Hi Paul,
another hypothesis...
If you take an ultra-high resolution structure from PDB (resolution
higher than 1.0A), then cut the data at 3A and do some refinement, you
will get unusually low R-factors.
This may suggest that your crystal can diffract to higher resolution and
3A is not the limit.
However, you mentioned twinning and I guess it would be wise to double
check how the R-factor is computed in this case, and how the total model
structure factor is defined. I recall some Garib's comments about the
difference of R-factor values related to twinning...
In addition, to make sure that what you observe is not refinement
program dependent or how the R-factor and Fmodel are defined, I would
try to re-compute the R-factors or do some quick refinement in another
package. For example, does this command:
phenix.model_vs_data model.pdb data.mtz
give you the same R-factors?
Good luck!
Pavel.
On 5/30/10 5:15 AM, 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
