Hi Jiamu,
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
