Extended Data Fig. 4: Cryo-EM data processing of the D4 map (PDB: 8Q04).

a, 2D classes after manual picking of 465 particles, used for autopicking from all grids. b, Representative micrograph shown without (left) and with (right) autopicked particles (green circles). Autopicking resulted in 237,035 particles that were used in subsequent 2D classification. c, Selected 2D classes after classification, resulting in 224,593 particles that were used for 3D classification. d, Top view of the five 3D classes following classification, shown at the same contour level (0.01). Class 3 was used for subsequent refinements to create the final D4 map. Arrows indicate the regions of additional low resolution density at the equator of Rubisco. e, Post-processed map following refinement of class 3 with C1 symmetry imposed during refinement. f, Post-processed map following refinement with D4 symmetry. Maps in e and f are shown at a contour level of 0.032. g, Post-processed map following CTF refinement and Bayesian polishing with D4 symmetry imposed during refinement. The map is displayed at a contour level of 0.0553. h, Phenix local resolution estimate for the D4 CsRubisco map. i, Example density of residues 238–245 of the CsRbcL with the corresponding model coordinates, carved with a radius of 2 at a contour level of 0.0415. j, Overlay of cryo-EM structures of Rubisco from Chlorella solved in this study and from Chlamydomonas reinhardtii solved in a previous study³². k, Fourier shell correlation (FSC) curve showing the resolution estimate for the D4 refined map with FSC cut-off of 0.143 (dashed lines).