Hi, I agree that Arcimboldo is a good idea, especially at such good resolution (assuming your space group is correct, an issue that others have commented on). But you could also try, directly, something that Isabel Uson has pointed out about molecular replacement with helices in Phaser. For such asymmetric objects, the rotational sampling tends to be too coarse to sample the orientations rotated around an axis perpendicular to the helix axis. So you could look at the rotational sampling chosen by Phaser and override it with something, say, 1/2 to 2/3 as large.
Another issue is that, with a long helix, there will be many nearly-correct solutions offset by partial turns. So the sequence register could be wrong. Good luck! Randy Read On 17 Oct 2011, at 18:09, Napoleão Valadares wrote: > Hi there! > I got crystals from some synthetic peptides I bought, they are 30 residues > long and are supposed to form a coiled coil. I collected various data sets > (home source, Brookhaven and Diamond), including some at the resolution of > 1.65 A, for which the space group appears to be C222 or C2221. The unit cell > is small, 22.67, 88.06, 26.13, and the Matheus Coefficient indicates that's > there's only one helix in the asymmetric unit and a 25% solvent content. > > I have tried A LOT of Molecular Replacement using Phaser and Phenix > AutoMR. I'm using a 80% identity coiled coil helix as search model. The > programs give me solutions with "reasonable" maps, but it is never possible > to refine to achieve Rvalues below 0.40. Additionally, maps from different > solutions look reasonable, so I'm thinking these are all bias. > > I have 5 other synthetic 30 residues peptides (that crystallize in > different space groups and diffract to lower resolutions), including a > SelenoMethionine (SM) derivative (but it does not have enough anomalous > signal, ASU is too big, it is possible that the SM are disordered). I'm stuck > on this since March. > > Regarding the search model, I already tried trimming some or all side > chains and removing 2, 3 or 5 residues on each/both sides. I also tried other > search models. Maybe some "magic" combination of parameters on Phaser or > other programs can help me. > > What is your advice regarding how to proceed with MR? Is there some > program, procedure, parameter, pray or human sacrifice that could help me? > Thank you. > Regards, > Napo ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
