Fig. 4. Cross-link violations tend to occur between or outside of structurally well determined regions.
a The predicted alignment error (PAE)2 for T. thermophila protein BBC118 (Uniprot identifier I7ME23) with satisfied and violated cross-links plotted onto the heatmap. Blue circles are the satisfied cross-link and red x’s are the cross-link violations. b We apply a watershed model to the PAE heatmap to segment the protein into individual rigid bodies. For BBC118, all cross-link violations occur between segmented rigid bodies. c The protein rigid bodies were broken up by the segmentation from the PAE and modeled using the intramolecular cross-links as distance restraints to find an arrangement that satisfied all but one of the cross-links. All models and PAE plots are provided at the supporting Zenodo web site.