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, dictionary files and
such.
In preparation for PDB deposition, I did a validation check and found that
there are 12 instances
where the angles of DNA res deviate. My question is how can I improve the angles
in my refinement so that it's close to ideal geometry? In Refmac refinement,
"geometric restraints/geometric parameters", what is the range of 'Angle
overall-wt'
that one can use? I have tried varying the 'wt' (upto 2.5) and found that the
angles
have improved geometry, while a few remained.
Expected
bond angle (°) Measured bond angle (°)
1/D 3/DC/C1' 3/DC/O4' 3/DC/C4' 110.1 ± 1.0 103.9
1/D 5/DA/OP1 5/DA/P 5/DA/OP2 119.6 ± 1.5 128.6
1/D 5/DA/O5' 5/DA/P 5/DA/OP2 105.7 ± 0.9 99.2
1/D 5/DA/C3' 5/DA/O3' 6/DA/P 119.7 ± 1.2 112.3
1/D 7/DT/O4' 7/DT/C1' 7/DT/N1 108.3 ± 0.3 110.3
1/D 7/DT/C3' 7/DT/O3' 8/DT/P 119.7 ± 1.2
111.1
1/D 9/EX/C3' 9/EX/O3' 10/DG/P 119.7 ± 1.2 112.3
1/E 1/DC/C3' 1/DC/O3' 2/DG/P 119.7 ± 1.2 110.5
1/E 4/6OG/C3' 4/6OG/O3' 5/DA/P 119.7 ± 1.2 111.8
1/E 5/DA/O5' 5/DA/P 5/DA/OP1 105.7 ± 0.9 98.2
1/E 6/DA/C1' 6/DA/O4' 6/DA/C4' 110.1 ± 1.0 103.8
1/E 6/DA/O4' 6/DA/C1' 6/DA/N9 108.3 ± 0.3 110.3
As a test, I have tried refining the same structure in Phenix.refine, and the
overall
geometry was better, but still have 4 angle violations. I do not want to use
phenix
in this case, as my refinement was carried out using Refmac.
Any thoughts? With regards to Refmac refinement, the geometry issues are
common for RNA/DNA refinements. Please correct me if I am wrong. In my specific
case,
it's a protein-DNA complex with about 410 amino acid and 24 nucleic acid
residues, and no angle deviations for protein residues!
Thanks,
Pradeep Pallan
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