An introduction to data reduction: space-group determination, scaling and intensity statistics

被引:1185
作者
Evans, Philip R. [1 ]
机构
[1] MRC, Mol Biol Lab, Cambridge CB2 0QH, England
来源
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY | 2011年 / 67卷
基金
英国生物技术与生命科学研究理事会; 英国医学研究理事会;
关键词
X-RAY DATA; MACROMOLECULAR CRYSTALLOGRAPHY; DIFFRACTION DATA; DATA QUALITY;
D O I
10.1107/S090744491003982X
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
This paper presents an overview of how to run the CCP4 programs for data reduction (SCALA, POINTLESS and CTRUNCATE) through the CCP4 graphical interface ccp4i and points out some issues that need to be considered, together with a few examples. It covers determination of the point-group symmetry of the diffraction data (the Laue group), which is required for the subsequent scaling step, examination of systematic absences, which in many cases will allow inference of the space group, putting multiple data sets on a common indexing system when there are alternatives, the scaling step itself, which produces a large set of data-quality indicators, estimation of vertical bar F vertical bar from intensity and finally examination of intensity statistics to detect crystal pathologies such as twinning. An appendix outlines the scoring schemes used by the program POINTLESS to assign probabilities to possible Laue and space groups.
引用
收藏
页码:282 / 292
页数:11
相关论文
共 18 条
[1]   iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM [J].
Battye, T. Geoff G. ;
Kontogiannis, Luke ;
Johnson, Owen ;
Powell, Harold R. ;
Leslie, Andrew G. W. .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2011, 67 :271-281
[2]   Improved R-factors for diffraction data analysis in macromolecular crystallography [J].
Diederichs, K ;
Karplus, PA .
NATURE STRUCTURAL BIOLOGY, 1997, 4 (04) :269-275
[3]   Scaling and assessment of data quality [J].
Evans, P .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2006, 62 :72-82
[4]   AN ALTERNATIVE METHOD OF SOLVING LAYER SCALING EQUATIONS OF HAMILTON ROLLETT AND SPARKS [J].
FOX, GC ;
HOLMES, KC .
ACTA CRYSTALLOGRAPHICA, 1966, 20 :886-&
[5]   TREATMENT OF NEGATIVE INTENSITY OBSERVATIONS [J].
FRENCH, S ;
WILSON, K .
ACTA CRYSTALLOGRAPHICA SECTION A, 1978, 34 (JUL) :517-525
[6]   STRUCTURE OF A SILICON CARBIDE POLYTYPE 24R [J].
HAMILTON, WC ;
ROLLETT, JS ;
SPARKS, RA .
ACTA CRYSTALLOGRAPHICA, 1965, 18 :129-&
[7]   IDENTIFICATION OF HEAVY-ATOM DERIVATIVES BY NORMAL PROBABILITY METHODS [J].
HOWELL, PL ;
SMITH, GD .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1992, 25 :81-86
[9]   Integration, scaling, space-group assignment and post-refinement [J].
Kabsch, Wolfgang .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2010, 66 :133-144
[10]   Intensity statistics in twinned crystals with examples from the PDB [J].
Lebedev, AA ;
Vagin, AA ;
Murshudov, GN .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2006, 62 :83-95