*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Apart from what the others already said, I think this could also be
some anomaly in the calculation of B values. Just like the weight for
geometric restraints needs to be adjusted for each individual case,
the weight for the B value calculation needs to be adjusted as well,
such that the rmsd's come to lie within a certain range. That was
particularly important for X-plor/CNS, and I think it somewhat still
is for Refmac. Perhaps, your weight is too high. This will give you
roughly the same average B value as with lower weights, but the
rmsd's will be high, because some atoms have very high B values, and
some have very low B values (i.e. 2.0). Try reducing the weight and
see if that solves your problem.
Now, before you ask what a good range is for rmsd's for B values, I
don't know what the current consensus is (as if our field ever
reaches a consensus on anything). Perhaps, others can offer some
enlightening advice.
Best - MM
On Apr 20, 2006, at 10:23 AM, Segura Pena, Dario wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Dear all,
Recently I obtained protein crystal that grew in 60 % MPD. The crystal
diffracts very well to 1.5 Ǻ. It seems that an MPD molecule is
in the
active center of the enzyme, however the atom C2 of the MPD
molecule has a
B factor of 2 after several cycles of refinement with Refmac.
Does anybody have any idea why the there is such a low B factor for
this
atom?.The electron density for the region corresponding to the atom
C2 of
the MPD molecule is visible at 5 sigma level in a 2fo-fc map while
at 3
sigma level there is not electron density for the rest of the
molecule.
I will appreciate any ideas or suggestions.
Sincerely,
Dario
------------------------------------------------------------------------
--------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
