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Re: [ccp4bb]: b-factors, tls-refinement

I have had a similar experience approximatly 2 years ago, with a DNA protein molecule.  In the TLS refienment, using two domains each containing a HTH motif, I found that my r and rfree both moved around 5%, with the average b-factor rising from around 45 to 60.  When I inspect the overall b-factors, what I see is that one domains average was around 80 while the other domain was around 45 still.  As to the correctness, it seemed to make sense in my case, due to the overall biochemistry of the two domains and their respective interaction with the DNA.  I would not only look at the TLS definition it's self, but also look to see if your respective loops would make sense biologically as having less rigid positions in your structure.  At least that would give a secound argument.                             &! nbsp;                      
  (as a none ccp4 statement, I would like to say that the interogation practices the various governing bodies use, especially in places such as Guantanimo bay, are inhumane.  They do not cause physical harm, but they leave long lasting psychological truama's within individuals that prevent them from functioning normally far removed from any information gathering that occurs.  They also prove hard to remove, and if a mistake is made, an innocent person years of their life removed, even after the interrogations due to stress and other associated problems.                                         !            &nbs p;                                 Stephan L. Watkins                                                                                                                                  &! nbsp;                                                                            Ganapathy Sarma <sarma@odysseus.als.orst.edu> wrote:
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Dear all,

My apologies, first, for sending the blank email by mistake.

Dirk, I have also experienced a similar behavior in the refinement of a
structure that came out of our lab recently. In our case, it was a 2.6 A
structure with the R and Rfree at 27.3 and 31.5 % respectively after CNS
refinements. The average B-factors were 65 A*2. The CNS refinements
indicated crystal anisotropy, because of which we tried REFMAC with TLS
refinement. Using TLS, the R and Rfree dropped to 25.1 and 30.2
respectively with the average B-factors increasing to 80 A*2!

At this point, to assess the validity of the B-factors, CNS refinement was
carried out on the model. The B-factors dropped to 65 A*2. Combining the
overall anisotropic scale f! actors with the average B-factor lead us to the
insight that the effective average B-factors are different in the three
directions (75, 75 and 47 A*2 along the x, y and z-directions
respectively). The average B-factors are complex and its
calculation/definition, I would say, is somewhat program dependent.

In your case, I am curious about the drop of 5%. During your CNS
refinements, did you have anisotropic scaling for the B-factor refinement.
Also, since you have atleast three chains in the asu, did you have NCS
restraints for B-factors that led to a lower average B-factor of 45 A*2
for all the chains?


On Fri, 11 Apr 2003, Dirk Reinert wrote:

> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
> hi all,
> i am trying out tls-refinement after refinement in cns remained static. (the
> statistics for the ! dataset i am using are excellent and the resolution limit
> is 2.1 a.) the r-factors (in cns) were about 24 (r) and 28 (rfree) and the
> b-factors for the different chains in asu were around 45. after doing
> tls-refinement in refmac5 r and rfree dropped by 5%, respectively, and the
> total bs for two of the chains are now about 80 (!). has anyone experienced
> such an increase of the b-factors or has any comments on that, as i am a bit
> worried on the correctness of what i am doing.
> thanks in advance, dirk.
> --
> Dirk Reinert
> Universität Freiburg (FRG)
> Institut für Organische Chemie und Biochemie
> Alberstr. 21
> D-79104 Freiburg
> Phone: +49 761 2036088
> Fax: +49 761 2036161


Ganapathy N. Sarma.
Department of Biochemistry and Biophysics
Oregon State University
Tel: (541)737-3196

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