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 deviations from ideal geometry are not surprising, I would even say they are expected. You can find a striking example of DNA conformation deviating from ideal by looking at any structure containing a nucleosome (for instance 1AOI, or 1KX5 if you want the one with highest resolution). Check the validation report of an entry with a nucleosome: you will see that many geometry "problems" like yours are listed in the report, but since they are supported by the map it’s fine to deposit like that. It won’t be a problem to have geometry outliers as long as you can convincingly show that they are supported by the map.
I hope this helps, Guillaume On 8 Apr 2022, at 14:24, Pallan, Pradeep S <000078fe4ea98718-dmarc-requ...@jiscmail.ac.uk<mailto:000078fe4ea98718-dmarc-requ...@jiscmail.ac.uk>> wrote: 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 När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## 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/
