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 <[log in to unmask]> 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

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Deepthi