It seems to be common for people to make the incorrect assumption that the average of the atomic B factors in the PDB file should equal the Wilson B. The Wilson B is actually a weighted average of the individual B factors where the weighting is rather mysterious, but the small B factors have much higher weight than the larger ones. While the Wilson B is simply a property of your data set the average of the atomic B factors will also depend on choices you have made in building your model.
In your case the core of your protein does have B factors that match your Wilson B. The fact that you have loops that have larger B's doesn't really mean there is a problem, because those atoms don't contribute much to the higher resolution reflections and don't come into the calculation of the Wilson B. The average of your B factors will increase if you choose to build model for more disordered regions, while the Wilson B will, of course, remain the same. The average B factor will be larger, for example, if you are more aggressive in building water molecules. This does not indicate a problem but is an unavoidable consequence of your choice to take more risks. Dale On 10/13/2016 12:16 AM, sunanda williams wrote: > Sorry for not making the problem clear! > The overall B factor for the 3.0 A structure is around 98.00 A*2. Most > of the deposited structures in the PDB site around this resolution > has an av B around 70 A*2.... > All other statistics looks fine. I got a warning message while trying to > upload the structure in PDB that 98 was higher than the norm! > The reason why the structure has such a high B factor could be due to > disordered loops... All the same I was wondering how acceptable this > structure would be to picky reviewers.. > And 'better the B factors' means bring them down...sorry couldn't phrase > it 'better'! I am going to try doing refinement with group B factors! > Would that help? > Thanks Robbie, I think this I need to make the best of the model I have. > Prof. Sekar will try PDB_redo..Thanks! > > > > On Thu, Oct 13, 2016 at 11:41 AM, Pavel Afonine <pafon...@gmail.com > <mailto:pafon...@gmail.com>> wrote: > > I fully agree with Dale in not understanding what the problem is. > Perhaps I have a better chance if you clearly explain what exactly > you mean by "is there any way to better the B factors". > Pavel > > > On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud > <de...@daletronrud.com <mailto:de...@daletronrud.com>> wrote: > > I'm sorry but I don't understand what your problem is. Do > you think > the B factors are too small for a 3A data set? A range of 70 to > 75 is a > little smaller than usual but probably not out of bounds. > > Dale Tronrud > > On 10/12/2016 7:59 PM, sunanda williams wrote: > > Hi all, > > I have a structure at 3.0 A and R/Rfree of 24/28. The mean B > value is > > around 98. The B value is especially high at the N terminus > and two loop > > regions (around 120-150 AA). > > The rest of the structure averaged around 70-75. Has anyone > faced such a > > scenario? How reliable is the structure and is there any way > to better > > the B factors. > > Any help is appreciated. > > Thank you!! > > >
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