Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structural-functional characterization of the MIRO1-TRAK1 complex
Cryo-EM data collection, refinement and validation statistics | |
|---|---|
Cryo-EM data collection | |
Microscope (Facility) | Titan Krios G3 (UPenn) |
Camera | K3 Summit |
Acquisition | EPU |
Magnification | 105000 |
Voltage, keV | 300 |
Defocus range, mm | −0.5 to −2.5 |
Pixel size, Å | 0.43 |
Electron exposure, e-/Å2 | 70 |
Micrographs | 14314 |
Initial no. particles | 821667 |
Map | |
Symmetry | C2 |
Final no. particles | 326239 |
Map resolution, Å FSC threshold 0.143 (0.5) | 3.57 (3.98) |
Resolution range, Å | 3.05 to 10.02 |
Refinement and validation | |
Initial models used (PDBs) | 6D71, 5KSZ |
Model resolution, Å FSC threshold 0.143 (0.5) | 3.51 (3.67) |
Sharpening B factor, Å2 | −238.9 |
Model composition | |
No. non-hydrogen atoms | 10282 |
No. residues | 1262 |
No. ligands | GTP:4, CA:4, MG:2 |
Correlation model vs. data | |
CC (mask, volume, box, peaks) | 0.84, 0.82, 0.75, 0.70 |
CC (ligands) | 0.80 |
R.m.s deviations | |
Bond lengths, Å (no. > 4σ) | 0.017 (12) |
Bond angles, °, (no. > 4σ) | 1.602 (44) |
Validation | |
MolProbity score | 1.39 |
Clashscore | 2.64 |
Rotamer outliers, % | 0.00 |
Ramachandran plot | |
Favored, % | 95.06 |
Allowed, % | 4.94 |
Disallowed, % | 0.00 |
ADP (B-factors) | |
Protein, Å2 (min/max/mean) | 26/196/103 |
Ligand, Å2 (min/max/mean) | 77/166/149 |
Accession codes | |
EMDB | 47460 |
PDB | 9E2P |
