How large B-factors can be in protein crystal structures

Area of Science:

• Structural Biology
• Biophysics
• Crystallography

Background:

• Protein crystal structures are often over-interpreted.
• Atomic B-factors are routinely refined without upper limits, leading to speculative atomic positions.
• High B-factors (>100 Ų) indicate atoms undetected in electron density maps.

Purpose of the Study:

• To develop a strategy for defining upper limits for atomic B-factors in protein crystal structures.
• To identify protein crystal structures that may be over-interpreted due to inflated B-factors.

Main Methods:

• Analyzed protein crystal structures from the Protein Data Bank (pre-2008).
• Determined the relationship between average B-factor and solvent volume percentage (pcVol).
• Extrapolated this relationship to pcVol = 100% to define a maximum B-factor limit (B_max).

Main Results:

• A method to establish an upper B-factor limit (B_max) was developed.
• Identified protein crystal structures with average B-factors exceeding B_max.
• These structures require cautious interpretation by users of the Protein Data Bank.

Conclusions:

• A strategy for setting B-factor upper limits (B_max) is presented.
• Structures with B-factors > B_max should be critically evaluated.
• This approach helps prevent scientifically deleterious over-interpretations of structural data.