[phenixbb] B-factors vs resolution
pafonine at lbl.gov
Wed Apr 6 20:47:31 PDT 2011
I guess in general your statements are valid, but in reality there are
more (important) variables in description of each phenomenon that we may
immediately/intuitively think of. Any discussion about B-factors is
sloppy (although it has a clear mathematical background to start with).
If we convolute it with such fundamental questions you asked we will end
up writing a (chapter for a) book -;)
All the best,
On 4/6/11 1:24 PM, miket at chem.ucla.edu wrote:
> Usually one will describe ordered parts of a protein vs disordered
> parts based on B factors. Is the higher resolution protein more ordered
> and that may have contributed to its stronger diffraction?
> Are the two crystals with different max resolution isomorphous? B-factors contain contributions from both dynamic and static disorder. Your difference in b-factors and resolution are both likely due to the fact that your higher-resolution data comes from a more ordered crystal, not a less dynamic protein. More ordered crystals diffract better, but if the two crystals were grown in the same conditions and the crystals are isomorphous I doubt that there is any difference in the dynamics of the molecules. If you are interested in which parts of your protein are more dynamically disordered you may want to consider (within a single dataset) which atoms have high b-factors relative to the average b-factor for all the atoms in that dataset.
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