Jiamu Du schrieb:
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?
Please check out <http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#help.2C_my_protein_has_high_B-factors.21>
2. If it can not be redueced, when I published it, is this value acceptable?
As there's nothing wrong with it, it can be published.
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.
Just look at the B-factors of new PDB entries which have a a resolution worse than 3 A (e.g., membrane proteins) - there are quite a few of those.
HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz
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