Results of comparisons between distances predicted by biochemical experiments and crystal coordinates of rRNA and proteins in the ribosome. The Y-axis shows the number of matching (shades of yellow) and mismatching (shades of blue) data points for different types of experiments.

Distribution of regions for which no crosslinking, footprinting, or cleavage information was available (dim gray in A, B, D and E) and ≥25% of the data available was in disagreement with crystal structures (blue in A, B, D and E). (A) Ratios of mismatches mapped into secondary structure of ribosomal 16S RNA. Proteins bearing >25% mismatches in crystallography vs. biochemistry comparisons (see the text) are shown as blue circles placed approximately near binding sites in RNA. (B) Interface of the 30S subunit. The same color scheme as in A, but rendered in three dimensions. (C) Ligand-binding regions (; ; ; ) and regions found to be flexible in comparative structural studies (see ; ; ; ; ) mapped into crystal structures of the 30S subunit (PDB identification: 1GIX; ). (D) Secondary structure diagram of the 23S RNA, 5S RNA, and associated proteins, colored in dark gold if data available for the region generally were in good agreement (<25% of mismatch); blue, >25% of mismatches; and gray, no data in our data set. (E) Interface of the 50S subunit. The same color scheme as in D, but rendered in three dimensions. (F) Ligand-binding regions and regions found to be flexible in comparative structural studies (; ; ; ) mapped into crystal structures of the 50S subunit (PDB identification: 1GIY; ). Landmarks show macroscopic features of the 30S and 50S subunits known from electron microscopy: h indicates head; bk, beak; sp, spur; and CP, central protuberance (where the 5S RNA is located); as well as proteins L1, L9, and L7/L12 dimer.

Vectors representing major clusters suggesting local movements (A–C) and exemplar subsets of coherent violation vectors suggesting more global motions (D–F) are shown for the 30S subunit (A, D), 50S subunit (B, E), and 70S ribosome (C, F). Color code for ribosomal subunits and intersubunit measurements is as follows: gold indicates 30S subunit; goldenrod, 50S subunit; blue, intrasubunit crosslinks; purple, footprints; turquoise, cleavage; and transparent black, intersubunit crosslinks. When shown on the 70S ribosome (C), 30S subunit vectors are shaded in red. Arrows of vectors shown in D–F are represented as balls of smaller radius (compared with initial points), circled in red. (Note that not all vectors are visible in the three-dimensional figure due to partial or complete overlapping.)