Well - I would look at the deviants in COOT and see if there is a proper
reason for the angels - water molecules too close? alternate conformation
for some near by sidechain? Any refinement program wants to get good
geometry unless there is an obstacle. If there is nothing obvious to fix
you could
Hello Pradeep,
Have you visually checked the model at these locations? Is this non-ideal
geometry of the DNA supported by the map? At 2.3 A resolution, the DNA should
be well resolved (both backbone and nucleic bases planes). Some (most?)
DNA-binding proteins distort DNA when binding to it, so
REFMAC5 refinement: nucleic acid residues with bad geometry
Hi All,
I am in the final refinement stage of an X-ray structure of a protein-DNA
complex,
2.3 A resolution, using Refmac5 (REFMAC 5.8.0267, CCP4Interface 7.1.018, Linux
platform).
I am confident about the space group, refinement steps,
