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I will try it soon. If it work, I will paste a sumary. Thanks On 4/30/07, Jacqueline Vitali <[log in to unmask]> 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 <[log in to unmask]> 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)