Sunanda,
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
Carlos
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
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!!
