Abstract:
BACKGROUND: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. RESULTS: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. CONCLUSIONS: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.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Carugo Odoi
10.1186/s12859-018-2083-8subject
Has Abstractpub_date
2018-02-23 00:00:00pages
61issue
1issn
1471-2105pii
10.1186/s12859-018-2083-8journal_volume
19pub_type
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