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

Jan jan.abendroth at gmail.com
Thu Feb 27 09:50:31 PST 2014

Hi all,
I am refining a pretty high resolution structure (1.65Å, P1) 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.


Jan Abendroth
Emerald BioStructures
Seattle / Bainbridge Island WA, USA
home: Jan.Abendroth_at_gmail.com
work: JAbendroth_at_embios.com

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