Fig. 3.

Comparison of atomic models of E. coli β-galactosidase derived by X-ray crystallography at 1.7-Å resolution and by cryo-EM at 3.2-Å resolution. (A) X-ray structure of E. coli β-galactosidase (PDB ID code 1DP0; ref. 21) after alignment to the cryo-EM structure shown in ribbon representation colored according to rmsd values [ranging from blue (low) to red (high)]. Each chain was aligned separately in Chimera, using the default algorithm (Needleman–Wunsch in BLOSUM-62 Matrix). Highlighted areas shown as red spheres correspond to regions marked with asterisks (* and **) with rmsd values for Cα over 2 Å that are involved in crystal contacts (Fig. S9). (B–D) Local deviations between the atomic model derived from X-ray crystallography (Left in gray sticks) and the atomic model derived from cryo-EM (Right in light blue sticks) superimposed on the cryo-EM density map (mesh representation). Zones of protein-protein contacts in the crystal lattice including residues 179–189 (marked * in A) are shown in B, and the region including residues 310–320 (marked ** in A) is shown in C. Example of local deviations near residues 50–55, which are not involved in crystal contacts but located at the periphery of the enzyme is shown in D. In all examples, displacement of side chains and the backbone regions is visible.