Extended Data Figure 9: Electron density maps of regions of the PSII dimer.

a–f, Electron density maps based on maximum likelihood structure factors (2mF_o-DF_c) obtained using the Bragg diffraction (model shaded green, left), the Bragg and continuous diffraction (model shaded blue, middle) and computed from pseudo-crystal refinement (model shaded brown, right). The maps are rendered at various density levels relative to the standard deviation of the overall density. a, b, Non-haem iron coordinated by two His residues from D1 (chain A) and two from D2 (chain D), contoured at 1.5σ (a) and 4σ (b). Neighbouring Tyr and Lys residues are displayed as well. c, Part of an α-helix (chain T), showing that the side chains (for example, Arg and Phe) fit better in the electron density when applying our new method (maps contoured at 1.5σ). d, Helices from chains Y and Z (maps contoured at 1.25σ). The density map shows more details and better agreement to the model when applying the analysis using the Bragg and continuous diffraction. e, Detailed view of a section of chain Z (maps contoured at 1.25σ). Using only the Bragg diffraction, no electron density is visible at this level around the side chains of Trp, Lys and Arg. Again, the model fits better into the map when using the continuous diffraction. f, Two chlorophylls and part of the transmembrane helix of chain C (maps contoured at 1.5σ). g, Matrix of Pearson correlation coefficients of electron density maps obtained from the model presented in ref. 2 (PDB, 3WU2), the model refined from Bragg diffraction and that obtained from the continuous diffraction.