Hands-on: Assessing individual outliers

Look at the following summary of outliers for a molecule of cystatin A in the validation report for PDB entry 3KSE. Let’s look at the detailed residue-level outliers underneath the percentile plots.

There are 11 residues with geometric outliers (bars coloured yellow) and one residue with a data (RSRZ) outlier.

We will focus on V48 and D61, both of which have single geometric outliers. The images below show the electron density for V48 (left) and D61 (right).

• Which of these outliers would you trust as being a true outlier and which would you expect is an incorrect modelling of the amino acid in the structure?
• Did the information in the validation report give you enough information to determine this without direct visualisation of the fit of the structure to the map?