The easy Q first:
Wilson plot B values are very unreliable for 4A data - b=20 is almost certainly wrong, but until you have a model to refine it is hard to get a proper estimate.

 Q2: With a decent model the ligand should show up as a blob, even at this resolution. You might have trouble fitting it, but at least you would know whether it had bound or not.

Q3: Why the MR doesnt work - I cant answer this..
Check the data for any serious problems - missing strong intensities can mislead. Is the spce group certain?

Is there any relationship between the P212121 and F222 cells?

Eleanor

w it ang 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