Dear James It seems that at this stage you may not be able to distinguish between these space groups. As I see they are subgroup of each other (more precisely P1 < C2 < I222 with the cell parameters you have) and it would not be easy to find out the exact space group at this stage. Highest space group may be more likely than others in the absence of other evidences. It seems that the problem is that the model is sufficiently far and refinement programs struggle to converge. We had some good results for this type of cases when we used jelly body refinement in refmac with 40-100 cycles and sigma set to 0.01. Phenix may have similar tricks. After that you can try either shelxe or arpwarp or one after another. Although at 2.3A they may not produce results as spectacular as in presentations, they may give you improved maps to work with.
regards Garib On 8 Jul 2012, at 22:11, James Garnett wrote: > Dear all, > > I have some troublesome data to ~2.3A and I hope someone can help. My data > indexes and scales equally well in I222, C2 and P1 > > I222 a=46.3 b=76.3 c=81.1 > C2 a=111.3 b=46.3 c=76.3 beta=133.2 (reset in I2 a=76.3 b=46.3 c=81.1 > beta=90.1) > C2 a=94.5 b=76.3 c=46.3 beta=119.6 (reset in I2 a=46.3 b=76.3 c=81.1 > beta=90.1) > P1 a=46.2 b=60.2 c=60.2 alpha=78.5 beta=67.4 gamma=67.4 > > I have found a molecular replacement solution in I212121 using an NMR > structure of the same protein and MR-ROSETTA/PHENIX (PHASER LLG=128 > TFZ=12.3), although I can not refine this below R ~45% and Rfree ~50%. The > maps look OK in parts but in other regions the connectivity is much reduced. > In case of model bias I have used density modification and also used > simulated annealing etc in case it is stuck in a local minima - these did not > help. This protein is an Ig-like fold (potential for pseudo-internal > symmetry) and so I have also played around with rotations of the structure > but this has not helped. Although twinning analysis in all spacegroups > suggest there is no twinning I have tried refinement in PHENIX and REFMAC > using twin laws but this does not help. > > I do not detect any off origin peaks in a native Patterson map but I do see > peaks suggesting NCS in self rotations in I222 (see below for peaks above 50% > origin) - there can only be 1 mol/au though. Does this suggest rotational > lattice defects? > > Eulerian angles Polar angles > > Alpha Beta Gamma Peak Omega Phi Kappa > Direction cosines > Symmetry: 1 2 > > > > Peak 1 > Origin peak 100.0 0.0 0.0 0.0 > > Peak 2 > 1 1 0.0 0.0 180.0 100.0 0.0 0.0 3.1 > 0.0000 0.0000 1.0000 > Origin peak 100.0 0.0 0.0 180.0 > > Peak 3 > 1 1 0.0 0.0 180.0 100.0 0.0 0.0 3.1 > 0.0000 0.0000 