Fig. 3.

Selection of TcdA1 particles and structural analysis. a–c Representative digital micrograph (micrograph number 0169) taken from the EMPIAR-10089 dataset. Red boxes indicate the particles selected by a Gauss-Boxer, b crYOLO, or c the generalized crYOLO network. Scale bar, 50 nm. d Summary of particle selection and structural analysis of the three datasets. All datasets were processed using the same workflow in SPHIRE. e Representative reference-free 2-D class averages of TcdA1 obtained using the ISAC and Beautifier tools (SPHIRE) from particles picked using crYOLO. Scale bar, 10 nm. f Fourier shell correlation (FSC) curves of the 3-D reconstructions calculated from the particles selected in crYOLO and Gauss-Boxer. The FSC 0.143 between the independently refined and masked half-maps indicates resolutions of ~3.4 and ~3.5 Å, respectively. g The final density map of TcdA1 obtained from particles picked by crYOLO is shown from the side and is colored by subunit. The reconstruction using particles from the generalized crYOLO network is indistinguishable