Extended Data Fig. 2: Restraint-based model reproduces cell-to-cell structural variability.
a Evolution of the number of input distance restraint violations from the experimental median distance matrix (Fig. 2a, left panel) when adding subsequent modeled structures to the ensemble obtained with the restraint-based approach. b End-to-end distance distributions for the experimental (gray) and modeled (red) ensembles. The boxes highlight the first, second and third quartiles, while the whiskers extend 1.5 times the interquartile range away from the box edges. Outliers are omitted. The plots come from 3,496 experimental and 70 modeled conformations. p = 0.16, two-sided Mann-Whitney test. c Root mean square deviation (rmsd) of bead/probe positions for best fitted modeled structures against each experimental structure (red, Nexp-model = 3,496), and null distribution of rmsd values between all experimental structures, after fitted / aligned (gray, Nnull = 6,109,260). p < 1e−16, two-sided Mann-Whitney test. The boxes highlight the first, second and third quartiles, while the whiskers extend 1.5 times the interquartile range away from the box edges. Outliers are omitted. d Variance from the first 10 principal components from PCA. e Projection of the displacement vectors onto the first 2 principal components from PCA. f 3D distance matrices for single structures extracted from experimental microscopy data18 (left) and from the ensemble obtained with the restraint-based model (right). The color scale ranges from 200 nm to 850 nm.
