On 00:00 Fri 31 Jul , Jiamu Du wrote:
> Dear All,
> I am refining a structure of a complex between of 50kD protein and a 20kD
> glycosylated protien. The data is of 2.9 A resolution. The wilson B factor
> is as high as 86.3 A^2.
> The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra
> high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor
> of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the
> electron density looks fine, even the sugar chain is seen clearly.
> My question is:
> 1. How to reduce the B factor to a reasonable level?
> 2. If it can not be redueced, when I published it, is this value acceptable?
> 3. In the same of similar resolutionIs, is there some other structures like
> this situation? A component or a subunit of the protein has a extra high B
> factor as high as 130.
Our group published a paper a few years ago with an average B of 80 A^2
(JMB 328:893 (2003)). One referee had some objections to this, so we
performed analyses of the whole Protein Data Bank for proteins at
2.5-3.0 A (see Fig. 2D in the paper). You may find this figure useful if
you need to convince anyone.
--
Thanks,
Donnie
Donnie Berkholz
P. Andrew Karplus lab
Oregon State University
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