B-anisotropic and bulk solvent correction
Simon Terzyan
terzyans at OMEGA.OMRF.OUHSC.EDU
Fri Nov 12 17:06:43 EST 1999
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Dear X-PLOR users,
I am in the late stages of refinement of a 2.3 angstrom Fab
structure
in P212121 with 2 molecules in the assymetric part. The R factors after
positional and B individual refinements in the resolution range 8.-2.3 A
are R=0.237 and Rfree= 0.314.
When I am using bulk solvent correction they become ( 25-2.3A) 0.231 and
0.303, correspondingly. But after it the electron density for the
residues on the surface of the molecules is worse than before.
Refinement of anisotropic B_overall ( without bulk solvent correction,
8-2.3A ) gives R factors 0.214 and 0.289. Further bulk solvent
correction and positional and B individual refinemt drops the R factors
to 0.199 and 0.266. As it was already mentioned in one of previos
letters from Christelle Sabatier (Message-ID:
<v03007800b02211264fa6@[128.206.29.205]>) this refinement increases the
mean value of B factors. And furthermore, if I go for a second cycle
then the B factors increase more.
I have used also suggestion of Ethan A Merritt and it seems that by this
way it is possible to overcome the problem. Although, the final
R-factors are about the same as without B anisotropic refinement.
So my question is, why B individual factors are growing when one tries
to use both B-anisotropic refinement and bulk solvent correction. Is
there a bug in X-plor 3.851?
If anyone has any thoughts on this I would appreciate it.
--
Dr. Simon Terzyan
Crystallography Department of OMRF
tel: (405) 2717543 fax: (405) 2713980
email:terzyans at omega.omrf.ouhsc.edu
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<html>
<br>Dear X-PLOR users,
<p> I am in the late stages of refinement
of a 2.3 angstrom Fab structure
<br>in P212121 with 2 molecules in the assymetric part. The R factors after
positional and B individual refinements in the resolution range 8.-2.3
A are R=0.237 and Rfree= 0.314.
<br>When I am using bulk solvent correction they become ( 25-2.3A) 0.231
and 0.303, correspondingly. But after it the electron density
for the residues on the surface of the molecules is worse than before.
<br>Refinement of anisotropic B_overall ( without bulk solvent correction,
8-2.3A ) gives R factors 0.214 and 0.289. Further bulk solvent correction
and positional and B individual refinemt drops the R factors to 0.199 and
0.266. As it was already mentioned in one of previos letters from Christelle
Sabatier (Message-ID: <v03007800b02211264fa6@[128.206.29.205]>) this
refinement increases the mean value of B factors. And furthermore, if I
go for a second cycle then the B factors increase more.
<br>I have used also suggestion of Ethan A Merritt and it seems that by
this way it is possible to overcome the problem. Although, the final R-factors
are about the same as without B anisotropic refinement.
<br>So my question is, why B individual factors are growing when one tries
to use both B-anisotropic refinement and bulk solvent correction.
Is there a bug in X-plor 3.851?
<br>If anyone has any thoughts on this I would appreciate it.
<br>
<pre>--
Dr. Simon Terzyan
Crystallography Department of OMRF
tel: (405) 2717543 fax: (405) 2713980
email:terzyans at omega.omrf.ouhsc.edu</pre>
</html>
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