As "common people", ... "agreement" don't means for me "equals" ...

So I hope I'm not so "incorrect" if I keep one mind the Wilson B as the model

refinement goes and the average B factor changes with different strategies.

If you are still worry about your Bfactor, you could try TLS, using the right approach could

improve your results.

All the best


On 10/13/16 18:42, Dale Tronrud wrote:
    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".

     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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