Satinder,
could it be a problem with the data? E.g., overloads were not thrown out? This
would not disturb the SAD phasing (only those bad reflections would have wrong
phases) but it might affect the refinement a lot.
I'd check the statistics of integration and scaling, _and_ try a different data
reduction program (that's always worth a try!).
HTH,
Kay
Satinder K. Singh schrieb:
> 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
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [log in to unmask] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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