Extended data Figure 9. Simulation of STORM data using EM particle reconstruction data.

a, Left panel, End-on view of reconstructed TORC1 helix fitted with 9 TORC1 particles in dark green, dark red and purple (c.f. Figure 3). Middle panel, Crystal structure of GFP (light green) was added to the reconstructed helix at sites identified as Raptor/Kog1 N-termini. Right panel, Crystal structure of anti-GFP nanobody (red) was added to a subset of the GFP structures, according to the labelling efficiency estimated for our experimental conditions (~20%). The localisation precision is indicated as a red cloud. b, 3D representation of the simulated starting model according to a. Red and blue spheres denote GFP positions. c, Simulated STORM images. Helices of different lengths were generated based on the distribution of focus sizes observed in vivo (Figure 2 and bar graph). Orientations of these helices were randomized in 3D (XYZ) space and then projected in 2D (XY). Coloured spheres denote GFP positions, a random fraction of which were considered labeled according to our experimentally determined labelling efficiency (see SMLM simulation in Methods for more details). d, Reconstructions of individual simulations from c, classified according to their eccentricity and presence of a cavity. Scale bar 100 nm. e, Particle averages obtained from the images in d. f, Plot of the eccentricity distribution of the simulated and experimental STORM dataset.