Table 1. Data collection, model building, refinement, and validation statistics for cryo-electron microscopy (cryo-EM) data obtained in this study.
| Human large ribosomal subunit (obtained from METTL18 KO cells) (PDB: 7F5S, EMD-31465) | |
|---|---|
| Data collection and processing | |
| Microscope | Tecnai Arctica |
| Camera | K2 Summit |
| Magnification | 39,000 |
| Voltage (kV) | 200 |
| Electron exposure (e-/Å2) | 50 |
| Exposure per frame | 1.25 |
| Number of frames collected | 40 |
| Defocus range (μm) | –1.5 to –3.1 |
| Micrographs (no.) | 5,517 |
| Pixel size (Å) | 0.97 |
| 3D processing package | RELION-3.1 |
| Symmetry imposed | C1 |
| Initial particle images (no.) | 381,227 |
| Final particle images (no.) | 118,470 |
| Initial reference map | EMD-9701 (40 Å) |
| RELION estimated accuracy | |
| Rotations (°) | 0.162 |
| Translations (pixel) | 0.287 |
| Map resolution | |
| masked (FSC = 0.143, Å) | 2.72 |
| Map sharpening B-factor | –63.0 |
| Refinement | |
| Model refinement package | phenix.real_space_refine |
| Initial model used | 6QZP |
| Model composition | |
| Chains | 45 |
| Non-hydrogen atoms | 138,634 |
| Residues | Protein: 6509; nucleotide: 3991 |
| Ligands | ZN: 5, MG: 297 |
| B factors (Å2) | |
| Protein | 62.85 |
| Nucleotide | 81.15 |
| r.m.s. deviations | |
| Bond lengths (Å) | 0.010 |
| Bond angles (°) | 0.834 |
| Validation | |
| Molprobity score | 1.92 |
| Clashscore | 9.61 |
| Poor rotamers (%) | 0.13 |
| CaBLAM outliers (%) | 3.35 |
| Ramachandran plot | |
| Favored (%) | 93.79 |
| Allowed (%) | 6.08 |
| Disallowed (%) | 0.12 |
| Map CC (CCmask) | 0.90 |