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)
>