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: A novel, flexible yet simple method to generate gigawatt X-ray free-electron-laser radiation with unprecedented spectral bandwidth above the 10% level is presented.
Abstract: A new and simple method to generate X-ray free-electron-laser radiation with unprecedented spectral bandwidth above the 10% level is presented. The broad bandwidth is achieved by sending a transversely tilted beam through a transverse-gradient undulator. The extent of the bandwidth can easily be controlled by variation of the beam tilt or the undulator gradient. Numerical simulations confirm the validity and feasibility of this method.
32 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...There is, however, a strong scientific interest in obtaining large-bandwidth XFEL pulses for some applications such as X-ray crystallography (Dejoie et al., 2013; Baradaran et al., 2012; Arthur et al., 2013), X-ray emission and absorption spectroscopy (Patterson et al., 2010), stimulated Raman…...
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...Introduction X-ray free-electron-laser (XFEL) facilities are leading-edge scientific instruments in multiple research fields like biology, material science, chemistry and physics....
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TL;DR: The three-membered silacyclic ring compounds LSi,[N(2)(Ph)(2)]tBu (1), LSi[HCN(Ph)( 2)]t Bu (2) and LSi [C(2)(NtBu))(2) (3) were obtained by the treatment of base stabilized monoalkylsilylenes LSitBu with PhN=NPh, PhN =CHPh and PhC≡CPh.
Abstract: The three-membered silacyclic ring compounds LSi[N2(Ph)2]tBu (1), LSi[HCN(Ph)2]tBu (2) and LSi[C2(Ph)2]tBu (3) were obtained by the treatment of base stabilized monoalkylsilylenes LSitBu (L = PhC(NtBu)2) with PhNNPh, PhNCHPh and PhCCPh. The reaction of PhNNPh and PhCCPh with LSitBu shows a different reactivity pattern with base stabilized monochlorosilylene LSiCl. The arrangement of the three-membered ring (SiNN) in 1 is the first structurally isolated example of a siladiaziridine compound.
32 citations
TL;DR: A new crystal-mounting method has been developed that involves a combination of controlled humid air and polymer glue for crystal coating that is particularly useful when applied to fragile protein crystals that are known to be sensitive to subtle changes in their physicochemical environment.
Abstract: Protein crystals are fragile, and it is sometimes difficult to find conditions suitable for handling and cryocooling the crystals before conducting X-ray diffraction experiments. To overcome this issue, a protein crystal-mounting method has been developed that involves a water-soluble polymer and controlled humid air that can adjust the moisture content of a mounted crystal. By coating crystals with polymer glue and exposing them to controlled humid air, the crystals were stable at room temperature and were cryocooled under optimized humidity. Moreover, the glue-coated crystals reproducibly showed gradual transformations of their lattice constants in response to a change in humidity; thus, using this method, a series of isomorphous crystals can be prepared. This technique is valuable when working on fragile protein crystals, including membrane proteins, and will also be useful for multi-crystal data collection.
31 citations
TL;DR: In this article, a non-crystallographic symmetry (NCS) dimer of salivary α-amylase (HSA) was determined using an affinity resin for α-class carbonic anhydrases.
Abstract: Human salivary α-amylase (HSA) is a major secretory protein component of saliva and has important biological functions, including the initial digestion of starch. HSA acts as a monomer and mediates the hydrolysis of α-1,4-glucosidic linkages in oligosaccharides. To date, all published crystal structures of HSA have been crystallized as monomers in space group P212121. Here, the serendipitous purification, crystallization and ultimate structure determination of a HSA non-crystallographic symmetry (NCS) dimer, while attempting to purify human carbonic anhydrase VI (HCA VI) from saliva using an affinity resin for α-class carbonic anhydrases, is presented. On further investigation, it was shown that HSA could only be copurified using the affinity resin in the presence of HCA VI which is glycosylated and not the non-glycosylated HCA II. The identification of the HSA crystals was carried out by peptide mapping and mass spectrometry. HSA was shown to have crystallized as an NCS dimer in space group C2, with unit-cell parameters a = 150.9, b = 72.3, c = 91.3 A, β = 102.8°. The NCS dimer crystal structure is reported to 3.0 A resolution, with a refined R cryst of 0.228. The structure is compared with the previously reported P212121 monomer structures and the crystal packing and dimer interface are discussed.
31 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Examination of the initial |Fo Fc| and 2|Fo Fc| electron-density maps clearly identified the N-terminal pyroglutamic acid, Ca2+ and Cl ions, which were subsequently manually built using the molecular-graphics program O v.7 (Jones, 1978)....
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TL;DR: Detailed procedures and key points in preparing frozen-hydrated biological specimens are reported for efficient cryogenic coherent X-rays diffraction imaging using an X-ray free-electron laser.
Abstract: Coherent X-ray diffraction imaging (CXDI) allows internal structures of biological cells and cellular organelles to be analyzed. CXDI experiments have been conducted at 66 K for frozen-hydrated biological specimens at the SPring-8 Angstrom Compact Free-Electron Laser facility (SACLA). In these cryogenic CXDI experiments using X-ray free-electron laser (XFEL) pulses, specimen particles dispersed on thin membranes of specimen disks are transferred into the vacuum chamber of a diffraction apparatus. Because focused single XFEL pulses destroy specimen particles at the atomic level, diffraction patterns are collected through raster scanning the specimen disks to provide fresh specimen particles in the irradiation area. The efficiency of diffraction data collection in cryogenic experiments depends on the quality of the prepared specimens. Here, detailed procedures for preparing frozen-hydrated biological specimens, particularly thin membranes and devices developed in our laboratory, are reported. In addition, the quality of the frozen-hydrated specimens are evaluated by analyzing the characteristics of the collected diffraction patterns. Based on the experimental results, the internal structures of the frozen-hydrated specimens and the future development for efficient diffraction data collection are discussed.
31 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...For instance, the values of nucleic acids, proteins and water are 0.55, 0.42 and 0.33 electrons Å 3, respectively (Stuhrmann & Miller, 1978; Svergun et al., 2013)....
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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.
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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.
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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'.
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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.
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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.
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