Table 1 Cryo-EM data collection, refinement, and validation statistics for Pd-CI-ND
From: Structure of the turnover-ready state of an ancestral respiratory complex I
Data collection and processing | Pd-CI-NDs | |
|---|---|---|
Voltage (kV) | 300 | |
Nominal magnification | 81,000× | |
Electron exposure (e– Å−2) | 46 [grids 1+2], 45 (grid 3) | |
Defocus range (μm) | −1.0 to −2.4 [grids 1+2], −0.9 to −2.5 (grid 3) | |
Calibrated pixel size (Å) | 1.066 [grids 1+2], 1.070 (grid 3) | |
Number of frames | 40 | |
Symmetry imposed | C1 | |
Number of micrographs | 11,994 (grid 1), 4820 (grid 2), 4561 (grid 3) | |
Initial particle images (no.) | 1,034,504 [grids 1 + 2], 320,429 (grid 3) | |
Final particle number (no.) | 103,186 [grids 1 + 2], 43,417 (grid 3) | |
Consensus Pd-CI-ND map (EMDB: 18324) | ND4-5 focus refined map (EMDB: 18325) | |
Map sharpening B factor (Å2) | −39.40 | −48.88 |
Map angular accuracy (°) | 0.234 | 0.468 |
Map translational accuracy (Å) | 0.215 | 0.540 |
Final map sampling | 0.745 | 0.745 |
Map resolution (Å) (FSC = 0.143) | 2.3 (0.143) | 2.5 (0.143) |
Map resolution range (Å) | 2.2–4.8 | 2.4–4.0 |
Refinement | ||
Initial model used | de novo (ModelAngelo) | Pd-CI-ND |
Model resolution (Å) (FSC = 0.5) | 2.4 | 2.6 |
Model composition | ||
Nonhydrogen atoms | 84,464 | 18,950 |
Protein residues | 5135 | 1118 |
Ligands | 49 | 15 |
Waters | 1080 | 115 |
B factors mean (Å2) | ||
Protein | 39.58 | 46.61 |
Ligand | 56.03 | 62.48 |
Water | 38.92 | 48.17 |
RMS deviations | ||
Bond lengths (Å) | 0.006 | 0.004 |
Bond angles (°) | 0.612 | 0.557 |
Validation | ||
MolProbity score | 1.15 | 1.10 |
EMRinger score | 5.74 | 5.61 |
Clashscore | 3.04 | 2.92 |
Rotamer outliers (%) | 0.36 | 0.45 |
Cß outliers (%) | 0.00 | 0.00 |
Ramachandran plot | ||
Favoured (%) | 97.74 | 97.93 |
Allowed (%) | 2.24 | 2.07 |
Outliers (%) | 0.02 | 0.00 |
Rama-Z (Ramachandran Z-score, RMSD) | ||
Whole (N = 5091) | 0.26 (0.11) | 0.76 (0.25) |
Helix (N = 2728) | 0.60 (0.10) | 0.98 (0.18) |
Sheet (N = 420) | 0.31 (0.25) | 1.18 (1.19) |
Loop (N = 1943) | -0.30 (0.14) | -0.74 (0.38) |
