Hello, I am having a few issues with a data set I have been working on recently, and was hoping to get some ideas on how to deal with it, if anyone is in the mood.
I have been working with a very small bacterocin (about 3 kDa) and set up some crystal trays in hope of getting some high diffracting crystals. I failed, but did manage to get a data set of reasonable quality to about 4A from crystals that reproduce very poorly. Now, this sounds horrendous, but the MR model I have available is of a similar bacteriocin, whose structure is predicted to be essentially identical (different ORF, but almost identical sequence). I was thinking it would be done in a day. The bravais lattice is P4, and 118 x 118 x 165 (which seems HUGE for such a small protein...indeed calling it a protein is generous...peptide). The data seems reasonably nice (nice spots, no visible overlap within 4A, but is very mosaic, about 1.5 degrees. The data integrates and scales nicely, with very good chi2, R-factors and % rejected reflections. It is hard to predict the correct space group, since all the tetragonal options have the same stats. The systematic absences seem to predict p41212 (as does pointless), but it wouldn't be the first time I screwed that up. I can't get a solution, no matter what I try. Is this the nature of such a small peptide in such a large unit cell (placing the first model is difficult for MR since there may be many copies in the AU), or are there some tricks? Is it likely that the unit cell is wrong? Self Rotation functions give 8 peaks, but this is considering a peak fairly generously (approx. 15-20% of origin). Are there some blatantly obvious red flags that I may be missing? Any advice would be great - even if that advice is that it may be time to move on. I should note that I have considered the idea that the peptide may be forming some sort of oligomeric structure such as a coiled coil, but it fails coiled coil predicting software, and there is no evidence that this should be the case. The homologous structure is very rigid, and I would say fairly confidently that mine is likely the same - I just want to confirm it. Thanks so much, Stephen Campbell Post Doctoral Fellow Department of Biochemistry McGill University
