How large B-factors can be in protein crystal structures

BMC Bioinformatics
Oliviero Carugo

Abstract

Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence. A strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps. It is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.

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Citations

Nov 30, 2018·PLoS Computational Biology·Brandon M ButlerS Banu Ozkan
Jul 10, 2019·Proceedings of the National Academy of Sciences of the United States of America·Lalima G AhujaSusan S Taylor
Mar 19, 2020·Briefings in Bioinformatics·Natesh SinghBruno O Villoutreix
Apr 7, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Robert C Penner
May 21, 2020·Scientific Reports·Maayan Bonjack, David Avnir
May 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Chulhwan KwakHyun-Woo Rhee
Aug 12, 2020·Antimicrobial Agents and Chemotherapy·Orville A PembertonYu Chen
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Aug 1, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Eliane BriandOlivier Taboureau
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Dec 11, 2020·Journal of Biomolecular Structure & Dynamics·Austė KanapeckaitėErik Verschueren
Jan 17, 2021·Molecular and Cellular Endocrinology·Thomas Alec LightningJonathan Wolf Mueller
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Jan 5, 2022·Acta Crystallographica. Section D, Structural Biology·Oliviero Carugo

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Methods Mentioned

BETA
X-ray

Software Mentioned

rwcontents
SEQRES
CCP4

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