The residual B factors are only one contribution to the mean square displacements, so don't read too much into the numbers. In particular, there is an ambiguity between the trace of T and the mean residual B factor - you can take a chunk out of Tr(T) and give it to all the atoms in the TLS group. TLS may even give a negative contribution. So you do need to run TLSANL.
There is nothing wrong in principle with using TLS at those resolutions, you have to do the normal validation. The 2 global numbers you quote (i.e. R and Rfree) suggest that TLS works well for the 3.2A structure, but leads to more overfitting for the 2.9A structure. But you should look at the maps, play with other TLS models, etc etc HTH Martyn On Mon, 2008-10-20 at 15:17 -0400, Jim Fairman wrote: > Hello everyone, > > I have two structures of a protein bound to two different small > molecules I am trying to refine with REFMAC5 from CCP4 v6.0.0. One > has a resolution of 3.2 and the other has a resolution of 2.9. If I > use TLS refinement parameters on these structures I can get the > Rwork/Rfree down to 19.5/26.4 (3.2 angstrom) and 20.7/27.5 (2.9 > angstrom). Without TLS refinement the Rwork/Rfree are 21.2/29.1 (3.2 > angstrom) 22.2/27.5 (2.9 angstrom). The question I have is in regards > to the Bfactors for these refinements. The average Bfactors are > approximately 100 for the 3.2 angstrom structure and 70 for the 2.9 > angstrom structure (These are the residual Bfactors before using > TLSANL to calculate the full Bfactor with the addition of the TLS > contribution) according to Baverage from CCP4. These Bfactors seem > very high to me, are they acceptable for publication? Is TLS > refinement appropriate in my case with my resolution (I read a paper > from Sandalova et al. 2001 PNAS p 9533-8 where they performed TLS > refinement at 3.0 angstrom resolution)? Any suggestions are welcome! > > Cheers, Jim > > -- > Jim Fairman > Graduate Research Assistant > Department of Biochemistry, Cellular, and Molecular Biology (BCMB) > University of Tennessee -- Knoxville > 216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED] > -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************
