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
[log in to unmask] 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:[log in to unmask]] On Behalf Of Dominik Possner
> Sent: Thursday, October 08, 2009 5:59 PM
> To: [log in to unmask]
> 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
