phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Chen, Vincent B.; Headd, Jeffrey J.; Moriarty, Nigel W.; Richardson, Jane S.; Richardson, David C.; Urzhumtsev, Alexandre; Zwart, Peter H.; Adams, Paul D.

doi:10.1107/s0021889810015608

Title: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

Journal Article · 21 May 2010 · Journal of Applied Crystallography

DOI: https://doi.org/10.1107/s0021889810015608 · OSTI ID:1625645

Afonine, Pavel V. ^[1]; Grosse-Kunstleve, Ralf W. ^[2]; Chen, Vincent B. ^[3]; Headd, Jeffrey J. ^[3]; Moriarty, Nigel W. ^[4]; Richardson, Jane S. ^[3]; Richardson, David C. ^[3]; Urzhumtsev, Alexandre ^[5]; Zwart, Peter H. ^[4]; Adams, Paul D. ^[6]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); DOE/OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Duke Univ., Durham, NC (United States). Medical Center. Biochemistry Dept.
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States
Centre National de la Recherche Scientifique (CNRS), Illkirch (France). INSERM-UdS. IGNBMC; Universite Nancy (France). Departement de Physique
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering

phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: AC03-76SF00098

OSTI ID:: 1625645

Journal Information:: Journal of Applied Crystallography, Journal Name: Journal of Applied Crystallography Journal Issue: 4 Vol. 43; ISSN 0021-8898; ISSN JACGAR

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

References (48)

