Table 1.
Cryo-EM data collection, refinement and validation statistics
| WT E2BeF3−, E2P-like (map 3, EMD-24214; PDB 7N70) | WT E2-AlF4−, E2-Pi-like (map 6, EMD-24217; PDB 7N72) | WT E2-Pi, post-hydrolysis (map 12, EMD-24223; PDB 7N78) | WT E1P-ADP-like (map 7, EMD-24218; PDB 7N73) | D508N E1-ATP (map 8, EMD-24219; PDB 7N74) | D458N/D962N E1-apo (map 9, EMD-24220; PDB 7N75) | D458N/D962N E1-apo (map 10, EMD-24221; PDB 7N76) | D458N/D962N E1-AlF4−, E1P-like (map 11, EMD-24222; PDB 7N77) | |
|---|---|---|---|---|---|---|---|---|
|
| ||||||||
| Data collection and processing | ||||||||
| Magnification | 64,000x | 64,000x | 64,000x | 64,000x | 64,000x | 64,000x | 64,000x | 36,000x |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 200 |
| Electron exposure (e−/Å2) | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 |
| Defocus range (μm) | −0.7 to −2.5 | −0.7 to −2.5 | −0.7 to −2.5 | −0.7 to −2.5 | −0.9 to −2.4 | −0.8 to −2.5 | −0.8 to −2.5 | −0.7 to −1.8 |
| Pixel size (Å) | 0.911 | 1.049 | 0.911 | 1.049 | 0.911 | 1.049 | 1.049 | 1.115 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 1,437,395 | 1,311,023 | n/a | 1,311,023 | 1,431,882 | 1,181,866 | 1,181,866 | 1,406,963 |
| Final particle images (no.) | 386,118 | 462,490 | 591,903 | 163,433 | 459,541 | 186,331 | 188,879 | 377,365 |
| Map resolution (Å) | 2.8 | 2.5 | 3.0 | 2.9 | 2.8 | 2.9 | 2.9 | 3.2 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.5–12 | 2.4–8 | 2.6–8 | 2.5–11 | 2.4–8 | 2.4–8 | 2.5–8 | 2.8–8 |
| Refinement | ||||||||
| Initial model used | De novo | Model 3 | Model 6 | Model 3 | Model 7 | Model 7 | Model 7 | Model 7 |
| Model resolution (Å) | 3.0 | 2.7 | 3.1 | 3.1 | 3.0 | 3.0 | 3.0 | 3.4 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| Map sharpening B factor (Å2) | 75 | 63 | 116 | 56 | 99 | 79 | 77 | 117 |
| Model composition | ||||||||
| Non-hydrogen atoms | 8,027 | 8,035 | 7,999 | 7,976 | 7,969 | 7,381 | 7,399 | 7,564 |
| Protein residues | 1,032 | 1,030 | 1,030 | 1,036 | 1,036 | 1,036 | 1,036 | 1,036 |
| Ligands | 4 | 11 | 11 | 6 | 4 | 0 | 0 | 4 |
| B factors (Å2) | ||||||||
| Protein | 49 | 66 | 74 | 76 | 44 | 56 | 73 | 29 |
| Ligand | 48 | 51 | 49 | 65 | 37 | - | - | 16 |
| R.m.s. deviations | ||||||||
| Bond lengths (Å) | 0.005 | 0.007 | 0.010 | 0.005 | 0.005 | 0.007 | 0.005 | 0.005 |
| Bond angles (°) | 0.649 | 0.745 | 0.783 | 0.631 | 0.735 | 0.689 | 0.647 | 0.698 |
| Validation | ||||||||
| MolProbity score | 1.43 | 1.33 | 1.55 | 1.55 | 1.46 | 1.61 | 1.53 | 1.73 |
| Clashscore | 7.93 | 5.99 | 8.15 | 7.76 | 7.46 | 7.91 | 5.80 | 9.56 |
| Poor rotamers (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ramachandran plot | ||||||||
| Favored (%) | 98.43 | 98.62 | 97.44 | 97.36 | 97.75 | 96.97 | 96.68 | 96.48 |
| Allowed (%) | 1.57 | 1.38 | 2.56 | 2.64 | 2.25 | 3.03 | 3.32 | 3.52 |
| Disallowed (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Rama-Z | 0.27 | 0.87 | 1.34 | 1.31 | 0.74 | 0.75 | 0.22 | 1.56 |
| CaBLAM outliers (%) | 0.80 | 0.80 | 1.00 | 0.59 | 0.49 | 0.89 | 0.49 | 0.99 |