twin/pseudo-symmetry question

11 Nov 2011

      Hello all-

I have a question regarding the possibility of twinning and or psuedo-symmetry. I have a crystal that processes well in R32, ie. less than 6% r-merge at 2.2 angstrom. We collected multiple potential derivatives and were able to get some phasing from one that was good enough to model in the helices. The strange thing is that when looking at the harker sections there were a lot of unexplained strong peaks. And there is a very narrow range of parameters that we could get the sites with Shelx and end up with interpretable maps(i know that this part might not be unusual). My first thought was that there could be twinning. Since there is no twin law for this space group, I thought that it might suggest that there was twinning in a lower symmetry space group and/or that we have a pseudo-R32 crystal. Processing works well in C2 and R3, as expected. In those cases Xtriage suggests that the real symmetry is likely to be R32. In the case of C-2, xtriage suggetss if it is twinned then it is about 45% twinned. That's the background. Fast forward with the help of phenix Autobuild and some manual correction, we have been able to refine the structure with the R32 processed data(with tls) to r_work = 0.1894, r_free = 0.2287, bonds = 0.007, angles = 0.908 at 2.2 angstrom with almost everything accounted for. 

I think I should be quite comfortable with this. BUT, I'm still wondering about those Harker sections. I've been reading the manuscripts of Dauter regarding twinning and I think I am at this point more curious than anything. But not leaving well enough alone, I went back to the data processed in C2. I can easily do molecular replacement, following refinement at 2.3 angstrom(I need a lot more frames for this sg so the cutoffs are a bit lower but r-merge is ~ the same as R32) with TLS I get r_work = 0.1850, r_free = 0.2249, bonds = 0.007, angles = 0.946. this doesn't seem significant to me. However if I refine with the two possible twin operations, the values drop with one being better than the other. both have the same starting model:

r_work = 0.1639 r_free = 0.1880 bonds = 0.006 angles = 0.902
r_work = 0.1582 r_free = 0.1866 bonds = 0.006 angles = 0.891

The twin fraction from the refined pdb header is 0.544 for the better statistical model and the r-values seem too low for 2.3 angstrom data. Is the high twin fraction suggestive of the higher symmetry space group or inconclusive towards that. of interest is that the maps look better to me than the r32 maps. by that i mean that the maps don't have what i would call minor dots of negative density for some(not a lot) of the side chains as we see for some side chains in the R32 case. also some side chains look better in the C2 twin refined case. Lastly for some of the monomers(there are now 6 copies versus 2 in the R32 case), I can add an additional residue or two on the termini which are not seen before. I wonder if this also suggests that the true space group is C2. Are these r-values too low? does the difference in values according to each twin law mean something?

In the end, the models are essentially the same in either space group (with the exception of a couple of residues at the termini). So, I don't think I learn much one way or the other. But the curiocity keeps coming back. So is it likely to be R32 or C2 or C2 with a hefty twin fraction? Anyone have an explanation?

Thanks in advance-
Todd

Green, Todd

Nathaniel Echols

Green, Todd

Peter Zwart

Green, Todd

Nathaniel Echols

Peter Zwart

Nathaniel Echols

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