Table 1B.
(Cont.). Cryo-EM data collection, refinement and validation statistics
| Pre2-KmAgogDtD (EMD-38412) (PDB: 8XK0) | Cleaved-KmAgogDtD (EMD-38414) (PDB: 8XK3) | Released-KmAgogDtD (EMD-38415) (PDB: 8XK4) | |
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 105 000 | 105 000 | 105 000 |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 54 | 54 | 54 |
| Defocus range (μm) | −1.0 ∼ −1.5 | −1.0 ∼ −1.5 | −1.0 ∼ −1.5 |
| Pixel size (Å) | 0.851 | 0.851 | 0.851 |
| Symmetry imposed | C1 | C1 | C1 |
| Initial particle images (no.) | 8 545 993 | 7 443 662 | 7 443 662 |
| Final particle images (no.) | 199 254 | 308 521 | 288 696 |
| Map resolution (Å) | 2.96 | 2.76 | 2.76 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.48–41.04 | 2.42–39.41 | 2.41–42.82 |
| Refinement | |||
| Initial model used | KmAgoapo | KmAgoapo | KmAgoapo |
| Model resolution (Å) | 2.91 | 2.72 | 2.75 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Model resolution range(Å) | n/a. | n/a. | n/a. |
| Map sharpening B factor (Å2) | −129.4 | −120.4 | −119.9 |
| Model composition | |||
| Non-hydrogen atoms | 6301 | 6309 | 6049 |
| Protein residues | 692 | 692 | 689 |
| Ligand | 2 | 3 | 3 |
| B-factors (Å2) | |||
| Protein | 28.95/102.36/48.40 | 24.12/71.89/41.39 | 40.02/118.37/60.99 |
| Nucleotide | 30.69/101.34/50.77 | 13.22/68.90/39.99 | 44.27/112.92/58.20 |
| Ligand | 40.00/53.16/46.58 | 36.44/49.50/42.26 | 51.88/73.39/65.68 |
| Water | 13.62/41.51/24.93 | 12.73/36.00/25.53 | 25.17/27.24/26.21 |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.006 | 0.003 | 0.003 |
| Bond angles (o) | 0.670 | 0.545 | 0.573 |
| Validation | |||
| MolProbity score | 1.85 | 1.63 | 1.67 |
| Clashscore | 5.94 | 5.29 | 7.56 |
| Poor rotamer (%) | 0.00 | 0.00 | 0.00 |
| Ramachandran plot | |||
| Favored (%) | 92.57 | 95.04 | 96.18 |
| Allowed (%) | 7.43 | 4.96 | 3.82 |
| Disallowed (%) | 0.00 | 0.00 | 0.00 |