Extended Data Fig. 5: Impact of the data quality on the resolving power of the maps.
From: Structures of the intermediates of Kok’s photosynthetic water oxidation clock
a–f, The data quality evidenced by 2F state models and 2mFobs − DFcalc maps contoured at 1.5σ. a, 5TIS (2F, 2.25 Å) model and map. Overlays indicate atom numbering in the OEC and the identities of selected coordinating sidechains. b, Current 2F model and map cut to 2.25 Å. c, Current 2F model and map at the full 2.07 Å resolution. Emergence of locations of O4 with improved data quality is indicated by bold arrow. d, As in a from a different angle and with mFobs − DFcalc density at 3σ indicating the lack of sufficient evidence for inserting an additional O atom at a chemically reasonable position. e, f, As in b, c from the same direction as d and with mFobs − DFcalc density at 3σ shown to 2.25 and 2.05 Å, respectively, after omitting the inserted Ox atom. Centring of the refined Ox position within the omit density gives a clear indication of the position of the inserted water in the S3 state with the current, higher-quality data, even when artificially cut to the same resolution as the previous data set. g, mFobs − DFcalc maps of the 2F data that compare the O6 model from Suga et al.9 and the Ox model from the current study. Map shows the mFobs − DFcalc density calculated with our current 2F data and our model adding the O6 position of Suga et al.9 (with the occupancy of 0.7 and B-factor of 30) (g-1), and with our Ox model (g-2). We see clearly a positive density for the missing Ox and a negative density at the O6 position in g-1. Schematics of the O6 and Ox S3 models are shown on the left.
