Homo crystallographicus--quo vadis?
- PMID: 11937051
- DOI: 10.1016/s0969-2126(02)00743-8
Homo crystallographicus--quo vadis?
Abstract
As macromolecular crystal structures are determined and refined in an increasingly automated fashion, careful assessment of the reliability and quality of the resulting models becomes increasingly important. Here, we analyze various issues related to the reliability and quality of macromolecular crystal structures deposited between 1991 and 2000. We find that the average resolution at which these structures are determined is essentially constant. In line with this observation, the average quality as measured by Ramachandran analysis does not improve as a function of time. On the other hand, an observed decrease of the average discrepancy between free and conventional R values suggests that the fit of model and data is improving. Finally, we present a surprising correlation between the tendency of crystallographers to deposit their experimental data and the free R values of their models.
Similar articles
-
Estimation of the quality of refined protein crystal structures.Protein Sci. 2015 May;24(5):661-9. doi: 10.1002/pro.2639. Epub 2015 Mar 11. Protein Sci. 2015. PMID: 25581292 Free PMC article.
-
Quality of protein crystal structures.Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):941-50. doi: 10.1107/S0907444907033847. Epub 2007 Aug 17. Acta Crystallogr D Biol Crystallogr. 2007. PMID: 17704562
-
Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.FEBS J. 2008 Jan;275(1):1-21. doi: 10.1111/j.1742-4658.2007.06178.x. Epub 2007 Nov 23. FEBS J. 2008. PMID: 18034855 Free PMC article. Review.
-
You are lost without a map: Navigating the sea of protein structures.Biochim Biophys Acta. 2015 Apr;1854(4):258-68. doi: 10.1016/j.bbapap.2014.12.021. Epub 2014 Dec 29. Biochim Biophys Acta. 2015. PMID: 25554228 Free PMC article. Review.
-
His-tag impact on structure.Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):295-301. doi: 10.1107/S0907444906052024. Epub 2007 Feb 21. Acta Crystallogr D Biol Crystallogr. 2007. PMID: 17327666
Cited by
-
PDB_REDO: automated re-refinement of X-ray structure models in the PDB.J Appl Crystallogr. 2009 Jun 1;42(Pt 3):376-384. doi: 10.1107/S0021889809008784. Epub 2009 Apr 3. J Appl Crystallogr. 2009. PMID: 22477769 Free PMC article.
-
Structural Basis of the Oncogenic Interaction of Phosphatase PRL-1 with the Magnesium Transporter CNNM2.J Biol Chem. 2017 Jan 20;292(3):786-801. doi: 10.1074/jbc.M116.759944. Epub 2016 Nov 29. J Biol Chem. 2017. PMID: 27899452 Free PMC article.
-
Homology-based hydrogen bond information improves crystallographic structures in the PDB.Protein Sci. 2018 Mar;27(3):798-808. doi: 10.1002/pro.3353. Epub 2017 Dec 8. Protein Sci. 2018. PMID: 29168245 Free PMC article.
-
A use of Ramachandran potentials in protein solution structure determinations.J Biomol NMR. 2003 Aug;26(4):355-66. doi: 10.1023/a:1024092421649. J Biomol NMR. 2003. PMID: 12815262
-
Implementing an X-ray validation pipeline for the Protein Data Bank.Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):478-83. doi: 10.1107/S0907444911050359. Epub 2012 Mar 16. Acta Crystallogr D Biol Crystallogr. 2012. PMID: 22505268 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials