[phenixbb] unusually high B-factors for selected -heavier- atoms

Nathaniel Echols nechols at lbl.gov
Thu Feb 27 10:23:35 PST 2014

Try resetting the B-factors to some suitably low value (i.e. below the
minimum for the entire structure), then refining.  If they're starting out
too high, it may be difficult for the minimizer to bring them down to the
true values (but going in the opposite direction is not a problem).


On Thu, Feb 27, 2014 at 9:50 AM, Jan <jan.abendroth at gmail.com> wrote:

> Hi all,
> I am refining a pretty high resolution structure (1.65Å, *P*1) with two
> tetramers of the protein in the ASU using Phenix dev 1630.
> Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very
> clear. However, several sulphur atoms of the protein, and in particular the
> phosphorous atoms of its cofactor NAD have inflated B-factors, along with
> distinct FoFc peaks. For instance B-factors for a Met with very well
> defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4
> For some of the residues it is comparable when I refine with or without
> TLS groups. I used one group per chain of this compact protein, the
> cofactor is part of each TLS group. Restraints for NAD were generated via
> eLBOW. When I refine the structure in refmac, using either the standard cif
> file or the eLBOW generated one, B-factors remain low.
> Any ideas? I am happy to share the data. It is a SSGCID target and will be
> in the PDB shortly anyway.
> Thanks,
> Jan
>  --
> Jan Abendroth
> Emerald BioStructures
> Seattle / Bainbridge Island WA, USA
> home: Jan.Abendroth_at_gmail.com
> work: JAbendroth_at_embios.com
> http://www.emeraldbiostructures.com
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