I use 2QNS for teaching. It is an egregious case of modeling ligand into noise. Also, the structure has many close contacts (e.g. HOH A351), poor stereochemistry (e.g. A58-A61), and incorrectly built water. Turn on symmetry to see the steric clash of the peptide ligand with itself. You can get the coordinates and maps from EDS.
http://www.ncbi.nlm.nih.gov/pubmed/18611381 http://www.ncbi.nlm.nih.gov/pubmed/21827955 http://retractionwatch.wordpress.com/2011/08/16/ties-that-dont-bind-group-retracts-parathyroid-hormone-crystallography-paper/ http://retractionwatch.wordpress.com/2012/01/26/pnas-retraction-marks-second-for-crystallography-group/ John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tanne...@missouri.edu<mailto:tanne...@missouri.edu> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html On Oct 17, 2013, at 8:51 AM, Lucas <lucasbleic...@gmail.com<mailto:lucasbleic...@gmail.com>> wrote: Dear all, I've been lecturing in a structural bioinformatics course where graduate students (always consisting of people without crystallography background to that point) are expected to understand the basics on how x-ray structures are obtained, so that they know what they are using in their bioinformatics projects. Practices include letting them manually build a segment from an excellent map and also using Coot to check problems in not so good structures. I wonder if there's a list of problematic structures somewhere that I could use for that practice? Apart from a few ones I'm aware of because of (bad) publicity, what I usually do is an advanced search on PDB for entries with poor resolution and bound ligands, then checking then manually, hopefully finding some examples of creative map interpretation. But it would be nice to have specific examples for each thing that can go wrong in a PDB construction. Best regards, Lucas
