Table 1.
Cryo-EM data collection, refinement and validation statistics.
| AtMSL1 in detergents (EMDB: 21444) (PDB: 6VXM) | AtMSL1 A320V in detergents (EMDB: 21445) (PDB: 6VXN) | AtMSL1 in nanodiscs (EMDB: 21447) (PDB: 6VXP) | |
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 105,000 | 105,000 | 105,000 |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 62 | 62 | 62 |
| Defocus range (μm) | −1.0 to −2.5 | −1.0 to −2.5 | −1.0 to −2.5 |
| Pixel size (Å) | 1.1 | 1.1 | 1.1 |
| Symmetry imposed | C7 | C7 | C7 |
| Initial particle images (no.) | 936,130 | 428,889 | 457,683 |
| Final particle images (no.) | 158,172 | 52,883 | 23,077 |
| Map resolution (Å) | 3.06 | 2.96 | 3.39 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.5–6.0 | 2.5–6.0 | 3.0–7.0 |
| Refinement | |||
| Initial model used (PDB code) | 5AJI | This study | This study |
| Model resolution (Å) | 3.0 | 3.1 | 3.5 |
| FSC threshold | 0.5 | 0.5 | 0.5 |
| Model resolution range (Å) | 2.7 | 2.7 | 3.1 |
| Model composition | |||
| Non-hydrogen atoms | 15,064 | 14,385 | 14,819 |
| Protein residues | 1939 | 1862 | 1939 |
| Ligands | 21 | 7 | 0 |
| B factors (Å2) | |||
| Protein | 36.2 | 93.1 | 73.6 |
| Ligand | 20 | 111 | N/A |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.006 | 0.008 | 0.008 |
| Bond angles (°) | 0.763 | 1.283 | 1.126 |
| Validation | |||
| MolProbity score | 1.57 | 1.28 | 1.64 |
| Clashscore | 5.58 | 5.31 | 6.59 |
| Poor rotamers (%) | 0 | 0 | 0 |
| Ramachandran plot | |||
| Favored (%) | 96.1 | 98.45 | 95.94 |
| Allowed (%) | 3.9 | 1.55 | 4.06 |
| Disallowed (%) | 0 | 0 | 0 |