Dear Jasmine (and all), Many thanks for the article. I have a question regarding the Z cutoffs used to flag geometry outliers in the PDB validation reports: geometry outliers are flagged with |Z|>2 for ligands (including carbohydrates), but with |Z|>5 for proteins. What is the rational for using different criteria for ligands vs proteins? After all isn’t this just one structure?
Cheers, Cyril PS. I am refining a 2.4 A resolution structure of a N-glycosylated protein and end up with a large number of geometry outliers for the sugars when I generate PDB validation reports (especially angle outliers). The huge majority of these outliers are flagged with |Z|<5 (ie they would not be flagged if they were protein bonds or angles). The electron density for the sugars is quite good and I made sure that correct LINKR records are used during refinement in Refmac. I must admit that I’m a bit struggling to improve this. From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Jasmine Young Sent: Thursday, 18 March 2021 2:46 am To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates A new article in Structure<https://doi.org/10.1016/j.str.2021.02.004> describes new features, including branched representations and 2D SNFG images for carbohydrates, identification of ligands of interest, 3D views of electron density fit, and 2D images of small molecule geometry. These enhancements and processes for validation of 3D small-molecular structures reflect recommendations from the wwPDB/CCDC/D3R Ligand Validation Workshop and the adoption of software through community collaborations. This manuscript also highlights enhancements made since the initial implementation of Validation Reports as described in Validation of the Structures in the Protein Data Bank (2017) Structure 25: 1916-1927 doi: 10.1016/j.str.2017.10.009<https://doi.org/10.1016/j.str.2017.10.009>. Enhanced Validation of Small-Molecule Ligands and Carbohydrates in the Protein Data Bank Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, Gérard Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko F. Aoki-Kinoshita, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley, and Jasmine Y. Young (2021) Structure doi: 10.1016/j.str.2021.02.004<https://doi.org/10.1016/j.str.2021.02.004> [undefined]<https://doi.org/10.1016/j.str.2021.02.004> <http://www.wwpdb.org/news/news?year=2021#top> -- Regards, Jasmine =========================================================== Jasmine Young, Ph.D. Biocuration Team Lead RCSB Protein Data Bank Research Professor Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway, NJ 08854-8087 Email: jasm...@rcsb.rutgers.edu<mailto:jasm...@rcsb.rutgers.edu> Phone: (848)445-0103 ext 4920 Fax: (732)445-4320 =========================================================== ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited. ######################################################################## 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/
