Assessing and maximizing data quality in macromolecular crystallography

被引:180
作者
Karplus, P. Andrew [1 ]
Diederichs, Kay [2 ]
机构
[1] Oregon State Univ, Dept Biochem & Biophys, Corvallis, OR 97331 USA
[2] Univ Konstanz, Fac Biol, D-78457 Constance, Germany
关键词
X-RAY DATA; MULTICRYSTAL ANOMALOUS DIFFRACTION; CRYSTAL-STRUCTURE; R-FACTOR; MODEL; IMPROVEMENT; COLLECTION; INCLUSION; SIGNAL; PHENIX;
D O I
10.1016/j.sbi.2015.07.003
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The quality of macromolecular crystal structures depends, in part, on the quality and quantity of the data used to produce them. Here, we review recent shifts in our understanding of how to use data quality indicators to select a high resolution cutoff that leads to the best model, and of the potential to greatly increase data quality through the merging of multiple measurements from multiple passes of single crystals or from multiple crystals. Key factors supporting this shift are the introduction of more robust correlation coefficient based indicators of the precision of merged data sets as well as the recognition of the substantial useful information present in extensive amounts of data once considered too weak to be of value.
引用
收藏
页码:60 / 68
页数:9
相关论文
共 48 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]   Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1 [J].
Akey, David L. ;
Brown, W. Clay ;
Konwerski, Jamie R. ;
Ogata, Craig M. ;
Smith, Janet L. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2014, 70 :2719-2729
[3]  
Bae B, PHAGE T7 GP2 INHIBIT
[4]   High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography [J].
Boutet, Sebastien ;
Lomb, Lukas ;
Williams, Garth J. ;
Barends, Thomas R. M. ;
Aquila, Andrew ;
Doak, R. Bruce ;
Weierstall, Uwe ;
DePonte, Daniel P. ;
Steinbrener, Jan ;
Shoeman, Robert L. ;
Messerschmidt, Marc ;
Barty, Anton ;
White, Thomas A. ;
Kassemeyer, Stephan ;
Kirian, Richard A. ;
Seibert, M. Marvin ;
Montanez, Paul A. ;
Kenney, Chris ;
Herbst, Ryan ;
Hart, Philip ;
Pines, Jack ;
Haller, Gunther ;
Gruner, Sol M. ;
Philipp, Hugh T. ;
Tate, Mark W. ;
Hromalik, Marianne ;
Koerner, Lucas J. ;
van Bakel, Niels ;
Morse, John ;
Ghonsalves, Wilfred ;
Arnlund, David ;
Bogan, Michael J. ;
Caleman, Carl ;
Fromme, Raimund ;
Hampton, Christina Y. ;
Hunter, Mark S. ;
Johansson, Linda C. ;
Katona, Gergely ;
Kupitz, Christopher ;
Liang, Mengning ;
Martin, Andrew V. ;
Nass, Karol ;
Redecke, Lars ;
Stellato, Francesco ;
Timneanu, Nicusor ;
Wang, Dingjie ;
Zatsepin, Nadia A. ;
Schafer, Donald ;
Defever, James ;
Neutze, Richard .
SCIENCE, 2012, 337 (6092) :362-364
[5]   Structure and Function of Human Xylulokinase, an Enzyme with Important Roles in Carbohydrate Metabolism [J].
Bunker, Richard D. ;
Bulloch, Esther M. M. ;
Dickson, James M. J. ;
Loomes, Kerry M. ;
Baker, Edward N. .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2013, 288 (03) :1643-1652
[6]   The interdependence of wavelength, redundancy and dose in sulfur SAD experiments [J].
Cianci, Michele ;
Helliwell, John R. ;
Suzuki, Atsuo .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2008, 64 :1196-1209
[7]   Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy [J].
Dauter, Z ;
Adamiak, DA .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2001, 57 :990-995
[8]   In-house measurement of the sulfur anomalous signal and its use for phasing [J].
Debreczeni, JÉ ;
Bunkóczi, G ;
Ma, QJ ;
Blaser, H ;
Sheldrick, GM .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2003, 59 :688-696
[9]   In-house phase determination of the lima bean trypsin inhibitor:: a low-resolution sulfur-SAD case [J].
Debreczeni, JE ;
Bunkóczi, G ;
Girmann, B ;
Sheldrick, GM .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2003, 59 :393-395
[10]   Improved R-factors for diffraction data analysis in macromolecular crystallography [J].
Diederichs, K ;
Karplus, PA .
NATURE STRUCTURAL BIOLOGY, 1997, 4 (04) :269-275