XChem fragment hits are detected and modelled using the PanDDA paradigm (Pearce et al, 2016), which explicitly treats the low occupancy binding of fragments as a superposition of bound and unbound states. This requires on the one hand a 3D density background correction to detect and model fragments; and on the other to model both bound and unbound states for refinement (Pearce et al, 2017).
While all these data are deposited in the PDB, both for calculating the evidence density ("event maps") and the superposed models, unfortunately the validation processes of the PDB do not yet correctly account for these data, so that the validation reports flag up the structures as extreme outliers.
Therefore, to check the electron density evidence for the fragment hits, you should consult the density and model quality evidence in the downloadable bundled html page served below, where we have collated the data that explain the model, in easily reviewable form. (This is a stop-gap while we work with the PDB to simplify the whole process on their pages.)
To review density and quality metrics for the Mpro XChem hits, download and unzip this file, and open the file index.html - it attempts to be self-explanatory.
Similarly, we currently deposit in the PDB only the "bound" structure, meaning we strip out the ground-state structure even though it is (often) included in refinement. As a result, parts of the protein might appear at the same non-unitary occupancy as the ligand; this is deliberate, because the full crystallographic model of the superposed bound and groud states is confusing for end-users (Essentially, the ground-state can be considered a crystallographic artefact, like the unit cell etc.)
Some browsers have recently implemented security features which mean the electron density maps do not load. If this happens, you need to enable "cross-origin requests" or CORS.
Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire.
Copyright © 2020 Diamond Light Source
Diamond Light Source Ltd
Harwell Science & Innovation Campus