Citations
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phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics
Pavel V. Afonine,Ralf W. Grosse-Kunstleve,Vincent B. Chen,Jeffrey J. Headd,Nigel W. Moriarty,Jane S. Richardson,David S. Richardson,Alexandre Urzhumtsev,Peter H. Zwart,Paul D. Adams,Paul D. Adams +10 more
TL;DR: Application of phenix.model_vs-data to the contents of the Protein Data Bank shows that the vast majority of deposited structures can be automatically analyzed to reproduce the reported quality statistics, but the small fraction that elude automated re-analysis highlight areas where new software developments can help retain valuable information for future analysis.
Journal ArticleDOI
Cisplatin binding to human serum albumin: a structural study
TL;DR: Structural data unambiguously prove that cisplatin mainly binds to His105 and Met329 side chains; additional binding sites are detected at His288, Met298, and Met548 and at His535, His67 and His247.
Journal ArticleDOI
Structural analysis of Bub3 interactions in the mitotic spindle checkpoint.
Nicholas A. Larsen,Jawdat Al-Bassam,Ronnie Wei,Ronnie Wei,Stephen C. Harrison,Stephen C. Harrison +5 more
TL;DR: It is proposed that the structure imposed on the GLEBS segment by its association with Bub3 enables recruitment to unattached kinetochores and causes checkpoint deficiency and chromosome instability.
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Optimization of data collection taking radiation damage into account
Gleb Bourenkov,Alexander Popov +1 more
TL;DR: Software implementing a new method for the optimal choice of data-collection parameters, accounting for the effects of radiation damage, is presented.
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Using SAD data in Phaser
Randy J. Read,Airlie J. McCoy +1 more
TL;DR: SAD data can be used in Phaser to solve novel structures, supplement molecular-replacement phase information or identify anomalous scatterers from a final refined model.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
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.
Journal ArticleDOI
Crystal structure refinement with SHELXL
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Journal ArticleDOI
Coot: model-building tools for molecular graphics.
Paul Emsley,Kevin Cowtan +1 more
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.
Journal ArticleDOI
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Journal ArticleDOI
Phaser crystallographic software
Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
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.