unusually high B-factors for selected -heavier- atoms
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. 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
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).
-Nat
On Thu, Feb 27, 2014 at 9:50 AM, Jan
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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Hi Jan, have a look at pages 8-14 here: http://phenix-online.org/presentations/faq.pdf If this does not help please send me model and data files (as well as ligand CIF files, if any) and I will help to solve this problem one way or another. This question is quite typical and in most cases the recipe above solves the problem. Problem of large B (that Nat mentioned) is a possibility, though B-factors should be above 100 to cause that sort of problems. Pavel On 2/27/14, 9:50 AM, Jan 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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participants (3)
-
Jan -
Nathaniel Echols -
Pavel Afonine