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. 2018 Feb 23;19(1):61.
doi: 10.1186/s12859-018-2083-8.

How large B-factors can be in protein crystal structures

Oliviero Carugo  1   2
Affiliations

How large B-factors can be in protein crystal structures

Oliviero Carugo. BMC Bioinformatics. .

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.

Keywords: Atomic displacement parameter; B-factor; Crystal structure; Matthews coefficient; Protein structure validation.

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The author declares that he has no competing interests.

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Figures

Fig. 1
Fig. 1
PDB entries with missing residues and large B-factors. Frequency with which different types of files have been deposited into the PDB during the last decades
Fig. 2
Fig. 2
B-factors and pcVol. Relationship between B-factors and pcVol (independently of crystallographic resolution)
Fig. 3
Fig. 3
B-factors, resolution and pcVol. Dependence of B-factors on resolution and dependence of resolution on pcVol indicate that the relationship between B-factors and pcVol (see Fig. 2) must be examined in datasets of structures that have similar resolution
Fig. 4
Fig. 4
B-factors-pcVol versus resolution. Relationship between B-factors and pcVol at various resolution ranges, indicated close to each curve
Fig. 5
Fig. 5
B-max examples. B_max values (Å2), at various resolution ranges, for the side chain atoms of lysine, serine, and methionine
See this image and copyright information in PMC

References

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