One of the great mysteries of refinement is that a model created using
high resolution data will fit a low resolution data set much better than
a model created only using the low resolution data. It appears that there
are many types of errors that degrade the fit to low resolution data that
can only be identified and fixed by using the information from high
resolution data.
The situation you describe (for a small molecule binding to a known
protein structure) is exactly what I would expect.
Btw, you can't compare the R value of the high resolution model to
that of the low resolution model in any meaningful way. Calculate the
R value of the high resolution model using only its 3A data and compare
that to the R value of your 3A model. I suspect you will find that the
R value is worst for the new model despite the small numbers you are
seeing. A 1.9A model will fit its 3A data very well.
Dale Tronrud
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
|