Multivariate phase combination improves automated crystallographic model building

被引:22
作者
Skubak, Pavol [1 ]
Waterreus, Willem-Jan [1 ]
Pannu, Navraj S. [1 ]
机构
[1] Leiden Univ, NL-2300 RA Leiden, Netherlands
来源
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2010年 / 66卷
关键词
CRYSTAL-STRUCTURE; MACROMOLECULAR STRUCTURES; RECIPROCAL-SPACE; STRUCTURAL BASIS; RESOLUTION; BINDING; REFINEMENT; SOFTWARE; SUBSTRUCTURES; RECOGNITION;
D O I
10.1107/S0907444910014642
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Density modification is a standard technique in macromolecular crystallography that can significantly improve an initial electron-density map. To obtain optimal results, the initial and density-modified map are combined. Current methods assume that these two maps are independent and propagate the initial map information and its accuracy indirectly through previously determined coefficients. A multivariate equation has been derived that no longer assumes independence between the initial and density-modified map, considers the observed diffraction data directly and refines the errors that can occur in a single-wavelength anomalous diffraction experiment. The equation has been implemented and tested on over 100 real data sets. The results are dramatic: the method provides significantly improved maps over the current state of the art and leads to many more structures being built automatically.
引用
收藏
页码:783 / 788
页数:6
相关论文
共 53 条
[1]   Bias reduction in phase refinement by modified interference functions: Introducing the gamma correction [J].
Abrahams, JP .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1997, 53 :371-376
[2]   Methods used in the structure determination of bovine mitochondrial F-1 ATPase [J].
Abrahams, JP ;
Leslie, AGW .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1996, 52 :30-42
[3]   THE CCP4 SUITE - PROGRAMS FOR PROTEIN CRYSTALLOGRAPHY [J].
BAILEY, S .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 :760-763
[4]   CRYSTALLIZATION AND PRELIMINARY-X-RAY DIFFRACTION STUDIES OF AN ALKALINE PROTEASE FROM BACILLUS-LENTUS [J].
BETZEL, C ;
DAUTER, Z ;
DAUTER, M ;
INGELMAN, M ;
PAPENDORF, G ;
WILSON, KS ;
BRANNER, S .
JOURNAL OF MOLECULAR BIOLOGY, 1988, 204 (03) :803-804
[5]   Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate binding module, TmCBM27 [J].
Boraston, AB ;
Revett, TJ ;
Boraston, CM ;
Nurizzo, D ;
Davies, GJ .
STRUCTURE, 2003, 11 (06) :665-675
[6]   Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].
Brunger, AT ;
Adams, PD ;
Clore, GM ;
DeLano, WL ;
Gros, P ;
Grosse-Kunstleve, RW ;
Jiang, JS ;
Kuszewski, J ;
Nilges, M ;
Pannu, NS ;
Read, RJ ;
Rice, LM ;
Simonson, T ;
Warren, GL .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921
[7]   Practical aspects of the integration of different software in protein structure solution [J].
Calderone, V .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2004, 60 :2150-2155
[8]   X-RAY-ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 A - NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR [J].
CARRELL, HL ;
GLUSKER, JP ;
BURGER, V ;
MANFRE, F ;
TRITSCH, D ;
BIELLMANN, JF .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1989, 86 (12) :4440-4444
[9]   Degradation pathway of the phosphonate ciliatine: Crystal structure of 2-aminoethylphosphonate transaminase [J].
Chen, CCH ;
Zhang, H ;
Kim, AD ;
Howard, A ;
Sheldrick, GM ;
Mariano-Dunaway, D ;
Herzberg, O .
BIOCHEMISTRY, 2002, 41 (44) :13162-13169
[10]   General quadratic functions in real and reciprocal space and their application to likelihood phasing [J].
Cowtan, K .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2000, 56 :1612-1621