ratios ranging from ∼ 0.6 to ∼ 1.7 are fully compatible with nanocrystalline and turbostratic tobermorite. Even at a ratio close or slightly higher than that of jennite (Ca/Si = 1.5) this latter mineral, which is required in some models to describe the structure of C-S-H, is not detected in the experimental XRD patterns. The 001 basal reflection from C-S-H, positioned at ∼ 13.5 A when the C-S-H structural Ca/Si ratio is low (< 0.9), shifts towards smaller d values and sharpens with increasing Ca/Si ratio, to reach ∼ 11.2 A when the Ca/Si ratio is higher than 1.5. Calculations indicate that the sharpening of the 001 reflection may be related to a crystallite size along c* (i.e. a mean number of stacked layers) increasing with the C-S-H Ca/Si ratio. Such an increase would contribute to the observed shift of the 001 reflection, but fails to quantitatively explain it. It is proposed that the observed shift could result from interstratification of at least two tobermorite-like layers, one having a high and the other a low Ca/Si ratio with a basal spacing of 11.3 and 14 A, respectively.
143 citations
TL;DR: Methods presented for growing protein–ligand complexes fall into the categories of co-expression of the protein with the ligand of interest, use of the ligands during protein purification, cocrystallization and soaking the liganded into existing crystals.
Abstract: Obtaining diffraction-quality crystals has long been a bottleneck in solving the three-dimensional structures of proteins. Often proteins may be stabilized when they are complexed with a substrate, nucleic acid, cofactor or small molecule. These ligands, on the other hand, have the potential to induce significant conformational changes to the protein and ab initio screening may be required to find a new crystal form. This paper presents an overview of strategies in the following areas for obtaining crystals of protein–ligand complexes: (i) co-expression of the protein with the ligands of interest, (ii) use of the ligands during protein purification, (iii) cocrystallization and (iv) soaks.
142 citations
TL;DR: In this paper, syntactic foams were fabricated by pressure-infiltrating liquid aluminum (commercial purity and 7075-Al) into a packed preform of silica-mullite hollow microspheres.
141 citations
TL;DR: A protein engineering approach is document to generate and optimize an extended polypeptide MSP, which will self-assemble phospholipids into larger Nanodiscs with diameters of 16-17 nm, which are characterized by size exclusion chromatography and solution X-ray scattering.
Abstract: High-density lipoproteins (HDLs) play an important role in human health through the metabolism and trafficking of cholesterol as well as providing the feedstocks for steroid hormone biosynthesis. These particles contain proteins, primarily Apo-AI and phospholipid and progress through various structural forms including ‘lipid-poor’, ‘discoidal’ and ‘spherical’ entities as cholesterol esters and lipid are incorporated. The discoidal form of HDL is stabilized in solution by two encircling belts of Apo-AI. Previous protein engineering of the Apo-AI sequence has led to a series of amphipathic helical proteins, termed membrane scaffold proteins (MSPs), which have shown great value in assembling nanoscale soluble membrane bilayers, termed Nanodiscs, of homogeneous size and composition and in the assembly of numerous integral membrane proteins for biophysical and biochemical investigations. In this communication we document a protein engineering approach to generate and optimize an extended polypeptide MSP, which will self-assemble phospholipids into larger Nanodiscs with diameters of 16–17 nm. We extensively characterize these structures by size exclusion chromatography and solution X-ray scattering.
139 citations