The penultimate rotamer library Lovell, Simon C.; Word, J. Michael; Richardson, Jane S. Proteins: Structure, Function, and Genetics, Vol. 40, Issue 3 https://doi.org/10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2	journal	January 2000
Thermal Motion and Conformational Disorder in Protein Crystal Structures: Comparison of Multi-Conformer and Time-Averaging Models Burling, F. Temple; Brünger, Axel T. Israel Journal of Chemistry, Vol. 34, Issue 2 https://doi.org/10.1002/ijch.199400022	journal	January 1994
Structure validation by Cα geometry: ϕ,ψ and Cβ deviation Lovell, Simon C.; Davis, Ian W.; Arendall, W. Bryan Proteins: Structure, Function, and Bioinformatics, Vol. 50, Issue 3 https://doi.org/10.1002/prot.10286	journal	January 2003
Protein Hydration Observed by X-ray Diffraction Jiang, Jian-Sheng; Brünger, Axel T. Journal of Molecular Biology, Vol. 243, Issue 1 https://doi.org/10.1006/jmbi.1994.1633	journal	October 1994
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms 1 1Edited by J. Thornton Word, J. Michael; Lovell, Simon C.; LaBean, Thomas H. Journal of Molecular Biology, Vol. 285, Issue 4 https://doi.org/10.1006/jmbi.1998.2400	journal	January 1999
Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography Niimura, N.; Arai, S.; Kurihara, K. Cellular and Molecular Life Sciences, Vol. 63, Issue 3 https://doi.org/10.1007/s00018-005-5418-3	journal	January 2006
The protein data bank: A computer-based archival file for macromolecular structures Bernstein, Frances C.; Koetzle, Thomas F.; Williams, Graheme J. B. Journal of Molecular Biology, Vol. 112, Issue 3 https://doi.org/10.1016/S0022-2836(77)80200-3	journal	May 1977
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Ensemble Refinement of Protein Crystal Structures: Validation and Application Levin, Elena J.; Kondrashov, Dmitry A.; Wesenberg, Gary E. Structure, Vol. 15, Issue 9 https://doi.org/10.1016/j.str.2007.06.019	journal	September 2007
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures Brünger, Axel T. Nature, Vol. 355, Issue 6359 https://doi.org/10.1038/355472a0	journal	January 1992
Version 1.2 of the Crystallography and NMR system Brunger, Axel T. Nature Protocols, Vol. 2, Issue 11 https://doi.org/10.1038/nprot.2007.406	journal	October 2007
Macromolecular crystal twinning, lattice disorders and multiple crystals1 Helliwell, J. R. Crystallography Reviews, Vol. 14, Issue 3 https://doi.org/10.1080/08893110802360925	journal	July 2008
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Davis, I. W.; Leaver-Fay, A.; Chen, V. B. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm216	journal	May 2007
The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W. Journal of Applied Crystallography, Vol. 35, Issue 1 https://doi.org/10.1107/S0021889801017824	journal	January 2002
PDB_REDO: automated re-refinement of X-ray structure models in the PDB Joosten, Robbie P.; Salzemann, Jean; Bloch, Vincent Journal of Applied Crystallography, Vol. 42, Issue 3 https://doi.org/10.1107/S0021889809008784	journal	April 2009
XABS 2: an empirical absorption correction program Parkin, S.; Moezzi, B.; Hope, H. Journal of Applied Crystallography, Vol. 28, Issue 1 https://doi.org/10.1107/S0021889894009428	journal	February 1995
A procedure compatible with X-PLOR for the calculation of electron-density maps weighted using an R -free-likelihood approach Urzhumtsev, A. G.; Skovoroda, T. P.; Lunin, V. Y. Journal of Applied Crystallography, Vol. 29, Issue 6 https://doi.org/10.1107/S0021889896007194	journal	December 1996
A short history of SHELX Sheldrick, George M. Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122 https://doi.org/10.1107/S0108767307043930	journal	December 2007
Improved Fourier coefficients for maps using phases from partial structures with errors Read, R. J. Acta Crystallographica Section A Foundations of Crystallography, Vol. 42, Issue 3 https://doi.org/10.1107/S0108767386099622	journal	May 1986
An efficient general-purpose least-squares refinement program for macromolecular structures Tronrud, D. E.; Ten Eyck, L. F.; Matthews, B. W. Acta Crystallographica Section A Foundations of Crystallography, Vol. 43, Issue 4 https://doi.org/10.1107/S0108767387099124	journal	July 1987
Description of overall anisotropy in diffraction from macromolecular crystals Sheriff, S.; Hendrickson, W. A. Acta Crystallographica Section A Foundations of Crystallography, Vol. 43, Issue 1 https://doi.org/10.1107/S010876738709977X	journal	January 1987
A systematic pairwise comparison of geometric parameters obtained by X-ray and neutron diffraction Allen, F. H. Acta Crystallographica Section B Structural Science, Vol. 42, Issue 5 https://doi.org/10.1107/S0108768186097823	journal	October 1986
Testing aspherical atom refinements on small-molecule data sets Hansen, N. K.; Coppens, P. Acta Crystallographica Section A, Vol. 34, Issue 6 https://doi.org/10.1107/S0567739478001886	journal	November 1978
On the rigid-body motion of molecules in crystals Schomaker, V.; Trueblood, K. N. Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, Vol. 24, Issue 1 https://doi.org/10.1107/S0567740868001718	journal	January 1968
Flat bulk-solvent model: obtaining optimal parameters Fokine, Andrei; Urzhumtsev, Alexandre Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 9 https://doi.org/10.1107/S0907444902010284	journal	August 2002
PHENIX : building new software for automated crystallographic structure determination Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11 https://doi.org/10.1107/S0907444902016657	journal	October 2002
Introduction to twinning Parsons, Simon Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11 https://doi.org/10.1107/S0907444903017657	journal	October 2003
On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps Afonine, Pavel V.; Lunin, Vladimir Y.; Muzet, Nicolas Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 2 https://doi.org/10.1107/S0907444903026209	journal	January 2004
The Uppsala Electron-Density Server Kleywegt, Gerard J.; Harris, Mark R.; Zou, Jin-yu Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12 https://doi.org/10.1107/S0907444904013253	journal	November 2004
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
REFMAC 5 dictionary: organization of prior chemical knowledge and guidelines for its use Vagin, Alexei A.; Steiner, Roberto A.; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12 https://doi.org/10.1107/S0907444904023510	journal	November 2004
A robust bulk-solvent correction and anisotropic scaling procedure Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Acta Crystallographica Section D Biological Crystallography, Vol. 61, Issue 7 https://doi.org/10.1107/S0907444905007894	journal	June 2005
Intensity statistics in twinned crystals with examples from the PDB Lebedev, Andrey A.; Vagin, Alexei A.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1 https://doi.org/10.1107/S0907444905036759	journal	December 2005
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 5 https://doi.org/10.1107/S0907444907009791	journal	April 2007
On macromolecular refinement at subatomic resolution with interatomic scatterers Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 11 https://doi.org/10.1107/S0907444907046148	journal	October 2007
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries Joosten, Robbie P.; Womack, Thomas; Vriend, Gert Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 2 https://doi.org/10.1107/S0907444908037591	journal	January 2009
Crystallographic model quality at a glance Urzhumtseva, Ludmila; Afonine, Pavel V.; Adams, Paul D. Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 3 https://doi.org/10.1107/S0907444908044296	journal	February 2009
Averaged kick maps: less noise, more signal…and probably less bias Pražnikar, Jure; Afonine, Pavel V.; Gunčar, Gregor Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 9 https://doi.org/10.1107/S0907444909021933	journal	August 2009
electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation Moriarty, Nigel W.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 10 https://doi.org/10.1107/S0907444909029436	journal	September 2009
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
The CCP4 suite programs for protein crystallography Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763 https://doi.org/10.1107/S0907444994003112	journal	September 1994
Difference refinement: obtaining differences between two related structures Terwilliger, T. C.; Berendzen, J. Acta Crystallographica Section D Biological Crystallography, Vol. 51, Issue 5 https://doi.org/10.1107/S0907444994013247	journal	September 1995
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination Brünger, A. T.; Adams, P. D.; Clore, G. M. Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 5 https://doi.org/10.1107/S0907444998003254	journal	September 1998
1.7 Å structure of the stabilized REI _v mutant T39K. Application of local NCS restraints Usón, Isabel; Pohl, Ehmke; Schneider, Thomas R. Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 6 https://doi.org/10.1107/S0907444999003972	journal	June 1999
Detecting outliers in non-redundant diffraction data Read, Randy J. Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 10 https://doi.org/10.1107/S0907444999008471	journal	October 1999

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Guha, S; Taylor, J H

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
Chemistry
Crystallography

Title: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

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