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
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 <pafon...@gmail.com
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
<de...@daletronrud.com <mailto:de...@daletronrud.com>> wrote:
I'm sorry but I don't understand what your problem is. Do
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.
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
> 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
> the B factors.
> Any help is appreciated.
> Thank you!!