Table 1.
Cryo-EM data collection, refinement, and validation statistics of mtHsp60 structures
| mtHsp60apo consensus (EMD-29813, PDB 8G7J) | mtHsp60apo focus (EMD-29814, PDB 8G7K) | mtHsp60ATP consensus (EMD-29815, PDB 8G7L) | mtHsp60ATP focus (EMD-29816, PDB 8G7M) | mtHsp60ATP-mtHsp10 consensus (EMD-29817, PDB 8G7N) | mtHsp60ATP-mtHsp10 focus (EMD-29818, PDB 8G7O) | |
|---|---|---|---|---|---|---|
| Data collection and processing | ||||||
| Microscope and camera | Glacios, K2 | Glacios, K2 | Glacios, K2 | Glacios, K2 | Glacios, K2 | Glacios, K2 |
| Magnification | 53,937 | 53,937 | 53,937 | 53,937 | 53,937 | 53,937 |
| Voltage (kV) | 200 | 200 | 200 | 200 | 200 | 200 |
| Data acquisition software | SerialEM | SerialEM | SerialEM | SerialEM | SerialEM | SerialEM |
| Exposure navigation | Image shift | Image shift | Image shift | Image shift | Image shift | Image shift |
| Electron exposure (e−/Å2) | 66 | 66 | 66 | 66 | 66 | 66 |
| Defocus range (μm) | −0.5 to −2.5 | −0.5 to −2.5 | −1.0 to −2.5 | −1.0 to −2.5 | −0.5 to −3.0 | −0.5 to −3.0 |
| Pixel size (Å) | 0.927 | 0.927 | 0.927 | 0.927 | 0.927 | 0.927 |
| Symmetry imposed | C7 | C1 | D7 | C1 | D7 | C1 |
| Initial particle images (no.) | 970,545 | 970,545 | 696,761 | 696,761 | 113,390 | 113,390 |
| Final particle images (no.) | 839,799 | 192,680 | 405,263 | 137,145 | 81,840 | 37,628 |
| Map resolution (Å) | 3.4 | 3.8 | 2.5 | 3.2 | 2.7 | 3.4 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.5–8 | 3–6 | 2–6 | 2.5–8 | 2–7 | 2.5–8 |
| Refinement | ||||||
| Model resolution (Å) | 3.6 | 4.1 | 2.7 | 3.4 | 2.8 | 3.6 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| Map sharpening B factor (Å2) | −221.8 | −157.4 | −127.9 | −120.0 | −120.6 | −91.8 |
| Model composition | ||||||
| Nonhydrogen atoms | 27,461 | 27,461 | 55,524 | 26,334 | 66,122 | 33,047 |
| Protein residues | 3,682 | 3,682 | 7,378 | 3,505 | 8,778 | 4,389 |
| Ligands | 0 | 0 | 42 | 21 | 42 | 7 |
| B factors (Å2) | ||||||
| Protein | 67.39 | 67.39 | 107.82 | 107.52 | 39.67 | 90.40 |
| Ligand | N/A | N/A | 23.99 | 44.80 | 11.75 | 61.26 |
| R. m. s. deviations | ||||||
| Bond lengths (Å) | 0.015 | 0.014 | 0.008 | 0.004 | 0.004 | 0.003 |
| Bond angles (°) | 1.525 | 1.509 | 1.350 | 0.940 | 0.972 | 0.572 |
| Validation | ||||||
| MolProbity score | 0.83 | 0.87 | 0.91 | 1.25 | 1.04 | 1.24 |
| Clashscore | 1.16 | 1.41 | 1.63 | 4.88 | 2.56 | 3.99 |
| Poor rotamers (%) | 0.00 | 0.00 | 0.79 | 0.00 | 0.20 | 0.00 |
| Ramachandran plot | ||||||
| Favored (%) | 99.24 | 98.99 | 99.37 | 99.17 | 99.04 | 97.78 |
| Allowed (%) | 0.68 | 0.82 | 0.63 | 0.83 | 0.96 | 2.22 |
| Disallowed (%) | 0.08 | 0.19 | 0.00 | 0.00 | 0.00 | 0.00 |