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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/