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

Kay Diederichs kay.diederichs at uni-konstanz.de
Thu Feb 27 11:36:08 PST 2014


could it be radiation damage? - that would affect the heavier atoms 
first/most ...

To prove/disprove, use zero-dose extrapolation and re-refine.


Am 27.02.14 20:13, schrieb phenixbb-request at phenix-online.org:
> Date: Thu, 27 Feb 2014 09:50:31 -0800
> From: Jan <jan.abendroth at gmail.com>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: [phenixbb] unusually high B-factors for selected -heavier-
> 	atoms
> Message-ID: <D87628CC-A657-4B4C-B14F-C230C0C2EF00 at gmail.com>
> 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

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