A test of enhancing model accuracy in high-throughput crystallography - PubMed (original) (raw)

Comparative Study

doi: 10.1007/s10969-005-3138-4.

Wolfram Tempel, Jane S Richardson, Weihong Zhou, Shuren Wang, Ian W Davis, Zhi-Jie Liu, John P Rose, W Michael Carson, Ming Luo, David C Richardson, Bi-Cheng Wang

Affiliations

• PMID: 15965733
• DOI: 10.1007/s10969-005-3138-4

Comparative Study

A test of enhancing model accuracy in high-throughput crystallography

W Bryan Arendall 3rd et al. J Struct Funct Genomics. 2005.

Abstract

The high throughput of structure determination pipelines relies on increased automation and, consequently, a reduction of time spent on interactive quality control. In order to meet and exceed current standards in model accuracy, new approaches are needed for the facile identification and correction of model errors during refinement. One such approach is provided by the validation and structure-improvement tools of the MOL: PROBITY: web service. To test their effectiveness in high-throughput mode, a large subset of the crystal structures from the SouthEast Collaboratory for Structural Genomics (SECSG) has used protocols based on the MOL: PROBITY: tools. Comparison of 29 working-set and 19 control-set SECSG structures shows that working-set outlier scores for updated Ramachandran-plot, sidechain rotamer, and all-atom steric criteria have been improved by factors of 5- to 10-fold (relative to the control set or to a Protein Data Bank sample), while quality of covalent geometry, R(work), R(free), electron density and difference density are maintained or improved. Some parts of this correction process are already fully automated; other parts involve manual rebuilding of conformations flagged by the tests as trapped in the wrong local minimum, often altering features of functional significance. The ease and effectiveness of this technique shows that macromolecular crystal structures from either traditional or high-throughput determinations can feasibly reach a new level of excellence in conformational accuracy and reliability.

PubMed Disclaimer

Similar articles

• Life in the fast lane for protein crystallization and X-ray crystallography.
  Pusey ML, Liu ZJ, Tempel W, Praissman J, Lin D, Wang BC, Gavira JA, Ng JD. Pusey ML, et al. Prog Biophys Mol Biol. 2005 Jul;88(3):359-86. doi: 10.1016/j.pbiomolbio.2004.07.011. Prog Biophys Mol Biol. 2005. PMID: 15652250 Review.
• The high-throughput protein-to-structure pipeline at SECSG.
  Liu ZJ, Tempel W, Ng JD, Lin D, Shah AK, Chen L, Horanyi PS, Habel JE, Kataeva IA, Xu H, Yang H, Chang JC, Huang L, Chang SH, Zhou W, Lee D, Praissman JL, Zhang H, Newton MG, Rose JP, Richardson JS, Richardson DC, Wang BC. Liu ZJ, et al. Acta Crystallogr D Biol Crystallogr. 2005 Jun;61(Pt 6):679-84. doi: 10.1107/S0907444905013132. Epub 2005 May 26. Acta Crystallogr D Biol Crystallogr. 2005. PMID: 15930619
• MolProbity: all-atom structure validation for macromolecular crystallography.
  Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. Chen VB, et al. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21. doi: 10.1107/S0907444909042073. Epub 2009 Dec 21. Acta Crystallogr D Biol Crystallogr. 2010. PMID: 20057044 Free PMC article.
• Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.
  Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS. Headd JJ, et al. J Struct Funct Genomics. 2009 Mar;10(1):83-93. doi: 10.1007/s10969-008-9045-8. Epub 2008 Nov 11. J Struct Funct Genomics. 2009. PMID: 19002604 Free PMC article.
• Current state of automated crystallographic data analysis.
  Lamzin VS, Perrakis A. Lamzin VS, et al. Nat Struct Biol. 2000 Nov;7 Suppl:978-81. doi: 10.1038/80763. Nat Struct Biol. 2000. PMID: 11104005 Review.

Cited by

• The first agmatine/cadaverine aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus.
  Cacciapuoti G, Porcelli M, Moretti MA, Sorrentino F, Concilio L, Zappia V, Liu ZJ, Tempel W, Schubot F, Rose JP, Wang BC, Brereton PS, Jenney FE, Adams MW. Cacciapuoti G, et al. J Bacteriol. 2007 Aug;189(16):6057-67. doi: 10.1128/JB.00151-07. Epub 2007 Jun 1. J Bacteriol. 2007. PMID: 17545282 Free PMC article.
• The distal pocket histidine residue in horse heart myoglobin directs the O-binding mode of nitrite to the heme iron.
  Yi J, Heinecke J, Tan H, Ford PC, Richter-Addo GB. Yi J, et al. J Am Chem Soc. 2009 Dec 23;131(50):18119-28. doi: 10.1021/ja904726q. J Am Chem Soc. 2009. PMID: 19924902 Free PMC article.
• Recommendations of the wwPDB NMR Validation Task Force.
  Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL. Montelione GT, et al. Structure. 2013 Sep 3;21(9):1563-70. doi: 10.1016/j.str.2013.07.021. Structure. 2013. PMID: 24010715 Free PMC article.
• Studying and polishing the PDB's macromolecules.
  Richardson JS, Richardson DC. Richardson JS, et al. Biopolymers. 2013 Mar;99(3):170-82. doi: 10.1002/bip.22108. Epub 2012 Sep 29. Biopolymers. 2013. PMID: 23023928 Free PMC article. Review.
• A new generation of crystallographic validation tools for the protein data bank.
  Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. Read RJ, et al. Structure. 2011 Oct 12;19(10):1395-412. doi: 10.1016/j.str.2011.08.006. Structure. 2011. PMID: 22000512 Free PMC article.

References

1. 1. Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1937-40 - PubMed
2. 1. Proteins. 2000 Aug 15;40(3):389-408 - PubMed
3. 1. Acta Crystallogr D Biol Crystallogr. 2002 Oct;58(Pt 10 Pt 2):1772-9 - PubMed
4. 1. Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2240-9 - PubMed
5. 1. Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):849-61 - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Ovid Technologies, Inc.
  • Springer