You may need to consider (assuming that space group is correct)
1) Twinning. In this case even wrong solution at the early stages
would give lower Rfactor and at the later stages higher Rfactor
without accounting for twinning
2) Pseudo translation. In this case the solution could be in wrong
origin (you can try zanuda from the YSBLprograms server)
3) you can try arp/warp and/or buccanneer and try to do automatic
model building
4) You can try SAD refinement
5) you can check anomolous difference map to see if Se-s are visible
6) If you have NCS you can do averaging
Experimental phasing is always a good idea
Garib
On 25 Jul 2008, at 18:05, Sampath Natarajan wrote:
Dear all,
Now I'm solving a structure with 1.6A resolution. The data seems
good with R-sym (12.4) and all other parameters. Actually the data
was collected with SAD phasing. When we checked the data we
couldn't find the Se atom in the structure. Since the data
resolution is good, we tried to do molecular replacement using
Balbes program. It was selected a model with 25% sequence identity
and we got the good solution too. I could find all residues in the
density and also checked the Ramachandran map which shows almost
all residues are in the allowed region.
The problem is, I have done refinement many times, the R-factor
(45.3) and R-free (51.4) is not reducing during the refinement and
also figure of merit is not increasing. Still it remains what I got
during the first refinement. The density is also not improving
much. Also I could find many cuts in the density.
My question is……..
1. Can we use SAD phasing data for MR solution?
2. Is there any other way to reduce the R/R-free?
3. Why the figure of merit is not increasing even after modeled
the residues exactly into the electron density?
Thanks,
Regards,
Sampath
