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Hello Iain, Do check very carefully your diffraction frames. Would you have by "chance" extremely weak lines of spots appearing between your diffraction spots (within lunes)? By extremely weak I mean that can hardly be distinguished from the background on the frames? These features, which are sometimes seen, indicate that you have a lattice that is X times larger than that chosen by autoindexing. Sometimes it is necessary to collect frames where your strong spots have indeed high density in order to view additional spots. If this is the case, the solution is to collect data again in such a way that all diffraction spots appear on the frames, process again with the enlarged cell parameters, and solve by MR. This is just one of the possibilities... Fred. On Mon, 3 Apr 2006, Kerr, Iain wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > I have a dataset that merges very nicely in C2 and I222 (Rmerges ~5% and ~8% > resp), 100% complete to 1.75A. The protein is a TIM-barrel enzyme, a couple > of loops are expected to be in different orientations or missing with respect > to the search model. The diffraction is very clean and appears to represent a > single lattice. The crystal is from a cluster with the same symmetry but > which presented multiple lattices upon diffraction...I just recently managed > to separate a single crystal and was very excited when I saw the diffraction > at the synchrotron.... > > The search model and target sequence have 75% identity and so I was expecting > this to be a routine MR problem. I have mutated the sequence of the search > model anyway to match the target sequence (I got tired of mutating the 25% > non-identical whilst fitting MR solutions..). Two loops are deleted (~30 > resdiues). I find oustanding solutions easily in both spacegroups (no > solutions in I212121), using a number of programs including MOLREP, PHASER > and CNS. None of these refine (REFMAC5 and CNS). For the best solutions I > have fit the model to the density and the refinement does not improve > (currently stuck at Rfree ~44%, Rfactor 40%). There are no obvious large > errors excepting some missing loops residues (~20 still). The best solution > (MOLREP) shows some difference density for one of the missing loops and > waters and overall the maps are good. I have checked for merohedral twinning > (C2) and pseudo-translational NCS; neither are present. > > The indexing output from MOSFLM: > > PENALTY > 7 158 mP 55.55 82.57 82.27 90.1 109.9 109.5 P2,P21 > 6 12 oI 55.55 102.35 116.68 89.6 89.8 90.0 I222,I212121 > 5 10 mC 116.44 116.68 55.55 89.8 118.5 89.8 C2 > 4 8 mC 129.04 102.35 55.55 90.0 115.3 90.3 C2 > 3 5 mC 154.73 55.55 102.35 90.0 131.1 89.8 C2 > 2 2 aP 55.55 82.27 82.57 90.1 109.5 109.9 P1 > 1 0 aP 55.55 82.13 82.57 76.8 70.5 70.4 P1 > > I have tried solutions 6 and 4 (solution 4 is found by HKL2000 and I tried > this first after I222). I have still to try 3 and 5 (3 looks non-standard > with the large beta angle though, ..), which I just noticed when I re-indexed > using MOSFLM today...at least with a similar crystal I have tried P1 and > didn't get an MR solution. > > In lieu of running another hundred MR jobs with multiple spacegroups I was > wondering if anyone had encountered anything like this before ?. Is there > something about C2 I am discounting ? I was expecting this problem to > disappear, having separated a single crystal from the cluster and therefore > removed the additional lattices from the diffraction pattern, but this is > apparently not the problem... > > Thank you very much in advance for any help. > > Cheers, > Iain -- s-mail: F.M.D. Vellieux (B.Sc., Ph.D.) Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: (+33) (0) 438789605 Fax: (+33) (0) 438785494 e-mail: [EMAIL PROTECTED]
