On Tuesday, 13 May, 2014 22:49:15 Kgosisejo, Oarabile wrote:
> Hi all,
>
> We have solved the structure of a protein at 2.3 A with the final R-work and R-free at 0.24 and 0.28, respectively. However, the B-factors are high, with an average of 72. There are 3 molecules in the asymmetric unit and the 3rd molecule is very disordered and I believe is the main contributor to high B-factors.
>
> Also is there a way I can improve the B-factors of my model?
The first thing I suggest is to check what is the Wilson B from your data processing.
If the data intensity distribution already indicates that the expected mean B is high,
then I wouldn't worry about it.
You could then test whether the high B factors are due to bulk motion of the molecules
rather than disorder or large motions of individual residues. Do this by placing each
chain into a single TLS group and refining the structure again in the presence of this
3-group TLS model.
> I was wondering if there is a way I can look at the B-factors of the molecules individually.
If you do go ahead and refine a 3-group TLS model, you can feed it to the
server at
http://skuld.bmsc.washington.edu/parvati/
Among other things, it will create a nice picture of your 3 chains colored by
B factor.
Ethan
>
> Best Regards,
>
> Oarabile Kgosisejo
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
