Figure 5: Cross-validation of different deposited MxiH needle models.
Histogram of shortest identified distances for (a) a final model obtained from the hybrid structure determination approach presented here (PDB ID 2MME) and (b) the model reported by Fujii et al.22 by fitting of the 7.7-Å cryo-EM density map (EMD 5352) alone (PDB ID 3J0R). For each observed cross-peak part of the calculation set (yellow, 996 correlations) and validation set (orange, 691 correlations), the shortest distance is calculated considering all possible chemical-shift assignments within the chemical-shift tolerance window (±0.15 p.p.m. for 13C chemical shifts) and all 7 possible subunit assignments (see Fig. 1b). By considering only the shortest distance, this procedure prevents the introduction of any bias in the cross-validation statistics arising from manual peak picking of the ssNMR spectra. The validation set was not used at any time in the structure calculations. Experimentally observed correlations that have an inter-nuclear distance above 12 Å in each model are classified as violations (red histograms). The present model (a) fits the validation data set by an average of 1.22 Å per distance constraint shorter than b (paired difference Student’s t-test, 95% confidence level).
