I will try it soon. If it work, I will paste a sumary. Thanks
On 4/30/07, Jacqueline Vitali <[EMAIL PROTECTED]> wrote:
Hello, I think it is because the peptide does not have full occupancy. I do not know if it is OK to fix occupancy to 0.5 and do the refinement. That would bring temp factor of peptide close to protein. After you get the responses, can you make a summary and post it in the newsgroup? I think your final refinement will be OK. Jackie Vitali On 4/29/07, Jiamu Du <[EMAIL PROTECTED]> 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) >
-- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
