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: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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