Maybe it was a bit early to turn on TLS. Pseudomerohedral twinning of a P21 crystal with a and c approximately equal often looks like C2221 with an appropriate transformation of the axes, that could explain the high R-values.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Tue, 16 Feb 2010, Eleanor Dodson wrote: > Two possible points. Could there be a problem with twinning, or spacegroup? > The Rfactors seem rather high.. > > You dont say whether you have a non-crystallographic translation, but it is > faintly possible with 2 molecules that the SG is actually C222 .. > > Or that twinning could be present - look at the ctruncate plots - espec the L > test - for infdications.. > > But re the TLS. You need to set the overall B to the wilson value more or > less. All B factors after REFMAC are relative to that initial starting B > > If you TLSANL you should get back sensible B values in the PDB slot, but of > course any which were restricted to the default value of " will be > corruppted.. > > Eleanor > > > > > Christophe Wirth wrote: > > Dear CCP Community, > > > > > > We have processed protein scattering data in space group C2221 to a > > resolution of 2.4 Å. The structure shows two protein molecules (chain A and > > B) in the asymmetric unit, related by a local two-fold symmetry axis. > > Initial rigid body refinement and subsequent full refinement of isotropic > > atomic B-factors (including all water and ligand molecules; using also > > non-crystallographic symmetry restraints) with the program REFMAC5 yielded R > > and Rfree values of 32.1and 33.9, respectively. > > > > In the next step, after setting the B-factor to 30 Å^2, we carried out 6 > > cycles of TLS refinement followed by 10 cycles of isotropic atomic B-factor > > refinement (two TLS-bodies were defined: the two symmetry-related > > streptavidin chains A and B in the asymmetric unit). As expected, the R and > > Rfree values droped down by 1-2% to 29.6 and 32.5%, respectively. Checking > > the residual atomic B-factors their global average had changed from 13 Å^2 > > (without TLS refinement) to 2 Å^2, the lower B-factor boundary. In fact, all > > atoms in the .pdb file showed B-values of 2 Å^2. > > Interestingly, when we previously processed the same molecule in C2 we did > > not have this TLS problem. > > > > Does anybody has an explanation why after TLS refinement, individual > > B-factor refinement is failing? Is this due to wrongly refined (i.e. too > > large) TLS parameters? Has this been observed before? Any suggestions to > > solve the problem? > > > > Many Thanks, > > > > > > Christophe > > > > > >
