Abstract
Historically, validation has been considered primarily as a gatekeeping function done at the end of a structure solution. Currently, the most interesting and important part of validation is the opportunity to correct diagnosed errors, provided mainly by local as opposed to global criteria, and available to you throughout the crystallographic process. Elsewhere in this book, you will hear about up-to-date methods in the data and model-to-data aspects of validation. This chapter addresses model validation and model improvement, first about current best-practice methodology (as done on the MolProbity website and elsewhere), and second about some important developments to anticipate in the near future.
Model validation has three primary parts: (a) geometry (bond lengths and angles, planarity, chirality), (b) conformation (rotamers, Ramachandran, ring pucker, RNA backbone conformers), (c) and sterics (clashes, H-bonds, packing). All of these both enhance and must be considered along with the information from electron density. The model criteria are primarily local, but their rate of occurrence can also be summarized as a global score.
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Web Sites
EDS (Electron Density Server): http://eds.bmc.uu.se/eds
MolProbity service: http://molprobity.biochem.duke.edu
PDB (at RCSB) Validation Server: http://validate.rcsb.org
PDBsum (ProCheck) is linked from the specific PDB page, eg for 1ubq: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?template=main.html&o=PROCHECK&c=999&pdbcode=1UBQ
Phenix: http://phenix-online.org
Richardson Lab for KiNG, Reduce, Suitename, Top8000, etc: http://kinemage.biochem.duke.edu
Verify3D profile analysis: http://nihserver.mbi.ucla.edu/Verify_3D
WhatCheck: http://swift.cmbi.ru.nl/gv/whatcheck
Wikipedia article: https://en.wikipedia.org/wiki/Structure_validation
wwPDB info about referee validation reports: http://www.wwpdb.org/validation.html
wwPDB link to Xray Validation Task Force: http://www.wwpdb.org/workshop/2011
Acknowledgments
Our work on model validation and improvement is supported by NIH grants: R01GM073919 for the MolProbity service, P01GM063210 for validation in Phenix, R01GM073930 for RNA validation, and R01GM088674 for improvement at low resolution.
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Richardson, J.S., Richardson, D.C. (2013). The Zen of Model Anomalies – Correct Most of Them. Treasure the Meaningful Valid Few. Live Serenely with the Rest!. In: Read, R., Urzhumtsev, A., Lunin, V. (eds) Advancing Methods for Biomolecular Crystallography. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6232-9_1
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