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
schul...@cornell.edu
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
