A Working Group consisting of the co-authors of this paper was established in 2020 to re-evaluate the standard valence geometry used for the validation of nucleic acid structure models in the Protein Data Bank (PDB). This Working Group re-examined the dependence of Cambridge Structural Database (CSD) derived targets on base and sugar type, sugar pucker, and phosphate and glycosidic conformation, before comparing those targets with the geometry of a quality-filtered reference set of nucleic acid crystal structural models held in the PDB. This revealed that the valence bond and angle mean values are close to the CSD targets, but many parameters have highly non-Gaussian or even multimodal distributions. One explanation is the inconsistency of restraints used over time and by different refinement programs. The Working Group recommends a new validation scheme for use by the PDB. For this purpose, we have developed a new three-tier scale for outlier detection-graded as Preferred, Allowed, and Of Concern intervals-based on a combination of quality-curated reference data from the CSD and the PDB. The proposed approach to validation should lead to improved nucleic acid models in (future) PDB-deposited macromolecular structures.

Department of Biochemistry Duke University Durham NC 27710 United States

Department of Biochemistry Vanderbilt University School of Medicine Nashville TN 37232 United States

Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey Piscataway NJ 08854 United States

Department of Crystallography Faculty of Chemistry Adam Mickiewicz University Poznan 61 614 Poland

Department of Quantitative and Computational Biology University of Southern California Los Angeles CA 90089 United States

Global Phasing Ltd Cambridge CB3 0AX United Kingdom

Institute for Quantitative Biomedicine Rutgers The State University of New Jersey Piscataway NJ 08854 United States

Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan 61 704 Poland

Institute of Biotechnology Czech Academy of Sciences 252 50 Vestec Czech Republic

Institute of Computing Science Poznan University of Technology Poznan 60 965 Poland

Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley CA 94720 United States

Oncode Institute and Division of Biochemistry The Netherlands Cancer Institute Amsterdam 1066CX the Netherlands

Ryvu Therapeutics Kraków 30 394 Poland

Scientific Computing Department UKRI Science and Technology Facilities Council Research Complex at Harwell Rutherford Appleton Laboratory Didcot OX11 0FA United Kingdom

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New targets and procedures for validating the valence geometry of nucleic acid structures