On Thursday, 17 October, 2013 10:51:08 Lucas 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?
4KAP is a nice cautionary example of failing to properly refine a ligand
after placement.
- Open coot, download 4KAP + map from EDS.
- Navigate to ligand and view difference density map.
- Oops.
- Now open up residue information for the ligand. Notice anything odd?
For bonus points, look up the known ligation chemistry of this site.
Notice that the binding pose of the 4KAP ligand does not match it.
Ethan
> 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
