Hi Paul,
I've seen that type of behaviour before for low resolution structures.
On such structures,
either I have a very hard time getting at the same time a good geometry,
"good" R-factors and satisfactory electron density,
or things go very smoothly and all the statistics (model geometry,
R-factors) plus electron density are fine.
Too bad I have no way of predicting when things will be going well.
Two examples where things went very smoothly:
glyceraldehyde-phosphate dehydrogenase from Trypanosoma brucei brucei
(PDB id: 2X0N re-refined fairly recently with Phenix);
malate dehydrogenase from Archaeoglobus fulgidus (PDB id: 2X0I also
re-refined with Phenix)
The only thing you have to check is that the relative weighting of the
X-ray term vs. the geometry term is appropriate, so that you do not
lower the R-factors while the geometry is getting worse.
HTH,
Fred.
Paul Lindblom wrote:
Hi everybody,
once more I need your help. I solved the structure of an enzyme at
resolution of 1.9 A. Now I was trying to get a complex and soaked some
ligand to my crystals. I could solve the structure (and see poor
density for my ligand or something else) at 3.0 A by molecular
replacement using my 1.9A structure as a starting model. But the
problem is now, that I got an R-work of 16.34 and an r-free of 20.23
for the new 3.0 A structure - without adding any waters or
solvent/ligand molecules. The r-factors are even better than the ones
I got for the 1.9A structure. So I think something is wrong with the
whole thing. I observed twinning for both data and used the twin
refinement option in refmac, but the results stay more or less the same.
Any suggestions what to do? Thanks a lot,
Paul
