Table 2.
Cryo-EM data collection, refinement, and validation statistics
| Data collection, refinement, and validation | Sb45+S-6P (1-up, 2-down) | Sb45+S-6P (2-up, 1-down) |
|---|---|---|
| EMDB ID | EMD-24105 | EMD-24106 |
| PDB ID | 7N0G | 7N0H |
| Data collection and processing | ||
| Magnification | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e−/Å) | 56 | 56 |
| Defocus range (μm) | −0.7 to −2.0 | −0.7 to −2.0 |
| Pixel size (Å/pixel) | 0.526 (1.052 binned) | 0.526 (1.052 binned) |
| Raw micrographs (No.) | 9725 | 9725 |
| Extract particles (No.) | 1,447,993 | 1,447,993 |
| Selected 2D particles (No.) | 662,994 | 662,994 |
| Refined particles (No.) | 417,460 | 417,460 |
| Particles for final map (No.) | 214,171 | 60,062 |
| Symmetry imposed | C1 | C1 |
| Map resolution (Å) | 3.02 | 3.34 |
| FSC threshold | 0.143 | 0.143 |
| Refinement | ||
| Initial model used | 6XKL, 7KGJ | 6XKL, 7KGJ |
| Model composition | ||
| Atoms | 29,062 | 27,974 |
| Residues | 3592 | 3469 |
| Ligands (NAG) | 73 | 64 |
| Overall B-factor (Å2) | ||
| Protein (min/max/mean) | 36.8/589.6/157.0 | 24.2/485.3/157.0 |
| Ligands (min/max/mean) | 55.3/340.1/129.9 | 51.8/358.8/144.5 |
| RMSDs | ||
| Bond length (Å) | 0.003 | 0.005 |
| Bond angle (°) | 0.548 | 0.972 |
| CC (mask/volume/peaks) | 0.84/0.84/0.77 | 0.83/0.83/0.77 |
| Validation | ||
| MolProbity score | 1.62 | 1.71 |
| Clashscore | 7.71 | 8.26 |
| Poor rotamers | 0.00 | 0.00 |
We did not use sharpened maps, and autosharpening by PHENIX did not improve the CC, so we kept the unsharpened maps for the refinement.