Extended Data Table 1. Cryo-EM data collection, refinement and validation statistics for the ShCas12k-sgRNA-target DNA complex structure and the ShTnsC-AMPPNP-dsDNA structure.
| ShCas12k-sgRNA-dsDNA (EMDB-13486) (PDB 7PLA) |
ShTnsC-AMPPNP-dsDNA (EMDB-13489) (PDB 7PLH) |
|
|---|---|---|
| Data collection and processing | ||
| Magnification | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 51.82 | 66.39 |
| Defocus range (μm) | -0.9 to -1.9 (0.1 steps) | -1.0 to -2.4 (0.2 steps) |
| Pixel size (Å) | 0.64 | 0.325 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 10,952 | 5,055 |
| Final particle images (no.) | 10,866 | 4,988 |
| Map resolution (Å) | 3.04 | 3.58 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 2.7-7.0 | 3.58-5.05 |
| Refinement | ||
| Initial model used (PDB code) | n. a. | 1W5T |
| Model resolution (Å) | 4.5 | 3.9 |
| FSC threshold | 0.5 | 0.5 |
| Map sharpening B factor (Å2) | -113.9 | -79.50 |
| Model composition | ||
| Non-hydrogen atoms | 8701 | 15542 |
| Protein residues | 437 | 1820 |
| Nucleotide residues | 244 | 44 |
| Ligands | 0 | MG :7 AMPPNP :7 |
| B factors (Å2) min/max/mean | ||
| Protein | 50.00/288.87/177.33 | 17.40/95.74/39.30 |
| Nucleotide | 20.00/30.00/29.96 | 20.00/20.00/20.00 |
| Ligand | 39.53/40.64/40.61 | |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.008 | 0.010 |
| Bond angles (°) | 1.152 | 1.659 |
| Validation | ||
| MolProbity score | 1.71 | 2.36 |
| Clashscore | 9.53 | 13.30 |
| Poor rotamers (%) | 0.26 | 8.98 |
| Ramachandran plot | ||
| Favored (%) | 96.74 | 98.06 |
| Allowed (%) | 3.26 | 1.94 |
| Disallowed (%) | 0.00 | 0.00 |
| Ramachandran Z score | ||
| whole | -0.03 | -2.29 |
| helix | 1.11 | -0.98 |
| sheet | -1.19 | -1.95 |
| loop | -1.32 | -2.19 |