The Wilson B and the average B are calculated differently so there
is no reason to expect that they will be equal. The derivation of
the Wilson B assumes that all B's in the model are equal. When there
really is a spread in the actual values in the PDB file the derivation
isn't really valid. Usually the average B will be larger than the
Wilson B because the atoms with very large B values will have stopped
diffracting at lower resolution than the shells used to calculate
the Wilson B.
If you want to compare you model to your Wilson B you should calculate
Fcalc from your PDB and calculate a Wilson B from those. The numbers
will almost certainly match. The refinement program has to be pretty
screwed up to cause the overall B of the model not to match the Fobs.
Dale Tronrud
[email protected] wrote:
Dear Dominik,
I do not see any problems with a mosaicity of 0.48°. Also the Wilson B-factor of 30.34 of
your data is ok, indicating no problems with the processing. Your problem is that the
average REFINED b-factor is much higher than your "observed" average b. The
first thing I would do is to calculate the average b-factor for your protein only. Adding
a lot of high b-factor water molecules can increase your average b-factor significantly.
If the average- and wilson B are then in the same ballpark, I would not worry too much
and rahter have a look at my waters to see if some of them could be removed. If the
descrepancy is still there for the protein only, I would look at the way the b-factors
are refined (individual, grouped, TLS, weights, restraints etc.) to see if there is a
problem somewhere.
Best regards,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Dominik
Possner
Sent: Thursday, October 08, 2009 5:59 PM
To: [email protected]
Subject: [ccp4bb] temperature factors, mosaicity and wilson plot
Hi,
I recently solved the structure of a mutant protein that contains a single amino acid substitution.
Here are some data about the mutant:
resolution: 2.65 A
completeness: 99.9 % (100.0 %)
Rwork/free: 22.3/27.8 %
Rsym 15.6 (47.7) %
avg. mosaicity: 0.48°
now whats confusing me:
Wilson b-factor: 30.34 A^2
Overall mean b-factor: 55.92 A^2
My questions are the following:
Where could the large difference of the b-factors come from? As noted, the crystal shows a mosaicity of avg. 0.48°.
Is there a way I could evaluate whether the high b-factors are completely
explained by the high mosaicity? What other factors could explain the high
b-factors? Does the b-factor correlate that clearly with the resolution?
I used XDS for data processing and REFMAC for refinement. Does either of these
programs consider the mosaicity so that i could exclude that the b-factors
origin from the mosaicity?
Thanks,
Dominik
