Extended Data Table 1.
Cryo-EM data collection, refinement and validation statistics.
| PAM/PAM bound complex (EMDB-23839) (PDB 7MI4) |
PAM/non-PAM bound complex (EMDB-23840) (PDB 7MI5) |
Sub-complex (EMDB-23847) (PDB 7MID) |
Full integration (EMDB-23843) (PDB 7MI9) |
Half-int, PAM intact, Cas4 remains. (EMDB-23845) (PDB 7MIB) |
Half-int, PAM cleaved, Cas4 dissociated. (EMDB-23849) (PDB N/A) |
|
|---|---|---|---|---|---|---|
| Data collection and processing | ||||||
| Magnification | 63,000 | 63,000 | 63,000 | 63,000 | 63,000 | 63,000 |
| Voltage (kV) | 200 | 200 | 200 | 200 | 200 | 200 |
| Electron exposure (e–/υ2) | 50 | 50 | 50 | 50 | 50 | 50 |
| Defocus range (μm) | 1.5~3.5 | 1.5~3.5 | 1.5~3.5 | 1.5~3.5 | 1.5~3.5 | 1.5~3.5 |
| Pixel size (Å) | 1.23 | 1.23 | 1.42 | 1.31 | 2.18 | 1.32 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 1214203 | 896858 | 896858 | 1711962 | 1711962 | 1711962 |
| Final particle images (no.) | 158665 | 120102 | 32228 | 62074 | 16563 | 25373 |
| Map resolution (Å) | 3.2 | 3.6 | 3.6 | 3.8 | 5.8 | 5.8 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 20-2.8 | 20-3.0 | 20-3.2 | 20-3.5 | 20-5.0 | 20-5.0 |
| Refinement | ||||||
| Initial model used (PDB code) | N/A | N/A | N/A | N/A | N/A | N/A |
| Model resolution (Å) | 3.2 | 3.6 | 3.6 | 3.8 | 5.8 | - |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | ||
| Model resolution range (Å) | 20-3.1 | 20-3.6 | 20-3.6 | 20-3.8 | 20-5.8 | - |
| Map sharpening B factor (Å2) | −50 | −50 | −50 | −50 | − | − |
| Model composition | ||||||
| Non-hydrogen atoms | 17162 | 15469 | 9789 | 15924 | 17216 | - |
| Protein residues | 2048 | 1852 | 1137 | 1706 | 1922 | - |
| Ligands | 10 | 8 | 6 | 4 | 6 | - |
| DNA base | 70 | 60 | 57 | 170 | 121 | - |
| B factors (Å2) | ||||||
| Protein | 71.98 | 146.39 | 71.96 | 54.24 | 54.24 | - |
| Ligand | ||||||
| R.m.s. deviations | ||||||
| Bond lengths (Å) | 0.009 | 0.009 | 0.009 | 0.006 | 0.008 | - |
| Bond angles (°) | 0.952 | 0.932 | 0.945 | 0.840 | 0.899 | - |
| Validation | ||||||
| MolProbity score | 2.7 | 2.8 | 2.7 | 2.9 | 2.8 | - |
| Clashscore | 13 | 33 | 14 | 30 | 57 | - |
| Poor rotamers (%) | 5.8 | 8.1 | 5.7 | 2.08 | 0.81 | - |
| Ramachandran plot | - | |||||
| Favored (%) | 91.45 | 90.47 | 91.32 | 86.9 | 87.54 | - |
| Allowed (%) | 8.44 | 9.42 | 8.68 | 12.97 | 12.45 | - |
| Disallowed (%) | 0.1 | 0.1 | 0.1 | 0.13 | 0.1 | - |