After we got the subtomogram average structure of the WT,motB-D24E,motB-D24N, ∆fliL, and CCCP treated WT motors, the regions around the 16 stator units (or corresponding regions) were rotationally aligned. Then 3D classification was based on the stator complex density in the extracted particles. Typically, we get three different class averages: class average with stator complex density, class average without stator complex density and class average that we are not sure whether there are stator complexes or not. Finally, the stator occupancy was calculated by dividing the particle numbers in the class average with stator complex densities over the total particle numbers. Three selected class averages from the classification results of WT (A-C), motB-D24E (D-F), motB-D24N (G-I) and ∆fliL(J-L), and CCCP treated WT (M-O) motor structures are shown here. (A, B, D, G, J, M, N, O) show class averages with stator complexes. (C, F, I and L) show class averages without stator complexes. (E, H and K) show class averages that we are not certain whether there are stator complexes or not.