Extended Data Figure 5 |. Image processing for the cryo-EM data of nucleotide-free LptB₂FGC in nanodiscs.

Different subsets of particle images were selected from different classification schemes to produce four refined cryo-EM maps: final LptB₂FGC map at 4.2-Å resolution, LptB₂FGC map with clear LPS density at 4.4-Å resolution, long-bjr LptB₂FGC map at 4.8-Å resolution and short-bjr LptB₂FGC map at 5.9-Å resolution. After the first round of 3D classification, all particles classified into the two best classes (#4 and #5) in the final 5 iterations (indicated as “5 cycles”) were kept for further processing.