Table 1.
Cryo-EM data collection, processing, model building, and validation statistics.
| Sample name | FtsH•HflK/C map a (DDM extracted) |
FtsH•HflK/C hat-like map (locally refined) | FtsH•HflK/C map I | FtsH•HflK/C map II | HflK/C | FtsH•HflK/C (Carboxy-DIBMA) |
|---|---|---|---|---|---|---|
| Description | Primary map analyzed | Locally refined map focused on HflK/C ‘hat’ | Classified map a with single FtsH6 | Classified map a with two FtsH6 | HflK/C overexpressed | Detergent-free solubilized sample |
| PDB code | 9CZ2 | 9CZ1 | n/a | n/a | n/a | n/a |
| EMDB ID | 46057 | 46056 | 46061 | 46059 | 46062 | 46058 |
| EMPIAR code | 12472 | 12471 | − | |||
| Defocus range (µm) | −0.05 to −1.75 | −0.5 to −2 |
−0.30 to 1.75 (1); −0.75 to −2.0 (2) |
|||
| Micrographs collected (#) | 25,179 | 16,055 | 11,899 (1); 32,907 (2) | |||
| Pixel size (Å) | 0.654 | 0.654 | 0.654 | |||
| Map reconstruction | ||||||
| Image processing package | cryoSPARC | |||||
| Total extracted particles | 334,256 | 334,256 | 295,185 | 47,449 | ||
| Final particle count | 184,019 | 184,019 | 17,473 | 76,491 | 230,567 | 24,011 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | |
| Resolution (Å) | ||||||
| GS-FSC (0.143) | ||||||
| unmasked | 7.0 | 7.0 | 12 | 8.0 | 9.7 | 15 |
| loose | 5.6 | 3.7 | 7.1 | 6.0 | 9.1 | 14 |
| tight | 4.4 | 3.5 | 6.6 | 4.5 | 7.7 | 12 |
| 3D-FSC sphericity (out of 1.0) | 0.89 | 0.82 | 0.712 | 0.906 | 0.926 | 0.870 |
| Model composition and refinement | ||||||
| Number of atoms | 114,335 | 40,604 | no models built | |||
| Protein residues | 7130 | 2556 | ||||
| Refinement package | Phenix and Coot | |||||
| Map-to-model cross-correlation | ||||||
| masked | 0.69 | 0.77 | ||||
| unmasked | 0.72 | 0.78 | ||||
| RMSD bond length (Å) [#>4σ] | 0.003 [0] | 0.003 [0] | ||||
| RMSD bond angles (o) [#>4σ] | 0.702 [0] | 0.664 [0] | ||||
| MolProbity score | 0.88 | 0.91 | ||||
| Clash score | 1.43 | 2.48 | ||||
| C-beta outliers (%) | 0.0 | 0.0 | ||||
| Rotamer outliers (%) | 0.03 | 0.0 | ||||
| Ramachandran favored (%) | 99.9 | 100 | ||||