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Building de novo cryo-electron microscopy structures collaboratively with citizen scientists

Fig 1

Comparison of model building for Afp7 in (A) an overall view and (B and C) views to compare side-chain fitting.

The Foldit structure is rendered in green, the microscopist structure in gray, the Phenix model in magenta, and Rosetta model in yellow. Because of the large deviations from the other structures, the Rosetta model is omitted in the zoomed-in views in parts B and C. The electron potential map is contoured at 2 σ. (D, E, and F) Comparison of key geometric and map fit parameters for each of the cases displayed here. (D) Comparison of Ramachandran outlier and allowed backbone conformations. (E) Comparison of Molprobity Clashscore—in both cases, lower is better. (F) Comparison of 3 different map-to-model correlation coefficients, in which higher values are better. More complete statistical analysis can be found in Table 1 and S8 Fig, with the underlying data provided in S1 Data. (G) Map-to-model FSC curves for Microscopist (gray), Foldit (green), Phenix (pink), ARP w/ARP (orange), and Buccaneer (blue) models. CCmask, CCbox, CCpeaks, and CCvolume are correlation coefficients calculated between the model and the map. The differences between these correlation coefficients arise from whether the entire map is used (CCbox), only the map around the atomic centers (CCmask), the molecular envelope defined by the model (CCvolume), or the strongest peaks in the model and map (CCpeaks) [14]. Afp7, antefeeding prophage 7; FSC, Fourier shell correlation; RMSD, root mean square deviation.

Fig 1

doi: https://doi.org/10.1371/journal.pbio.3000472.g001