Hello,
I have a SAD data set to 2.9A and a native data set on the same protein to
2.3A. I have built 70% of the model (polyalanine) into the SAD experimental map
that has been subjected to 2-fold NCS averaging and phase-extended to 2.3 A.
From the maps, the model looks like it fits the density fine, but when I try to
refine (either rigid-body or positional refinement in REFMAC or simulated
annealing in CNS), I get an R-factor of ~60%, worse than random. Similarly, a
SigmaA run ("combine isomorphous phase with partial structure") on the model
yields an R-factor of ~60%. However, when I run DM on the original
phase-combined file (before NCS averaging and phase extension) in omit mode, I
get an R-free of 34.6%, which suggests that the map files itself is okay.
I also checked the space group of the processed data, and it is definitely
P21212.
Does anyone have any suggestions of what I may be doing wrong?
Thanks in advance for your help.
Kind regards,
Satinder
