Extended Data Figure 2: Cryo-EM map generation and atomic model refinement.

a, An example micrograph (drift-corrected, dose-weighted, and low-pass filtered to 20 Å) of the nanodisc-reconstituted ABCG2–5D3(Fab) data set. White scale bar, 1,000 Å. b, Averages of the 28 most prevalent two-dimensional class averages of the final round of two-dimensional classification, sorted in decreasing order by the number of particles assigned to each class. c, Map obtained from the RELION three-dimensional auto-refine procedure shown at a lower (white, transparent) and higher (blue, non-transparent) threshold. Density corresponding to the nanodisc is indicated with an arrow. d, Same as c but rotated. e, Angular distribution plot for the final reconstruction. The refinement map is shown at two different thresholds as in c, in the same orientation. f, FSC from the RELION auto-refine procedure of the unmasked half-maps (yellow), the random-phase corrected half-maps (green), the half-maps after masking (blue), and the half-maps after masking and correction for the influence of the mask (red). A horizontal line (black) is drawn for the FSC = 0.143 criterion. For both the unmasked and the corrected FSC curves, their intersection with the FSC = 0.143 line is indicated by an arrow, and the resolution at this point is indicated. g, FSC of the final model versus the map calculated with all data after local-resolution filtering, against which it was refined, (dark blue) and of the final model with introduced shifts (up to 0.3 Å) refined against the first unfiltered half-map (half-map 1) versus the same unfiltered half-map (violet) and versus the other unfiltered half-map (half-map 2) against which it was not refined (grey).