1.0000 > Origin peak 100.0 180.0 0.0 180.0 > > Peak 4 > 1 1 0.0 180.0 180.0 100.0 90.0 0.0 3.1 > 1.0000 0.0000 0.0000 > 1 2 0.0 180.0 0.0 100.0 90.0 90.0 3.1 > 0.0000 1.0000 0.0000 > Origin peak 100.0 90.0 0.0 180.0 > > Peak 5 > 1 1 0.0 180.0 180.0 100.0 90.0 0.0 3.1 > 1.0000 0.0000 0.0000 > 1 2 0.0 180.0 0.0 100.0 90.0 90.0 3.1 > 0.0000 1.0000 0.0000 > Origin peak 100.0 90.0 180.0 180.0 > > Peak 6 > 1 1 0.0 180.0 0.0 100.0 90.0 90.0 3.1 > 0.0000 1.0000 0.0000 > 1 2 0.0 180.0 180.0 100.0 90.0 0.0 3.1 > 1.0000 0.0000 0.0000 > 1 3 0.0 0.0 180.0 100.0 0.0 0.0 3.1 > 0.0000 0.0000 1.0000 > Origin peak 100.0 90.0 90.0 180.0 > > Peak 7 > 1 1 270.0 89.9 90.0 51.9 90.0 0.0 89.9 > 1.0000 0.0000 0.0000 > 1 2 270.0 89.9 270.0 51.9 45.0 270.0 180.0 > 0.0000 -0.7067 0.7075 > 1 3 90.0 90.1 270.0 51.9 90.0 180.0 90.1 > -1.0000 0.0000 0.0000 > 1 4 90.0 90.1 90.0 51.9 135.0 270.0 180.0 > 0.0000 -0.7075 -0.7067 > 2 1 90.0 89.9 90.0 51.9 135.0 270.0 180.0 > 0.0000 -0.7067 -0.7075 > 2 2 90.0 89.9 270.0 51.9 90.0 180.0 89.9 > -1.0000 0.0000 0.0000 > 2 3 270.0 90.1 270.0 51.9 135.0 90.0 180.0 > 0.0000 0.7075 -0.7067 > 2 4 270.0 90.1 90.0 51.9 90.0 360.0 90.1 > 1.0000 0.0000 0.0000 > 3 1 90.0 90.1 270.0 51.9 90.0 180.0 90.1 > -1.0000 0.0000 0.0000 > 3 2 90.0 90.1 90.0 51.9 45.0 90.0 180.0 > 0.0000 0.7075 0.7067 > 3 3 270.0 89.9 90.0 51.9 90.0 360.0 89.9 > 1.0000 0.0000 0.0000 > 3 4 270.0 89.9 270.0 51.9 135.0 90.0 180.0 > 0.0000 0.7067 -0.7075 > 4 1 270.0 90.1 270.0 51.9 45.0 270.0 180.0 > 0.0000 -0.7075 0.7067 > 4 2 270.0 90.1 90.0 51.9 90.0 360.0 90.1 > 1.0000 0.0000 0.0000 > 4 3 90.0 89.9 90.0 51.9 135.0 270.0 180.0 > 0.0000 -0.7067 -0.7075 > 4 4 90.0 89.9 270.0 51.9 90.0 180.0 89.9 > -1.0000 0.0000 0.0000 > > Peak 8 > 1 1 90.0 89.9 270.0 51.9 90.0 180.0 89.9 > -1.0000 0.0000 0.0000 > 1 2 90.0 89.9 90.0 51.9 135.0 270.0 180.0 > 0.0000 -0.7067 -0.7075 > 1 3 270.0 90.1 90.0 51.9 90.0 360.0 90.1 > 1.0000 0.0000 0.0000 > 1 4 270.0 90.1 270.0 51.9 135.0 90.0 180.0 > 0.0000 0.7075 -0.7067 > 2 1 270.0 89.9 270.0 51.9 45.0 270.0 180.0 > 0.0000 -0.7067 0.7075 > 2 2 270.0 89.9 90.0 51.9 90.0 360.0 89.9 > 1.0000 0.0000 0.0000 > 2 3 90.0 90.1 90.0 51.9 45.0 90.0 180.0 > 0.0000 0.7075 0.7067 > 2 4 90.0 90.1 270.0 51.9 90.0 180.0 90.1 > -1.0000 0.0000 0.0000 > 3 1 270.0 90.1 90.0 51.9 90.0 360.0 90.1 > 1.0000 0.0000 0.0000 > 3 2 270.0 90.1 270.0 51.9 45.0 270.0 180.0 > 0.0000 -0.7075 0.7067 > 3 3 90.0 89.9 270.0 51.9 90.0 180.0 89.9 > -1.0000 0.0000 0.0000 > 3 4 90.0 89.9 90.0 51.9 135.0 270.0 180.0 > 0.0000 -0.7067 -0.7075 > 4 1 90.0 90.1 90.0 51.9 45.0 90.0 180.0 > 0.0000 0.7075 0.7067 > 4 2 90.0 90.1 270.0 51.9 90.0 180.0 90.1 > -1.0000 0.0000 0.0000 > 4 3 270.0 