Hello, James Holton can probably tell more about this, but it is possible to create a library of potential coiled coil structures with differences in number of residues, superhelical radius, and residues per superhelical turn. A library of 300 theoretical coiled coils was generated and, in conjunction with EPMR, was used successfully to solve the structure of a KCNQ tetrameric coiled coil.
See: Howard et al (2007) Neuron 53(5),663-675. And I second Sergei Strelkov's comment: what should be an expected tetramer could show up as a trimer, etc... so you may want to check via ultracentrifugation that you have the expected stoichiometry. Regards, Filip On Mon, Oct 17, 2011 at 10:09 AM, Napoleão Valadares <n...@ifsc.usp.br>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 > -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
