PMC

Flexible fitting benchmark. Shown are the RMSD values for the final results of flexible fitting with ISD (light blue) and Flex-EM (dark blue) in comparison to the RMSD of the initial structure to the target structure (green). (A) Flexible fitting results for 1uwo, 1g5y, 1ccz, 1jxm. (B) Flexible fitting results for 1ake, 1cll, 1c1x.

Multi-body modeling of GroEL/ES. Shown is the RMSD between structural models obtained by posterior sampling with ISD and the crystal structure (PDB code 1aon). (A) RMSD for GroEL subunits for both 7-membered rings (chains A–G and chains H–N) and for the entire 14-mer (chains A–N). (B) RMSD for GroES (chains O–U) (C) RMSD for the entire 21-mer. (D) Correlation between the overall RMSD (21-mer) and the cross-correlation coefficient.

Estimation of the precision λ of the GroEL/ES map. (A–D) Show the distribution of the “error” (or discrepancy) between the experimental and calculated maps ρ_n − ρ(x_n; θ, σ). Error distribution for the full map (A), full map after cropping (B), the downsampled and cropped map (C), the downsampled, cropped and masked map (D). (E) Estimated precision for the different input maps used in multi-body fitting.

Flexible fitting of adenylate kinase into a 10 Å map. (A) Evolution of the RMSD to the initial structure (4ake) shown in dark blue and the target structure (1ake) shown in light blue. (B) Evolution of the cross-correlation coefficient during flexible fitting. (C) RMSD reduced to Cα atoms that are part of the same rigid domain.

Major structural clusters of the GroEL 14-mer generated from the prior distribution confined to a box. Subunits are color coded. The lowest energy clusters are shown on top (structures 1–3). The second lowest energy structures are clusters 4 and 5. Structure 6 is a rare high energy configuration that is also generated by replica-exchange Monte Carlo.