Table 1.
Cryo-EM data collection, refinement, and validation statistics.
| RNase Z-HS (EMDB-50050) (PDB 9EY0) | RNase ZH548A-HS (EMDB-50051) (PDB 9EY1) | RNase Z-HCCA (EMDB-50052) (PDB 9EY2) | RNase Z-HCCA TRMT10C/SDR5C1 focus (EMDB-51230) (PDB 9GCH) | |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 165,000 | 165,000 | 165,000 | 165,000 |
| Voltage (kV), source | 300, XFEG | 300, XFEG | 300, E-CFEG | 300, E-CFEG |
| Electron exposure (e–/Å2) | 59 | 59 | 59 | 59 |
| Underfocus range (μm) | 0.2–2 | 0.2–2 | 0.2–2 | 0.2–2 |
| Pixel size (Å) | 0.505 | 0.505 | 0.505 | 0.505 |
| Symmetry imposed | P1 | P1 | P1 | P1 |
| Initial particle images (no.) | 293,145 | 643,629 | 4,773,315 | 4,773,315 |
| Final particle images (no.) | 28,771 | 15,961 | 4346 | 293,773 |
| Map resolution (Å)a | 2.94 | 2.92 | 2.96 | 1.90 |
| Global refinement | 2.78b | 2.69b | 3.1c | |
| ELAC2 focus | 3.07b | 3.34b | 3.2c | |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å)d | ||||
| Min, 25th percentile | 2.204, 3.110, 3.872 | 2.204, 3.153 | 1.486, 3.372 | 1.545, 2.007 |
| Median, 75th percentile | 6.156, 44.472 | 3.845, 5.530, 46.799 | 4.560, 7.171, | 2.392, 3.750, 26.869 |
| Max | 48.229 | |||
| Refinement | ||||
| Initial model used (PDB code) | 7ONU | 7ONU | 7ONU | 7ONU |
| Model resolution (Å) | 3.0 | 2.8 | 3.1 | 1.9 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 |
| Model composition | ||||
| Non-hydrogen atoms | 16,691 | 16,783 | 16,556 | 11,235 |
| Protein/RNA residues | 2008/65 | 2009/69 | 1982/68 | 1304/68 |
| Ligands | GTP:1 Zn:2 SAM:1 | GTP:1 Zn:1 SAM:1 | GTP:1 Zn:2 SAM:1 | GTP:1 Mg:1 SAM:1 |
| B factors (Å2) | ||||
| Protein | 22.1/186.4/74.99 | 0/106.2/35.1 | 24.69/419.90/52.20 | 2.08/144.89/25.72 |
| RNA | 40.5/147.0/90.5 | 9.8/167.9/70.0 | 28.66/141.64/58.40 | 5.91/158.23/44.49 |
| Ligand | 42.8/189.2/85.3 | 78.55/171.39/91.80 | 35.69/164.93/76.06 | 13.90/145.87/70.29 |
| Water | 18.21/34.63/26.14 | |||
| r.m.s. deviations | ||||
| Bond lengths (Å) | 0.004 | 0.005 | 0.004 | 0.003 |
| Bond angles (°) | 0.540 | 0.634 | 0.504 | 0.489 |
| Validation | ||||
| MolProbity score | 1.36 | 1.38 | 1.38 | 1.19 |
| Clashscore | 4.49 | 4.90 | 6.16 | 4.05 |
| Poor rotamers (%) | 0.18 | 0.43 | 0.00 | 0.00 |
| Ramachandran plot | ||||
| Favored (%) | 97.29 | 97.34 | 97.81 | 98.22 |
| Allowed (%) | 2.71 | 2.66 | 2.09 | 1.78 |
| Disallowed (%) | 0.00 | 0.05 | 0.10 | 0.00 |
aGold-standard 0.143 FSC resolution calculated with 3DFSC (Tan et al, 2017). The masks for FSC calculation were generated in CryoSPARC using a relative threshold of 0.5.
bGold-standard 0.143 FSC resolution calculated by CryoSPARC with the auto-tightened refinement mask.
cGold-standard 0.143 FSC resolution calculated by RELION postprocess using the refinement mask.
dMap resolution range calculated with CryoSPARC v4.3.1 BlocRes and FSC threshold of 0.5.