| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | | |
|
|
Re: [ccp4bb] extra high B factor |
|
CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 30 April 2007Subject: Re: extra high B factor From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU Date: 2007-04-30 is the high B-value of your protein due to motions, which are not modeled appropiately ? Which program by the way are you using for refinement ? Then the TLSMD server might help you here. Monomer or multimer in the asu ? NCS used, if so checked that they actually follow NCS and you're not forcing them ? How does your difference density map look like around your ligand ? Jürgen Jiamu Du wrote: > Dear All: > I am refining a protein-peptide complex struture at 2.6 angstrom > resolution. > The data was obtain from a co-crystal and the wilson B factor of the > data is about 70. > The affinity between protein and peptide is about 10E-7 to 10E-8 molar. > Protein fragment of the structure has a common B facor about 50. > But surprisingly, the average B factor of the peptide is as high as > 130, although the peptide can be clearly traced from the the electron > density map. All residues of the peptide have such a high B factor. > My question is how can I reduce the abnormal high B factor to a common > level or if this high B factor acceptable. > And another question is if this high B fator will influence the final > refiment level. > > Thanks. > > -- > Jiamu Du > State Key Laboratory of Molecular Biology > Institute of Biochemistry and Cell Biology Shanghai Institutes for > Biological Sciences > Chinese Academy of Sciences (CAS) -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 30 April 2007 |
| ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd |