I tried opening the model with other spacegroups MTZ file. The map doesn't fit well for other spacegroups. The initial model was refined using Phenix Autobuild software. I tried MR with every spacegroup possible in primitive hexagonal. Only p3221 worked. There is no twinning in the crystal. I will try using other softwares for refinement but this is annoying. I also tried mutating the model to poly alanines and refine but this made it worse. The R-free went up to 0.546. I initially thought it might be a space group problem but trying other space groups doesn't work either.
Thank youvery much for the help Deepthi On Wed, Jul 18, 2012 at 9:36 AM, Vellieux Frederic <frederic.velli...@ibs.fr > wrote: > Hi there, > > Not much information provided. How was the initial model refined ? Phenix > ? It could be a problem with the Refmac refinement protocol (difficult to > say with so little information) if you switched from Phenix to Refmac. > > How certain are you 1 - of the space group; 2 - that the crystal wasn't > twinned ? You can have both and it can be "annoying". > > Further, at this resolution I think you could use one of the SHELXes > (forgot the terminology) for refinement, that could be more appropriate. > > F.V. > > > Deepthi wrote: > >> Hi all >> >> I am working with a small mutant protein which is 56 amino acids long. >> The crystal diffracted at 1.4A0 and the space group is p3221. I did >> molecular replacement using Phenix software with all the data (1.4A0) and >> got a solution. Phenix did auto building with waters and R-free was 0.3123. >> >> I mutated some residues which don't align with the model protein to >> Alanines. When i change the residues back to their respective side chains >> Refmac5 won't refine it well. The maps looks clear( you can guess its >> 1.4A0 data) but R-free is shooting up to 0.41. It is not accepting any >> changes to the Phenix generated model. I have no idea what is going on. Can >> anyone help me? >> >> Thank You in advance >> Deepthi >> >> >> -- Deepthi
