Table 1.
Cryo-EM data collection, refinement, and validation statistics.
| Sample name | AtAgo10-guide RNA |
AtAgo10-guide- target |
AtAgo10-guide- target |
|---|---|---|---|
| (central duplex) | (bent duplex) | ||
| EMDB ID | EMD-25446 | EMD-25472 | EMD-25482 |
| PDB ID | 7SVA | 7SWF | 7SWQ |
| Microscope | Talos Arctica | Talos Arctica | |
| Detector (Mode) | Gatan K2 Summit, counting mode | Gatan K2 Summit, counting mode | |
| Voltage (kV) | 200 | 200 | |
| Magnification (nominal) | 73,000x | 45,000x | |
| Total electron fluence (e−/Å2) | 66.51 | 66.88 | |
| Defocus range (μm) | −0.8 to −1.3 | −1.0 to −1.7 | |
| Pixel size (Å) | 0.566 | 0.91 | |
| Total exposure time (sec) | 11 | 8.4 | |
| Total frames/micrograph | 55 | 42 | |
| Exposure per frame (e−/Å2/frame) | 1.21 | 1.59 | |
| Micrographs collected (no.) | 2,656 | 2,049 | |
| Total extracted particles (no.) | 736,209 | 1,935,081 | |
| Particles used for 3D analyses (no.) | 381,087 | 405,690 | 190,349 |
| Final refined particles (no.) | 53,766 | 38,833 | 28,499 |
| Symmetry imposed | C1 | C1 | C1 |
| Map Global Resolution (Å) | 3.26 | 3.79 | 3.79 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| FSC Sphericity | 0.963 | 0.964 | 0.949 |
| Local resolution range (Å) | 3.0 – 6.0 | 3.5 – 6.5 | 3.5-6.5 |
| Map Sharpening B factors (Å2) | −115.7 | −70 | −88.3 |
| Refinement | |||
| Refinement package (s) | Phenix | Phenix | Phenix |
| Model composition | |||
| Non-hydrogen atoms | 6515 | 6873 | 6998 |
| Protein residues | 792 | 778 | 791 |
| RNA residues | 11 | 34 | 35 |
| Mg2+ ions | 1 | 1 | 1 |
| Model resolution (Å) | |||
| FSC 0.5 | 3.4 | 3.9 | 3.9 |
| FSC 0.143 | 3.1 | 3.6 | 3.6 |
| B factors (Å2) | |||
| Protein | 40.38 | 83.05 | 34.47 |
| Nucleotide | 39.44 | 93.19 | 90.16 |
| Map Correlation Coefficient | |||
| Global | 0.82 | 0.82 | 0.76 |
| Local | 0.79 | 0.80 | 0.74 |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.004 | 0.010 | 0.004 |
| Bond angles (°) | 0.957 | 0.976 | 0.739 |
| Validation | |||
| EMRinger score | 3.41 | 2.89 | 2.76 |
| MolProbity score | 1.85 | 2.31 | 2.19 |
| Clashscore | 8.64 | 15.32 | 12.99 |
| Rotamer outliers (%) | 0.29 | 1.33 | 0.00 |
| Cβ deviations (%) | 0.00 | 0.00 | 0.00 |
| Ramachandran plot | |||
| Favored (%) | 94.36 | 90.89 | 89.35 |
| Allowed (%) | 5.64 | 9.11 | 10.65 |
| Disallowed (%) | 0.00 | 0.00 | 0.00 |