Fig. 4: Comparison of different data analysis approaches for detecting low occupancy binding of SolQ2Br. | Nature Communications

Fig. 4: Comparison of different data analysis approaches for detecting low occupancy binding of SolQ2Br.

From: A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

Fig. 4

The chosen T2R-TTL system comprises two binding sites for the photochemical affinity switch SolQ2Br and we refer to those as: high occupancy site 1 (left panel: A and B) and low occupancy site 2 (right panel: C, D, E and F). A Standard omit (Fo-Fc) map against apo protein state. B Refined electron density (2Fo-Fc) map. C Standard omit (Fo-Fc) map against apo protein state. D Electron density (2Fo-Fc) map refined against a model containing alternative conformations of ligand bound and apo protein state. E Isomorphous difference density (Fo-Fo) map against apo protein state. F Extrapolated electron density (2Fextra-Fc) map; the ratio of ligand bound state was determined to ~30%. The SolQ2Br structure is overlayed in all shown standard omit maps and isomorphous difference density maps for better visualization. The apo protein state is presented by the flipped in residue Asn247 of site 1 or 2 respectively. For comparability, all standard omit maps and isomorphous difference density maps are shown at a sigma level of 3.0, all electron density maps are shown at a sigma level of 1.5.

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