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!