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

   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.


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 <
> <>> 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
>     < <>> 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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