Extended Data Table 1.
Cryo-EM data collection, refinement, and validation statistics
| Sample name | EfPiwi-piRNA-target (2–16) | EfPiwi-piRNA | EfPiwi (MID/PIWI)-piRNA-long-target (2–25) |
|---|---|---|---|
|
| |||
| EMDB ID | EMD-23063 | EMD-23061 | EMD-23062 |
|
| |||
| PDB ID | 7KX9 | 7KX7 | |
|
| |||
|
| |||
| Microscope | Talos Arctica | Talos Arctica | |
|
| |||
| Detector (Mode) | Gatan K2 Summit, counting mode | Gatan K2 Summit, counting mode | |
|
| |||
| Voltage (kV) | 200 | 200 | |
|
| |||
| Magnification (nominal / at detector) | 36,000× / 43,478× | 36,000× / 43,478× | |
|
| |||
| Total electron fluence (e−/Å2) | 47.33 | 47.33 | |
|
| |||
| Electron flux (e−/pixel/sec) | 3.91 | 5.22 | |
|
| |||
| Defocus range (μm) | −1.0 to −1.6 | −1.0 to −1.6 | |
|
| |||
| Pixel size (Å) | 1.15 | 1.15 | |
|
| |||
| Total exposure time (sec) | 16 | 12 | |
|
| |||
| Total frames/micrograph | 64 | 48 | |
|
| |||
| Exposure per frame (e−/Å2/frame) | 0.74 | 0.99 | |
|
| |||
| Micrographs collected (no.) | 1,881 | 1,765 | |
|
| |||
| Total extracted particles (no.) | 2,551,046 | 3,280,351 | |
|
| |||
| Particles used for 3D analyses (no.) | 1,571,175 | 1,862,936 | 608,488 |
|
| |||
| Final refined particles (no.) | 118,493 | 125,041 | 116,655 |
|
| |||
| Accuracy of rotations (deg.) / translations (pixels) | 1.972 / 0.581 | 2.748 / 0.785 | 8.374 / 1.739 |
|
| |||
| Symmetry imposed | C1 | C1 | C1 |
|
| |||
| Global Resolution (Å) | |||
|
| |||
| FSC 0.5 (masked/unmasked) | 3.8/4.0 | 4.3/4.5 | 8.6 / 10.8 |
| FSC 0.143 (masked/unmasked) | 3.4/3.6 | 3.8/3.9 | 8.6 / 10.8 |
|
| |||
| FSC Sphericity | 0.97 | 0.91 | |
|
| |||
| Local resolution range (Å) | 3.5 – 6.0 | 3.5 – 6.0 | |
|
| |||
| Map Sharpening B factors (Å2) | −80 | −80 | |
|
| |||
| Model composition | |||
|
| |||
| Non-hydrogen atoms | 6578 | 5828 | |
|
| |||
| Protein residues | 734 | 729 | |
|
| |||
| RNA residues | 40 | 7 | |
|
| |||
| Mg2+ ions | 2 | 2 | |
|
| |||
| Refinement | |||
|
| |||
| Refinement package (s) | Phenix | Phenix | |
|
| |||
| Map Correlation Coefficient | |||
|
| |||
| Global | 0.79 | 0.82 | |
|
| |||
| Local | 0.78 | 0.83 | |
|
| |||
| R.m.s. deviations | |||
|
| |||
| Bond lengths (Å) | 0.008 | 0.008 | |
|
| |||
| Bond angles (°) | 1.183 | 1.092 | |
|
| |||
| Validation | |||
|
| |||
| EMRinger score | 2.84 | 2.98 | |
|
| |||
| MolProbity score | 2.22 | 2.18 | |
|
| |||
| Clashscore | 13.11 | 13.87 | |
|
| |||
| Rotamer outliers (%) | 0.17 | 0.34 | |
|
| |||
| Cβ deviations (%) | 0 | 0 | |
|
| |||
| Ramachandran plot | |||
|
| |||
| Favored (%) | 88.46 | 90.57 | |
|
| |||
| Allowed (%) | 11.54 | 9.43 | |
|
| |||
| Disallowed (%) | 0 | 0 | |
|
| |||
| CaBLAM outliers (%) | 3.74 | 3.8 | |