Improved resolution of the averaged CA structure. (A and B) Tomographic slices of the averaged 32-nm repeat of the Chlamydomonas WT CA viewed in cross section to compare data recorded with either a CCD camera (A) or a direct electron detector and Volta Phase Plate (K2/VPP; B). Thin white lines in A and B indicate the locations of the slices shown in E and G, respectively. (C) FSC curves of the CA averages show that the resolution is improved from 3.5 nm for CCD data to 2.3 nm for K2/VPP data (0.5 criterion). (D–G) Tomographic slices to compare the C2 microtubule-associated structures between the CCD (D and E) and the K2/VPP data (F and G) in cross-sectional (D and F) and longitudinal (E and G) views. Note the clear visualizations of (a) filamentous, microtubule-associated proteins between protofilaments 9–12 (white arrowheads in F and G), (b) two distinct domains of the microtubule inner protein (MIP) C2a (black arrows in G), and (c) the tubulin lattice of the microtubule wall (G) in the K2/VPP data, which were not observed or were blurred in the CCD data. (H) Isosurface rendering shows the averaged Chlamydomonas WT CA (K2/VPP data) in cross-sectional view. Naming and coloring of CA projections adopted from Mitchell and Sale (1999) and Carbajal-González et al. (2013). CA protofilaments were not previously numbered; here we assigned protofilament #1 of C1 and C2 to where the C1a and C2a projections attach, respectively. In all figures, cross sections are viewed from proximal (i.e., cell body) to the ciliary tip, and in longitudinal views the proximal side is on the right (except for Fig. 1, E and G; and Fig. S1, A–E). Scale bar in B, 20 nm (valid for A and B); in G, 20 nm (valid for D–G).