since the ligands bare being soaked into a known solved structure, why
is MR necessary? Why not just start out with some rigid body refinement
of the native structure to account for possible slight differences in
the cell dimensions?
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
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On 06/07/10 15:17, yang li wrote:
> Dear colleagues,
> We are now trying to soak some ligands into a protein, which is
> about 60kd in size and the structure has been solved
> before. But the molecular replacement cannot give a right solution.
> Below is some contrast of the data:
>
> Native 2A P212121 monomer
> Soaked 4A F222 monomer (more than 70% solvent) or
> dimer(more possible)
>
> I wonder if it is possible to find the ligand in the case of such low
> resolution, provided the ligand is not so small. What facts
> could probably lead to the failure of MR? Molrep gave a model of
> monomer but the rfree is as high as 0.7, while phaser could
> get no result. I tried phenix.explore_metric_symmetry to find the two
> spacegroups are not compatible, and the Rmerge of the
> data seems reasonable.
> One more question is: the wilson B of the data is lower than 20 from
> ccp4. Is it common for a 4A data? Since I donnot have
> the experience of handling this low resolution data yet.
> By the way, any suggestions about refinement methods in low resolution
> will be appreciated!
>
> Best wishes
> Yang
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