Hello everyone,
I am puzzled about differences I see when I refine the very same
structure against data processed with xscale or scala.
I got data to 2.55A from a protein-ligand complex. The data were
processed with xds/xscale (1) or xds/scala (2)
Free R was imported from a previously solved structure with a different
ligand, first to (1) and from there to (2).
After MR and refinement (Refmac/Phenix), I get some difference density
peaks (a bit pos and neg), near the ligand when I refine against (1)
and it converges more or less around R/Rfree of 20.9 and 24.8. I do not
get these pos and negative density blobs when I refine the same
coordinates against (2), with a tiny bit higher R/Rfree of 21.6/26.1?
So the data processed with scala, where I get slightly better refinement
statistics, I end up with some pos/neg density peaks. They don't show up
when I apply a high resolution cut-off of 2.65A during refinement.
Symmetry is orthorhombic and the statistics are OK (Rsym 0.09 and 0.38
in highest shell, redundancy ~5, I/sigI =1.9, mean I/sigI = 5.2 ) and
in both files appear to be more or less the same number of reflections.
I also did simulated annealing, omitting the region around the ligand in
a 15A radius and the density is nicely coming up. But it doesn't make a
difference: after refinement I always end up with the result as
discribed above? And there isn't really a difference between the two
structures in the end.
Has anyone an idea whats going on?
Sabine
