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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