Hi Satinder,
Did you checked if your SAD dataset (2.9A) and the dataset you're using in
the refinement (2.3A) are in the same setting? The 'cad' program can do that
for you.
Cheers,
Miguel
2007/7/27, Satinder K. Singh <[EMAIL PROTECTED]>:
>
> 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
>
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