Hi Eleanor Thanks a lot for your advice
I will reprocess my data and try and use the UCLA anisotropy server (open to suggestions here). I have done most of my work so far in the small cell and Yes I would say there is an indication of twinning A) xtriage and SFcheck both say twinning is probable B) H test for twin laws found by xtriage have alpha ~0.48 C) MR in P32 finds 4 solutions of equal scores and they all have different orientations in the unit cell (maybe this is a result of a tetramer in the ASU) D) MAD phases look like garbage and MR solutions cannot be refined Yes the P32 and P 32 1 2 solutions are the same. in fact I could not find a solution in P 32 searching with a single component it was not until I used two copies of the dimer found in P32 1 2 to make a tetramer which was subsequently used for MR in P32 thank you kindly for your input Ben On 9/24/09 2:43 AM, Eleanor Dodson wrote: > First - I would integrate to the 2A limit - you can apply an anisotropic > cut off to limit data in the weak direction if you like, but the higher > resolution reflections will certainly improve your maps.. > > Second: I would work in the smaller cell till you get a good model. > > Do you get an indication of twinning in that cell? > > And is the P32 solution equivalent to the P32 12 solution. > > And the SFCHECK result: > > pseudo-translation vector: 0.000 0.000 0.500 (12.3%) from 'SFcheck' (what > does the % mean?) > > It means the peak height in the Patterson at 0 0 0.5 is 12.5% of the > origin peak.. > Eleanor > > Ben Flath wrote: > > > > > > Hi > > > > Firstly thanks to all who replied to my original post. > > > > The clear consensus was to look for pseudo symmetry. > > > > I must admit there is more to the story. Here goes the long version. > > > > Crystals are Hexagonal bi-pyramids (under ideal conditions they are very > > beautiful nice crisp edges etc. non ideal conditions crystals still > > grow > > however they lose the nice edges and look kind of like a football, and > > do > > not diffract well). Two different unit cells have been observed for > > these > > crystals; 1) a,b=50, c=150, 2) a,b=50, c=300. 90 90 120 > > > > The data for both cells is highly anisotropic and has apparent 622 > > symmetry > > (self rotation function). Due to the anisotropy data can only be > > merged to > > ~3 A even though there is data to ~2 A in the strong reflecting > > direction. > > > > There is no pseudo symmetry detected in the small cell however there is > > pseudo translation detected in the big cell: > > > > pseudo-translation vector: 0.000 0.000 0.500 (12.3%) from 'SFcheck' > > (what > > does the % mean?) > > > > Not surprisingly intensity statistics to detect twinning are kind of all > > over the place but xtriage does find three twin laws (alpha for all 3 > > laws > > 0.48) and suspects the data to be twinned (in consensus with SFcheck). > > Using data processed in P3 at the end of xtriage log there is this > > statement. > > > > [ The results of the L-test indicate that the intensity statistics > > Show more centric character than is expected for acentric data.] > > > > I have a MR model with 45% identity. No solutions are found in the big > > cell. In the small cell solutions can be found in P3212 and P32 (2 and 4 > > mol/ASU respectively). Refinement stalls at ~42% and there is missing > > density for much of the model. I have attempted perfect twin refinement > > with > > CNS but I get huge divergence in R-Rfree 30 - 52. > > > > SeMet protein has been crystallized but so far has only exhibited the > > small > > cell. Sites appear to have been found with SOLVE/RESOLVE and SHELX, > > however > > the maps just look like noise. > > > > Questions: > > > > What can cause acentric data to have centric characteristic? > > > > Is there an option to do perfect twin refinement with phenix? > > > > In the case of the small cell (no pseudosymmetry) perfect twin test > > still > > has values well above 2. any other ideas besides pseudo symmetry? the > > data > > also has these values in resolution shells that do not suffer form > > anisotropy. > > > > All comments,questions and suggestions welcome > > > > Sincerely > > > > > > > > > > > > > > > > > > > > > > > > > > > > --------------------------------- > > > > Benjamin Flath > > College of Pharmacy and Nutrition > > University of Saskatchewan > > 320 Thorvaldson Building > > 110 Science Place > > Saskatoon, SK > > S7N 5C9 > > >
