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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: 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....

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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


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....

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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


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....

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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


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…...

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  • ...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....

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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


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)....

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  • ...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…...

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References
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Journal ArticleDOI
01 Jan 2016-IUCrJ
TL;DR: The results of refinements using a Transferable Aspherical Atomic Model of electron density (TAAM) appear to be in far better agreement with neutron results than the corresponding Independent Atom Model (IAM) results for all parameters, all resolutions and all compounds.

30 citations

Journal ArticleDOI
TL;DR: Solvent dependent double C-H activation in an Ir(NHC)(2) system generates an agostically stabilized 14-electron complex featuring a face-capping bis(alkyl) tethered NHC ligand that can be applied to the dehydrogenation of BN-containing substrates.

30 citations

Journal ArticleDOI
TL;DR: A crystal structure analysis of the synthetic deoxydodecamer d(CGCAAATTIGCG) which contains two adenosine (A.I) mispairs has revealed that, in this sequence, the A.I base-pairs adopt a A(anti).I(syn) configuration.
Abstract: A crystal structure analysis of the synthetic deoxydodecamer d(CGCAAATTIGCG) which contains two adenosineinosine (AI) mispairs has revealed that, in this sequence, the AI base-pairs adopt a A(anti)I(syn) configuration The refinement converged at R = 0158 for 2004 reflections with F greater than or equal to 2 sigma(F) in the range 70-25A for a model consisting of the DNA duplex and 71 water molecules A notable feature of the structure is the presence of an almost complete spine of hydration spanning the minor groove of the whole of the (AAATTI)2 core region of the duplex pH-dependent ultraviolet melting studies have suggested that the base-pair observed in the crystal structure is, in fact, a protonated AH+ (anti)I(syn) species and that the AI base-pairs in the sequence studied display the same conformational variability as AG mispairs in the sequence d(CGCAAATTGGCG) The AH+(anti)I(syn) base-pair predominates below pH 65 and an A(anti)I(anti) mispair is the major species present between pH 65 and 80 The protonated base-pairs are held together by two hydrogen bonds one between N6(A) and O6(I) and the other between N1(A) and N7(I) This second hydrogen bond is a direct result of the protonation of the N1 of adenosine The ultraviolet melting studies indicate that the A(anti)I(anti) base-pair is more stable than the A(anti)G(anti) base-pair but that the AH+(anti)I(syn) base pair is less stable than its AH+(anti)G(syn) analogue Possible reasons for this observation are discussed

30 citations

Journal ArticleDOI
TL;DR: The effect of modifying the N-aryl substituent of the phosphinoamide ligands linking Zr and Co in tris(phosphinoamide)-linked heterobimetallic complexes has been investigated and reveals similar structural features but with a less sterically hindered Zr apical site in complex 4.
Abstract: The effect of modifying the N-aryl substituent (aryl = mesityl vs. m-xylyl) of the phosphinoamide ligands linking Zr and Co in tris(phosphinoamide)-linked heterobimetallic complexes has been investigated. Treatment of the metalloligand (iPr2PNXyl)3ZrCl (2) (Xyl = m-xylyl) with CoI2 affords the iodide-bridged product ICo(iPr2PNXyl)2(μ-I)Zr(η2-iPr2PNXyl) (3) rather than the C3-symmetric isomer observed using the N-mesityl derivative, ICo(iPr2PNMes)3ZrCl. Upon two-electron reduction of complex 3, ligand rearrangement occurs to generate the three-fold symmetric reduced complex N2Co(iPr2PNXyl)3Zr(THF) (4). Comparison of 4 with the previously reported mesityl-substituted complex N2Co(iPr2PNMes)3Zr(THF) (1) reveals similar structural features but with a less sterically hindered Zr apical site in complex 4. An obvious electronic difference between these two complexes is also present based on the drastically different infrared N2 stretching frequencies of 1 and 4. These notable differences lend themselves to different reactivity in both stoichiometric and catalytic reactions. Alkyl halide addition to complex 4 results in homo-coupling products resulting from alkyl radicals rather than the alkyl-bridged or intramolecular C–H activation products formed upon addition of RX to 1. This difference in reactivity with alkyl halides renders complex 3 a less effective catalyst for the Kumada cross-coupling of alkyl halides with n-octylMgBr than ICo(iPr2PNMes)3ZrCl, as a greater proportion of homocoupling products are formed under catalytic conditions.

30 citations

Journal ArticleDOI
TL;DR: A data set has been collected using the Laue technique on a trigonal crystal of Torpedo californica AChE soaked with the reversible inhibitor edrophonium, which clearly reveals the bound ligand, as well as a structural change in the conformation of the active-site Ser200 induced upon binding.
Abstract: Acetylcholinesterase (AChE) is one of nature's fastest enzymes, despite the fact that its three-dimensional structure reveals its active site to be deeply sequestered within the molecule. This raises questions with respect to traffic of substrate to, and products from, the active site, which may be investigated by time-resolved crystallography. In order to address one aspect of the feasibility of performing time-resolved studies on AChE, a data set has been collected using the Laue technique on a trigonal crystal of Torpedo californica AChE soaked with the reversible inhibitor edrophonium, using a total X-ray exposure time of 24 ms. Electron-density maps obtained from the Laue data, which are of surprisingly good quality compared with similar maps from monochromatic data, show essentially the same features. They clearly reveal the bound ligand, as well as a structural change in the conformation of the active-site Ser200 induced upon binding.

30 citations