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Maybe I did not make the questions clear, which leading to the misleadings. Firstly, I have collected the mad data and get the phase at synchrotron, the phased Se is quite good for modelling, and get over 70% of the molecule run with resolve autobuilding.The density seems also good for building. But when finally refining the model, the gap between the R(0.22) and free_R(0.32 )is big, even though modelled the Se-methionine. Before collecting the mad data at synchrotron, I already have another native data set collected at home diffractometer (rigku, with R-axis IV++). To my surprise, when I using the same model(first model) and run with this data set, it is quite good( with 2.7A resolution, R=0.24 and Rf=0.28 and further refine to R=0.22 and Free_R=0.25), and I got the final model.The geometry of the first model and final model(actually no big difference of the two models)is quite good with procheck.The omit map says good enough with both of the two models. So I wondering what happened with the peak data? Did the anomolous signal have much effect on the data? and anyone have the similar experience? > First it is always best to refine your model against the highest > resolution good quality data that you have available. There was > correspondence about the geometric weighting - could you have weighted > the Xray data too high and have bad geometry - see previous Emails! > > And the Free R seems rather low for the Se data. > Did you transfer the same Free R set from the native to the Se data? > Eleanor > > > Peng Zhang wrote: >> Dear friends, >> >> Recently, I have solved a structure using mad method. When using the >> peak >> data(2.3A) as the native for structure refinement, the gap between R >> factor and R free is big, about 0.1(0.22 and 0.32). I modelled the >> selenomethionine but the gap still exists. When I changed the data for a >> real native one(2.7A),it seems OK with R=0.24 and Rf=0.28. >> >> Does anyone have the similar experience? >> what should I pay attention to when using the sad/mad data as the native >> one for modelling and refinement? >> >> Thanks in advance. >> >> >> > > > -- Peng Zhang, Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 20031 P.R. China Tel: 021-5492-1117 Fax: 021-5492-1116 Email: [log in to unmask]