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Re: [ccp4bb] difficulties to determine the space group |
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CCP4bb navigationCCP4bb <-- 2007 <-- May 2007 <-- 08 May 2007Subject: Re: difficulties to determine the space group From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2007-05-08 Leaving aside the screwyness presumably it processed as PG422 OK. Checks 1) NCS translation? 2) Twinned? ( both can be checked with SFCHECK - it will tell you if there is pseudo translation and make a guess at whether there is twinning.. The log file is terse but should give you this info.) Then check axial reflections - scala has given an indication, or use: mtzutils hklin scala-op.mtz AXIS h00 00l This will list the axial reflections and might help you decide P41 21 2 or P43 21 2 or P4i 2 2 Are you likely to have one or two molecule in PG 422? It is possible there is pseudo symmetry mixing up the 21 or 2 axes but that isnt consistent with having a self rotation function which shoews anything other than the crystal symmetry.. Eleanor Schneider Sabine wrote: > > Hi everyone, > > > > I have got a dataset to 2.8A which according to Mosflm/XDS have P4 > (etc) or P222 (etc) symmetry with a=b=71 c = 228 (same penalty in both > programs). > > > > According to Matthews coefficient and self-rotation function (GLRF and > Molrep at kappa=180) I have 2 molecules in ASU, related through NCS. > Looking at systematic absences in hklview it seem to be P4. I > initially processed the data in P4 and pointless suggested P41 21 > 2/P43 21 2, so I reprocessed the data in P41 21 2. > > > > As a molecular replacement model I used an ensemble of 3 structures > each with (unfortunately) only ~20% sequence ID and search was carried > out with one molecule. Residues that in the search model that were not > identical were stripped back to C gamma by chainsaw and the B-factors > were reset to 10 (mc) and 20 (sc). > > > > I run Phaser searching in all alternative space groups and 2 molecules > in the ASU and it found a solution in P43 21 2. When I input the data > again in P43 21 2 into Phaser searching all spacegroups I get a > solution in P43 2 2? The difference in the two solutions is > association of the two molecules in the asymmetric unit along b. I > reprocessed the data in P43 2 2 and run phaser again against all space > groups and am finding P43 21 2? > > > > I thought I might have mistaken the NCS as crystallographic symmetry > and have processed them in a to high symmetry space group. The data > are merging OK in P222 (Rmerge 5.3%) and P4322/P43212 (6%/6.5%). > > I run Phaser with the data processed in P 2 2 2 against all possible > space groups and it found a solution in P2 2 21. > > > > In all solutions (orthorhombic and tetragonal) I have clashes with the > symmetry molecules looking at the results in Coot. > > > > The rotation function Z-scores and translation function Z-scores are > low as expected with 2.7 -2.9 and 4.7-5, respectively. And of course > the maps from Phaser are rather poor, but there are bits and pieces > which seem to make sense and I was hoping that I could at least > determine the space group. > > > > Any comments are much appreciated! > > > > Sabine > > > > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses, which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > CCP4bb navigationCCP4bb <-- 2007 <-- May 2007 <-- 08 May 2007 |
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