Jan, could it be radiation damage? - that would affect the heavier atoms first/most ... To prove/disprove, use zero-dose extrapolation and re-refine. Kay Am 27.02.14 20:13, schrieb [email protected]:

Date: Thu, 27 Feb 2014 09:50:31 -0800 From: Jan To: PHENIX user mailing list Subject: [phenixbb] unusually high B-factors for selected -heavier- atoms Message-ID: Content-Type: text/plain; charset="iso-8859-1"

Hi all, I am refining a pretty high resolution structure (1.65?, 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.

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