89.9 270.0 51.9 135.0 90.0 180.0 > 0.0000 0.7067 -0.7075 > 4 4 270.0 89.9 90.0 51.9 90.0 360.0 89.9 > 1.0000 0.0000 0.0000 > > Peak 9 > 1 1 90.0 90.0 90.0 51.5 135.0 270.0 180.0 > 0.0000 -0.7072 -0.7070 > 1 2 90.0 90.0 270.0 51.5 90.0 180.0 90.0 > -1.0000 0.0000 0.0000 > 1 3 270.0 90.0 270.0 51.5 45.0 270.0 180.0 > 0.0000 -0.7070 0.7072 > 1 4 270.0 90.0 90.0 51.5 90.0 0.0 90.0 > 1.0000 0.0000 0.0000 > 2 1 270.0 90.0 90.0 51.5 90.0 360.0 90.0 > 1.0000 0.0000 0.0000 > 2 2 270.0 90.0 270.0 51.5 135.0 90.0 180.0 > 0.0000 0.7072 -0.7070 > 2 3 90.0 90.0 270.0 51.5 90.0 180.0 90.0 > -1.0000 0.0000 0.0000 > 2 4 90.0 90.0 90.0 51.5 135.0 270.0 180.0 > 0.0000 -0.7070 -0.7072 > 3 1 270.0 90.0 270.0 51.5 135.0 90.0 180.0 > 0.0000 0.7070 -0.7072 > 3 2 270.0 90.0 90.0 51.5 90.0 360.0 90.0 > 1.0000 0.0000 0.0000 > 3 3 90.0 90.0 90.0 51.5 45.0 90.0 180.0 > 0.0000 0.7072 0.7070 > 3 4 90.0 90.0 270.0 51.5 90.0 180.0 90.0 > -1.0000 0.0000 0.0000 > 4 1 90.0 90.0 270.0 51.5 90.0 180.0 90.0 > -1.0000 0.0000 0.0000 > 4 2 90.0 90.0 90.0 51.5 135.0 270.0 180.0 > 0.0000 -0.7070 -0.7072 > 4 3 270.0 90.0 90.0 51.5 90.0 360.0 90.0 > 1.0000 0.0000 0.0000 > 4 4 270.0 90.0 270.0 51.5 45.0 270.0 180.0 > 0.0000 -0.7072 0.7070 > > Peak 10 > 1 1 270.0 90.0 270.0 51.5 45.0 270.0 180.0 > 0.0000 -0.7072 0.7070 > 1 2 270.0 90.0 90.0 51.5 90.0 360.0 90.0 > 1.0000 0.0000 0.0000 > 1 3 90.0 90.0 90.0 51.5 135.0 270.0 180.0 > 0.0000 -0.7070 -0.7072 > 1 4 90.0 90.0 270.0 51.5 90.0 180.0 90.0 > -1.0000 0.0000 0.0000 > 2 1 90.0 90.0 270.0 51.5 90.0 180.0 90.0 > -1.0000 0.0000 0.0000 > 2 2 90.0 90.0 90.0 51.5 45.0 90.0 180.0 > 0.0000 0.7072 0.7070 > 2 3 270.0 90.0 90.0 51.5 90.0 360.0 90.0 > 1.0000 0.0000 0.0000 > 2 4 270.0 90.0 270.0 51.5 45.0 270.0 180.0 > 0.0000 -0.7070 0.7072 > 3 1 90.0 90.0 90.0 51.5 135.0 270.0 180.0 > 0.0000 -0.7070 -0.7072 > 3 2 90.0 90.0 270.0 51.5 90.0 180.0 90.0 > -1.0000 0.0000 0.0000 > 3 3 270.0 90.0 270.0 51.5 135.0 90.0 180.0 > 0.0000 0.7072 -0.7070 > 3 4 270.0 90.0 90.0 51.5 90.0 360.0 90.0 > 1.0000 0.0000 0.0000 > 4 1 270.0 90.0 90.0 51.5 90.0 360.0 90.0 > 1.0000 0.0000 0.0000 > 4 2 270.0 90.0 270.0 51.5 135.0 90.0 180.0 > 0.0000 0.7070 -0.7072 > 4 3 90.0 90.0 270.0 51.5 90.0 180.0 90.0 > -1.0000 0.0000 0.0000 > 4 4 90.0 90.0 90.0 51.5 45.0 90.0 180.0 > 0.0000 0.7072 0.7070 > > Any suggestions and advice are very welcome. > > Cheers > > James > > Dr James Garnett > Centre for Structural Biology > Division of Molecular Biosciences > > Level 5 Sir Ernst Chain Building > South Kensington Campus > Imperial College London > London SW7 2AZ > Tel: +44 (0) 207 594 5464 > Fax: +44 (0) 207 594 3057 Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
