Extended Data Table 1:
Data collection and refinement statistics.
| E. coli disome-SmrB stalled 70S; validation against focus refined map (EMDB-13956) (PDB 7QGN) | E. coli disome-SmrB collided 70S with SmrB and mRNA; validation against focus refined map (EMDB-13958) (PDB 7QGR) | E. coli disome stalled 70S ribosome; validation against focus refined map (EMDB-13952) (PDB 7QG8) | E. coli disome collided 70S ribosome; validation against focus refined map (EMDB-13955) (PDB 7QGH) | E. coli tri some (EMDB-13964) | B. subtilis disome stalled 70S ribosome (EMDB-13959) (PDB 7QGU) | B. subtilis disome collided 70S ribosome (EMDB-13961) (PDB 7QH4) | |
|---|---|---|---|---|---|---|---|
| Data collection and processing | |||||||
| Magnification | 130,000 | 130,000 | 75,000 | 75,000 | 75.000 | 75,000 | 75.000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e-/Å2) | 42.4 | 42.4 | 40 | 40 | 40 | 25 | 25 |
| Defocus range (μm) | 0.5–3.5 | 0.5–3.5 | 0.5–4 | 0.5–4 | 0.5–4 | 0.5–4 | 0.5–4 |
| Pixel size (Å) | 1.059 | 1.059 | 1.09 | 1.09 | 1.09 | 1.084 | 1.084 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 651,789 | 651,789 | 238,082 | 238,082 | 448,847 | 2,761,261 | 2,761,261 |
| Final particle images (no.) | 32,412 | 32,412 | 75,081 | 75,081 | 45,952 | 12,739 | 12,739 |
| Map resolution (Å) | 3.37 | 3.78 | 3.97 | 4.48 | 13.29 | 4.75 | 5.45 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.9–17 | 3.3–18.6 | 3.5–14 | 3.7–15.6 | 4.4–25.7 | 4.8–21.6 | |
| Refinement | |||||||
| Initial model used | 5NWY | 5NWY | 5NWY | 5NWY | 3J9W | 3J9W | |
| (PDB code) | 6WD1 (bL9, L1 stalk) | 6WD1 (bL9, L1 stalk) | 6WD1 (bL9, L1 stalk) | 6WD1 (bL9, L1 stalk) | |||
| 3L0U (tRNA) | 3L0U (tRNA) | 3L0U (tRNA) | 3L0U (tRNA) | ||||
| Model resolution (Å) | 3.4 | 4.3 | 4.9 | 5.0 | 4.5 | 5.1 | |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | |
| Map sharpening B factor (Å2) | −53.6 | −63.0 | −145.2 | −167.3 | −158.1 | −198.7 | |
| Model composition | |||||||
| Non-hydrogen atoms | 147,306 | 149,850 | 147,112 | 147,973 | 136,024 | 136,043 | |
| Protein residues | 5,975 | 6,223 | 5,936 | 6,046 | 5,791 | 5,573 | |
| Nucleotide residues | 4,695 | 4,746 | 4,695 | 4,716 | 4,656 | 4,733 | |
| R.m.s. deviations | |||||||
| Bond lengths (Å) | 0.016 | 0.016 | 0.016 | 0.016 | 0.009 | 0.009 | |
| Bond angles (°) | 1.647 | 1.641 | 1.648 | 1.642 | 1.462 | 1.452 | |
| Validation | |||||||
| MolProbity score | 1.95 | 1.96 | 1.95 | 1.95 | 2.14 | 2.07 | |
| Clashscore | 4.89 | 5.83 | 4.85 | 5.43 | 12.74 | 11.82 | |
| Poor rotamers (%) | 1.61 | 1.38 | 1.61 | 1.41 | 0.53 | 0.19 | |
| Ramachandran plot | |||||||
| Favored (%) | 90.40 | 90.33 | 90.35 | 90.20 | 91.02 | 92.01 | |
| Allowed (%) | 8.60 | 8.66 | 8.63 | 8.79 | 6.64 | 6.06 | |
| Disallowed (%) | 1.01 | 1.01 | 1.01 | 1.01 | 2.34 | 1.93 | |
| Map vs. Model CC | 0.23 | 0.25 | 0.45 | 0.45 | 0.63 | 0.49 |