This reminds me of a potential problem with low resolution data that
you might have: if any strong reflection (or a couple of them) is only
partially measured, because it is in the half-shadow of the beamstop,
then the measured intensity is too small, which in turn results in a
too low overall B-factor. For bulk-solvent correction, the Bsol is
then usually at its lower limit and the overall B might still be too
low. An easy way to check this is to re-run TLS, bulk solvent
correction and refinement excluding the lowest resolution shell (say,
use 20, 30, 40 A instead of 50 A or 100 A, or whatever) and check
whether the overall Bs are still too small. If not, you could try to
find out which reflections are the culprits and exclude them.
Good luck,
Dirk.
Am 03.12.2008 um 12:17 schrieb Eleanor Dodson:
Then I think it is the problem of fitting the TF parameters into low
resolution data.
REFMAC tries to use the lowest ( < 9A) data to get the solvent B
factor and then after applying that correction to get an overall B.
Many Wilson plot programs only use the data from 4A out, with the
belief that the lower resolution stuff is so entangled with cell
content distribution and solvent scattering that it is un-scramble-
able.
For higher resolution data sets the two methods usually agree pretty
well. At low resolution I am not sure which is the better.. Arp/wARP
tries to be smarter but onerarely uses it at that resolution..
So it is a bit like comparing apples and pears - I doubt if any
sensible conclusions can be drawn.
Eleanor
Wim Burmeister wrote:
Eleanor Dodson a écrit :
Wim Burmeister wrote:
Dear all,
I have a 3 A structure refined with REFMAC which gives
consistently average atomic B-factors of 40 A2, whereas the B
factor from a Wilson plot is about 60 A2. Is there any
explanation for such a discrepancy?
There are no obvious problems:
No twinning, spacegroup P21 with two molecules in the asu, no
proper ncs symmetry. No pathologic Wilson plot, complete and
redundant dataset (although collected on several crystals with
serious problems due to radiation damage).
Interestingly, the Wilson plot of the Fcalc values is about 60 A2
as for Fobs in the output dataset.
Yours
Wim
Are you using TLS? B factors in the pdb are always relativre to
the TLS paramters unless you have run TLSANL
Eleanor
Dear Eleanor, there is no TLS used.
Yours
Wim
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