TABLE 1.
CryoEM data collection, single-particle reconstruction maps, and model statistics
| State 2 | State 1 | |
|---|---|---|
| Data collection information | PNCC #160258 – Krios-3 | |
| Nominal magnification | 105,000× | |
| Voltage (kV) | 300 | |
| Electron dose (e−/Å2) | 40.94 | |
| Physical pixel size (super-res) (Å) | 0.65 (0.325) | |
| Movies amount | 8,337 | |
| Defocus average and range (µm) | 1.2 (0.5–2.0) | |
| Frames | 51 | |
| Single-particle reconstruction information | EMD-44533 | EMD-45392 |
| Initial particles picked | 997,400 | 997,400 |
| Particles in the final map | 98,135 | 145,659 |
| Initial model used | Ab initio | Ab initio |
| Symmetry imposed | C1 | C1 |
| Map overall resolution - FSC0.143 (Å) | 2.63 | 2.59 |
| Map resolution range (Å) | 2.5–3.5 | 2.5–3.5 |
| Map sharpening B-factor (Å2) |
59.4 | 63.4 |
| Built model information | PDB 9BH5 | PDB 9CAI |
| Chains | 130 | 79 |
| Atoms (non-H) | 332,769 | 330,203 |
| Protein residues | 10,633 | 10,629 |
| Nucleotides | 4,925 | 4,849 |
| Ligands | SPD:1 | SPD:1 |
| 3HE:1 | 3HE:1 | |
| Bonds (RMSD) | ||
| Length (Å, # > 4σ) | 0.006 (10) | 0.004 (10) |
| Angles (°, # > 4σ) | 0.607 (29) | 0.571 (29) |
| Mean B-factor (Å2) | 190332/0 | 188673/0 |
| Protein (min/max/mean) | 36.34/200.37/88.15 | 41.59/226.71/97.25 |
| Nucleotide (min/max/mean) | 31.68/261.66/83.13 | 35.27/260.86/88.57 |
| Ligand (min/max/mean) | 46.86/78.64/60.50 | 45.85/86.75/66.62 |
| MolProbity score | 1.80 | 1.66 |
| Clashscore | 5.41 | 6.35 |
| Ramachandran plot | ||
| Favored (%) | 96.78 | 97.16 |
| Allowed (%) | 3.20 | 2.83 |
| Outliers (%) | 0.02 | 0.01 |
| Rama-Z (Ramachandran plot Z-score, RMSD) | ||
| Whole (N = 3625) | 0.54 (0.08) | 0.64 (0.08) |
| Helix (N = 1443) | 1.61 (0.09) | 1.73 (0.09) |
| Sheet (N = 472) | 0.26 (0.12) | 0.30 (0.12) |
| Loop (N = 1710) | 0.27 (0.08) | 0.24 (0.09) |
| Rotamer outliers (%) | 2.52 | 1.59 |
| Cβ outliers (%) | 0.00 | 0.00 |
| Peptide plane (%) | ||
| Cis proline/general | 2.9/0.0 | 2.9/0.0 |
| Twisted proline/general | 0.2/0.0 | 0.2/0.0 |
| CaBLAM outliers (%) | 1.52 | 1.53 |
| Occupancy | ||
| Mean | 1.00 | 1.00 |
| occ = 1 (%) | 100.00 | 100.00 |
| 0 < occ < 1 (%) | 0.00 | 0.00 |
| occ > 1 (%) | 0.00 | 0.00 |
| Model versus data | ||
| Mean CC for ligands | 0.86 | 0.83 |
| CC (peaks) | 0.73 | 0.70 |
| CC (volume) | 0.88 | 0.86 |
| CC (box) | 0.78 | 0.76 |
| CC (mask) | 0.89 | 0.86 |
