A New Generation of Crystallographic Validation Tools for the Protein Data Bank

被引：355

作者：

Read, Randy J. ^{[1
]}

Adams, Paul D. ^{[2
]}

Arendall, W. Bryan, III ^{[3
]}

Brunger, Axel T. ^{[4
,5
,6
,7
,8
]}

Emsley, Paul ^{[9
]}

Joosten, Robbie P. ^{[10
,11
]}

Kleywegt, Gerard J. ^{[12
,13
]}

Krissinel, Eugene B. ^{[13
,14
]}

Luetteke, Thomas ^{[10
,15
]}

Otwinowski, Zbyszek ^{[16
]}

Perrakis, Anastassis ^{[11
]}

Richardson, Jane S. ^{[3
]}

Sheffler, William H. ^{[17
]}

Smith, Janet L. ^{[18
]}

Tickle, Ian J. ^{[19
]}

Vriend, Gert ^{[10
]}

Zwart, Peter H. ^{[2
]}

机构：

[1] Univ Cambridge, CIMR, Cambridge CB2 0XY, England

[2] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA

[3] Duke Univ, Dept Biochem, Durham, NC 27710 USA

[4] Stanford Univ, James H Clark Ctr, Howard Hughes Med Inst, Stanford, CA 94305 USA

[5] Stanford Univ, James H Clark Ctr, Dept Mol & Cellular Physiol, Stanford, CA 94305 USA

[6] Stanford Univ, James H Clark Ctr, Dept Neurol & Neurol Sci, Stanford, CA 94305 USA

[7] Stanford Univ, James H Clark Ctr, Dept Struct Biol, Stanford, CA 94305 USA

[8] Stanford Univ, James H Clark Ctr, Dept Photon Sci, Stanford, CA 94305 USA

[9] Univ Oxford, Dept Biochem, Oxford OX1 3QU, England

[10] Radboud Univ Nijmegen, Med Ctr, NCLMS, CMBI, NL-6525 GA Nijmegen, Netherlands

[11] NKI, Dept Biochem, NL-1066 CX Amsterdam, Netherlands

[12] Uppsala Univ, Biomed Ctr, Dept Cell & Mol Biol, SE-75124 Uppsala, Sweden

[13] European Bioinformat Inst, Cambridge CB10 1SD, England

[14] STFC Rutherford Appleton Lab, Didcot OX11 0QX, Oxon, England

[15] Univ Giessen, Inst Vet Physiol & Biochem, D-35392 Giessen, Germany

[16] Univ Texas SW Med Ctr Dallas, Dallas, TX 75390 USA

[17] Univ Washington, Dept Biochem, Seattle, WA 98195 USA

[18] Univ Michigan, Dept Biol Chem, Inst Life Sci, Ann Arbor, MI 48109 USA

[19] Astex Therapeut, Cambridge CB4 0Q4, England

来源：

STRUCTURE | 2011年 / 19卷 / 10期

基金：

美国国家科学基金会; 英国生物技术与生命科学研究理事会; 瑞典研究理事会; 英国惠康基金;

关键词：

SIDE-CHAIN CONFORMATION; CRYSTAL-STRUCTURE; NUCLEIC-ACIDS; REFINEMENT; LIGAND; PARAMETERS; MODELS; MOLPROBITY; GEOMETRY; PACKING;

D O I：

10.1016/j.str.2011.08.006

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：

This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a now assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.

引用

页码：1395 / 1412

页数：18

共 89 条

[81] Sorting the chaff from the wheat at the PDB [J].