Protein Data Bank depositions from synchrotron sources

被引:22
作者
Jiang, JS [1 ]
Sweet, RM [1 ]
机构
[1] Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA
关键词
PDB deposition; synchrotron radiation facilities; structural genomics;
D O I
10.1107/S0909049504013792
中图分类号
TH7 [仪器、仪表];
学科分类号
0804 ; 080401 ; 081102 ;
摘要
A survey and analysis of Protein Data Bank (PDB) depositions from international synchrotron radiation facilities, based on the latest released PDB entries, are reported. The results (http://asdp.bnl.gov/asda/Libraries/) show that worldwide, every year since 1999, more than 50% of the deposited X-ray structures have used synchrotron facilities, reaching 75% by 2003. In this web-based database, all PDB entries among individual synchrotron beamlines are archived, synchronized with the weekly PDB release. Statistics regarding the quality of experimental data and the refined model for all structures are presented, and these are analysed to reflect the impact of synchrotron sources. The results confirm the common impression that synchrotron sources extend the size of structures that can be solved with equivalent or better quality than home sources.
引用
收藏
页码:319 / 327
页数:9
相关论文
共 18 条
[1]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242
[2]   PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES [J].
BERNSTEIN, FC ;
KOETZLE, TF ;
WILLIAMS, GJB ;
MEYER, EF ;
BRICE, MD ;
RODGERS, JR ;
KENNARD, O ;
SHIMANOUCHI, T ;
TASUMI, M .
JOURNAL OF MOLECULAR BIOLOGY, 1977, 112 (03) :535-542
[3]   FREE R-VALUE - A NOVEL STATISTICAL QUANTITY FOR ASSESSING THE ACCURACY OF CRYSTAL-STRUCTURES [J].
BRUNGER, AT .
NATURE, 1992, 355 (6359) :472-475
[4]   Free R value: Cross-validation in crystallography [J].
Brunger, AT .
MACROMOLECULAR CRYSTALLOGRAPHY, PT B, 1997, 277 :366-396
[5]   Automated crystallographic system for high-throughput protein structure determination [J].
Brunzelle, JS ;
Shafaee, P ;
Yang, XJ ;
Weigand, S ;
Ren, Z ;
Anderson, WF .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2003, 59 :1138-1144
[6]   Structural genomics: A pipeline for providing structures for the biologist [J].
Chance, MR ;
Bresnick, AR ;
Burley, SK ;
Jiang, JS ;
Lima, CD ;
Sali, A ;
Almo, SC ;
Bonanno, JB ;
Buglino, JA ;
Boulton, S ;
Chen, H ;
Eswar, N ;
He, GS ;
Huang, R ;
Ilyin, V ;
McMahan, L ;
Pieper, U ;
Ray, S ;
Vidal, M ;
Wang, LK .
PROTEIN SCIENCE, 2002, 11 (04) :723-738
[7]   ACCURATE BOND AND ANGLE PARAMETERS FOR X-RAY PROTEIN-STRUCTURE REFINEMENT [J].
ENGH, RA ;
HUBER, R .
ACTA CRYSTALLOGRAPHICA SECTION A, 1991, 47 :392-400
[8]   Synchrotron radiation facilities [J].
Helliwell, JR .
NATURE STRUCTURAL BIOLOGY, 1998, 5 (Suppl 8) :614-617
[9]   Automated protein crystal structure determination using ELVES [J].
Holton, J ;
Alber, T .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (06) :1537-1542
[10]  
JIANG JS, 2004, UNPUB ACTA CRYST D, V60