Table 2 ∣.
Cryo-EM data collection, refinement and validation statistics of PCSK9-RNC
| PCSK9-RNC_AP tRNA (EMD-0596, PDB 6OM0) |
PCSK9-RNC_AA tRNA (EMD-0597, PDB 6OM7) |
PCSK9-RNC_PP tRNA (EMD-0598, PDB 6OLZ) |
|
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 43,478 | 43,478 | 43,478 |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 50 | 50 | 50 |
| Defocus range (μm) | 1.0 to 2.5 | 1.0 to 2.5 | 1.0 to 2.5 |
| Pixel size (Å) | 1.15 | 1.15 | 1.15 |
| Symmetry imposed | C1 | C1 | C1 |
| Initial particle images (no.) | 148,817 | 148,817 | 148,817 |
| Final particle images (no.) | 43,666 | 9,564 | 7,214 |
| Map resolution (Å) | 3.1 | 3.7 | 3.9 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.5 to 7.5 | 3 to 9 | 3 to 9 |
| Refinement | |||
| Initial model used (PDB code) | |||
| 40S subunit | 6ek0 | 6ek0 | 5aj0 |
| 60S subunit | 5aj0 | 5aj0 | 5aj0 |
| tRNA | 3j7r | 3j7r | 5aj0 |
| Model resolution (Å) | 3.1 | 3.7 | 3.9 |
| FSC threshold | 0.5 | 0.5 | 0.5 |
| Model resolution range (Å) | 2.5 to 7.5 | 3 to 9 | 3 to 9 |
| Map sharpening B factor (Å2) | −75 | −77 | −80 |
| Model composition | |||
| Nonhydrogen atoms | |||
| Protein residues | |||
| Ligands | |||
| B factors (Å2) | |||
| Protein | |||
| Ligand | |||
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.007 | 0.020 | 0.009 |
| Bond angles (°) | 1.036 | 1.190 | 1.222 |
| Validation | |||
| MolProbity score | |||
| Clashscore | 4.86 | 6.36 | 7.51 |
| Poor rotamers (%) | 1.25 | 1.03 | 0.83 |
| Ramachandran plot | |||
| Favored (%) | 90.02 | 87.57 | 88.18 |
| Allowed (%) | 9.54 | 12.11 | 11.36 |
| Disallowed (%) | 0.45 | 0.32 | 0.45 |