Hi Dirk,
this seems to be the case indeed (*):
Resolution_range Wilson_B Average_B Number_of_structures
0.00 - 1.00 9.77 13.11 94
1.00 - 1.25 10.58 16.44 401
1.25 - 1.50 13.50 19.14 1050
1.50 - 1.75 17.20 21.76 3600
1.75 - 2.00 22.27 26.82 5510
2.25 - 2.50 35.70 39.42 3385
2.50 - 2.75 43.71 44.73 2844
2.75 - 3.00 53.86 51.94 1628
3.00 - 3.25 65.11 60.76 780
3.25 - 3.50 81.69 78.70 165
3.50 - 3.75 92.67 88.84 100
3.75 - 4.00 111.83 102.29 30
(*) Wilson_B is computed using phenix.model_vs_data
Average_B is computed using phenix.model_vs_data from PDB file
(TLS is accounted for)
Structures selected such that the recomputed R-factor matches the
one in PDB file header within 1%.
I've never looked at this statistics before, so I'm a bit surprised - I
was expecting a larger discrepancy between Wilson B and average B at low
resolution. Although this is probably because PHENIX uses Peter Zwart's
likelihood-based Wilson B estimation (Peter - what's the reference?),
which is supposed to be better.
Pavel.
On 7/1/10 12:52 AM, Dirk Kostrewa wrote:
Dear Murugan,
at higher resolution, the Wilson plot captures mainly the contribution
of atoms with lower B-factors which leads to a systematic
underestimation of the true B-factor distribution. Accordingly, the
average B-factor of refined structures tend to be higher then the
Wilson B-factor, at least in my experience. In your case, it is the
other way around. One possible problem could be, apart from the fit of
the Wilson plot as James Holton suggested, that you have reflections
at very low resolution with underestimated intensities due to cut
overloads or measurement in the half-shadow of the beamstop. This
would result in a too low overall B-factor for the model in order to
try to fit the usually stronger low resolution reflections at the cost
of the weaker high resolution data. One quick check of this hypothesis
is to cut the low resolution at, say, 10 A instead of 50 A and run a
test-refinement. If this results in more realistic model B-factors,
you should have a closer look at the low resolution data and exclude
the ill-measured ones.
Best regards,
Dirk.
Am 30.06.10 19:31, schrieb Vandu Murugan:
Dear all,
If one could find a difference of more than 15 between Wilson B
factor of the data ( 55) and Mean B factor of the structure, (30)
what could be the possible reasons? I am seeing it in my structure.
Could someone tell me why it could be?? Thanks in advance.
Yours faithfully,
Murugan
