Extended Data Fig. 4: Cryo-EM for apoferritin.
a, Representative electron micrograph. Scale bar is 20 nm. b, 2D class average images. c, Local resolution map. d, Fourier Shell Correlation (FSC) between the two independently refined half-maps. e, FSC between the model and the map as calculated for the model refined against the full reconstruction against that map (black); the model refined in the first half-map against that half-map (FSCwork; blue); and the model refined in the first half-map against the second half-map (FSCtest; dashed orange). FSCwork and FSCtest curves are shown for three different models: with hydrogens and anisotropic B-factors (solid lines); with hydrogens and isotropic B-factors (dashed lines); and without hydrogens and with isotropic B-factors (dotted lines). Including hydrogens and using anisotropic B-factors gives a better fit to the data at medium resolution, but lead to a small amount of overfitting at high resolution. Atomic models were refined including spatial frequencies up to 1.15 Å. f, The beam tilt in X (blue) and Y (orange); the resolution (res.) for subsets of 5,000 consecutive particles (black); and RELION's rlnGroupScaleCorrection values for individual micrographs (blue dots) during the data acquisition experiment. Events like CFEG flashing (red), liquid nitrogen filling (black) and moving the grid to another grid square (dark blue) are indicated with vertical lines. The cutoff in scale correction values used to discard part of the micrographs is indicated with a dashed grey line.
