Automatic protein structure solution from weak X-ray data

被引:226
作者
Skubak, Pavol [1 ]
Pannu, Navraj S. [1 ]
机构
[1] Leiden Univ, Dept Biophys Struct Chem, NL-2333 CC Leiden, Netherlands
关键词
FREE R-VALUE; REFINEMENT; ACCURACY; SOFTWARE;
D O I
10.1038/ncomms3777
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 angstrom RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.
引用
收藏
页数:6
相关论文
共 21 条
[1]   PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].
Adams, Paul D. ;
Afonine, Pavel V. ;
Bunkoczi, Gabor ;
Chen, Vincent B. ;
Davis, Ian W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Hung, Li-Wei ;
Kapral, Gary J. ;
Grosse-Kunstleve, Ralf W. ;
McCoy, Airlie J. ;
Moriarty, Nigel W. ;
Oeffner, Robert ;
Read, Randy J. ;
Richardson, David C. ;
Richardson, Jane S. ;
Terwilliger, Thomas C. ;
Zwart, Peter H. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221
[2]   FREE R-VALUE - A NOVEL STATISTICAL QUANTITY FOR ASSESSING THE ACCURACY OF CRYSTAL-STRUCTURES [J].
BRUNGER, AT .
NATURE, 1992, 355 (6359) :472-475
[3]   Free R value: Cross-validation in crystallography [J].
Brunger, AT .
MACROMOLECULAR CRYSTALLOGRAPHY, PT B, 1997, 277 :366-396
[4]   Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution [J].
Brunger, Axel T. ;
Adams, Paul D. ;
Fromme, Petra ;
Fromme, Raimund ;
Levitt, Michael ;
Schroeder, Gunnar F. .
STRUCTURE, 2012, 20 (06) :957-966
[5]   The Buccaneer software for automated model building.: 1.: Tracing protein chains [J].
Cowtan, Kevin .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2006, 62 :1002-1011
[6]   Recent developments in classical density modification [J].
Cowtan, Kevin .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2010, 66 :470-478
[7]   Matrix methods for solving protein substructures of chlorine and sulfur from anomalous data [J].
de Graaff, RAG ;
Hilge, M ;
van der Plas, JL ;
Abrahams, JP .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2001, 57 :1857-1862
[8]  
EMSLEY P, 2008, ACTA CRYSTALLOGR D, V66, P486
[9]  
Hendrickson W. A., 1970, Acta Crystallographica, Section B (Structural Crystallography and Crystal Chemistry), Vb26, P136, DOI 10.1107/S0567740870002078
[10]   MOLSCRIPT - A PROGRAM TO PRODUCE BOTH DETAILED AND SCHEMATIC PLOTS OF PROTEIN STRUCTURES [J].
KRAULIS, PJ .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1991, 24 :946-950