You don't say whether you have any indication of non cryst translation or likely dimer NC axes? The self rotation can help sometimes to select likely pairings - for instance if one (or both) domain(s) is forming a dimer.
Eleanor On 26 Oct 2012, at 13:43, Bosch, Juergen wrote: > We had recently a similar case. > Indexed in P2x2x2x but truly was P21 with variable amount of twin fraction > depending on the dataset & beamline between 9% and 40%. > We were able to solve it using phenix.ensembler using all available known > structures plus our various homology models. > We still have not gone back and done a postmortem analysis of why we failed > with a highly similar homolog to find a solution in the first place with > either Phaser, Molrep or Phenix using single models. > It might help to process your data in XDS to take care of the overlaps a bit > better in case you have not done so already. > > Here's a link <advertisement on> Hain et al. 2012 > http://www.ncbi.nlm.nih.gov/pubmed/22982544 </advertisement off>. > > Jürgen > ...................... > Jürgen Bosch > Johns Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Office: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://lupo.jhsph.edu > > On Oct 26, 2012, at 8:27 AM, Seijo, Jose A. Cuesta wrote: > >> Hi all, >> >> I am dealing with a molecular replacement problem for a 60KDa protein >> composed of 2 rigid domains joined by a flexible linker which can move >> relative to each other. Sequence identity for my best model is 46% evenly >> spread, so in principle this should be a tractable problem. >> Then the problems start to pile up: >> a) The unit cell is 56.7Å, 288.5Å, 69.4Å, 90 93.5, 90. Spacegroup P21. >> Rmerge 12% to 2.4Å. The data also merges relatively well (Rmerge 16%) in >> P222 with the same a, c and b axes, now of course in that order. In the P21 >> case, that corresponds to 4 monomers in the asymmetric unit with a solvent >> content of approx. 50%, giving me 8 domains to find if I separate them. >> b) The 288 axis means that my data show some overlap in almost all >> orientations (might be corrected in the future with new datasets), so that >> my low resolution data are likely unreliable. >> c) Intensity distributions suggest twinning in either point groups. >> Actually, they are beyond the perfect twinning case, which I attribute to >> the reflection overlaps making the strong reflections weaker (integration >> box too small) and the small stronger (from tails of adjacent strong ones). >> Of course the latest would mean that the twin fraction estimation is >> unreliable, but all moments, etc show perfect twin statistics, so I am >> assuming that there is indeed perfect twinning of some sort. >> >> So, the question is, what is the best strategy to deal with this many (4 or >> 8) body / noisy / twinned problem? >> >> I am trying EPMR with many bodies, but I suspect the twinning would throw it >> out of the right track, and one domain seems to be too little of the >> diffracting matter to show any sort of discriminations between solutions and >> non-solutions if do the usual serial searches. I plan to let autotracing >> programs be the judge of success, but I am not sure of how well those can >> deal with twinning. Can Arp-Warp use twinned data? >> >> Thanks in advance for any tips. >> >> Jose. >> >> ======================================== >> Jose Antonio Cuesta-Seijo, PhD >> Carlsberg Laboratory >> Gamle Carlsberg Vej 10 >> DK-1799 Copenhagen V >> Denmark >> >> Tlf +45 3327 5332 >> Email [email protected] >> ======================================== > > > >
