Fig. 2.
Results of different refinements for the OEC in PSII and omit maps. (A and B) To explore the feasibility of a model for the OEC in the 2F data that contains no additional bridging oxygen ligand Ox, we performed refinements against our 2F data (6w1v; ref. 2) starting with a Mn4O5Ca cluster with O5 placed in a position approximately similar to the position suggested by Wang et al. (1) and explored different refinement strategies. Upon refinement with phenix.refine (8), employing loose restraint settings (sigma values of 0.5 Å), the O5 atom moved back into a position closer to Mn4 and Mn3 and more distant from Mn1, closer to the model we obtained in our original work (2). The resulting refined model (final Rfree of 0.2483) with O5 distances in Å and the Fo-Fc density contoured at ±3σ (blue/orange) is shown in A. To force O5 to stay close to the starting position, we had to tightly restrain it to this position (sigma values of 0.005 Å). The resulting structural model (final Rfree of 0.2454) together with the Fo-Fc density is shown in B. Upon tightly restraining O5, a new positive Fo-Fc peak is visible between O5 and Mn4, indicating that this model does not properly explain the experimental data. We further evaluated the proposed model by generating omit maps (C and D). We first used our published model 6w1v (C) and omitted O5 and Ox separately. The resulting omit map is shown in magenta (O5) and blue (Ox) at 5σ contour level. In addition, both O5 and Ox were omitted together, and the resulting omit map is shown as green mesh at 3σ contour level. The shape of this density clearly indicates that the experimental data cannot be described by a single atom. In comparison, we computed Fo-Fc maps assuming a position of O5 as suggested by Wang et al. (D). The resulting Fo-Fc map with O5 placed in the model is shown in blue/orange at ±3σ. In addition, the omit map obtained by removing O5 from the model is shown as green mesh contoured at 3σ. The Fo-Fc map with O5 present in a position close to what Wang et al. suggested shows a strong positive peak to the right (toward Mn1), indicating that an additional atom needs to be included in the model. In addition, a weaker positive peak is visible to the left of O5 (toward Mn4, red dashed circle), indicating that O5 should move closer to Mn4.