Table 1 Cryo-EM data collection, refinement and validation statistics. C1 cpzA3H–VCBC (EMDB-47805), (PDB 9E9V) and C2 (EMDB-47752), (PDB 9E93)
Data collection and processing | ||
---|---|---|
Microscope | Talos Arctica | Talos Arctica |
Detection camera | Gatan K3 | Gatan K3 |
Voltage (kV) | 200 | 200 |
Magnification | 100,000 | 100,000 |
Electron exposure (e − / Å2) | 45 | 45 |
Defocus range (μm) | 0.8 − 2.2 | 0.8 − 2.2 |
Pixel size (Å) | 0.81 | 0.81 |
Symmetry imposed | C2 | C1 |
Initial particle images (no.) | 10,231,372 | 6,580,020 |
Final particle images (no.) | 201,593 | 215,818 |
Map resolution (Å) | 3.63 | 4.0 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.97-8.0 | 3.5-7.7 |
Model building and refinement | ||
Initial model used (PDB code) | 4N9F, 5Z98 | 4N9F, 5Z98 |
Model resolution (Å) | 4.0 | 4.55 |
FSC threshold | 0.5 | 0.5 |
Model resolution range (Å) | 3.0-6.0 | 3.4-6.6 |
Map sharpening B factor (Å)a | -135.9 | -143.6 |
B factors (Å2) | ||
Protein | 83.51 | 160.61 |
Nucleotide | 84.91 | 107.42 |
Ligand | 102.2 | 182.24 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.002 | 0.001 |
(outliers >4 sigma) | 0 | 0 |
Bond angles (°) | 0.397 | 0.405 |
(outliers >4 sigma) | 2 | 6 |
Validation | ||
MolProbity score | 1.29 | 1.34 |
Clashscore | 5.46 | 4.31 |
Rotamer outliers (%) | 0.0 | 0 |
CaBLAM outliers (%) | 1.3 | 1.19 |
Cβ outliers (%) | 0 | 0 |
Ramachandran plot | ||
Favored (%) | 98.52 | 97.35 |
Allowed (%) | 1.48 | 2.65 |
Outliers (%) | 0.0 | 0.0 |
Model composition | ||
Nonhydrogen atoms | 8,773 | 10,936 |
Protein residues | 965 | 1241 |
Nucleotide residues | 32 | 32 |
Ligands | ZN: 4 | ZN: 4 |
Real-space correlation | ||
CCvolume | 0.75 | 0.6 |
CCmask | 0.75 | 0.61 |