Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structural basis for lipid transport at membrane contact sites by the IST2–OSH6 complex
IST2716GDN | IST2716ND narrow | IST2716ND wide | IST2fl | |
|---|---|---|---|---|
Data collection and processing | ||||
Magnification | ×130,000 | ×130,000 | ×130,000 | ×130,000 |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e− per Å2) | 62.43 | 62.43 | 62.43 | 62.43 |
Defocus range (μm) | −1 to −2.4 | −1 to −2.4 | −1 to −2.4 | −1 to −2.4 |
Pixel size (Å) | 0.651 | 0.651 | 0.651 | 0.651 |
Symmetry imposed | C2 | C2 | C1 | C2 |
Initial particle images (no.) | 3,981,000 | 5,700,000 | 5,700,000 | 420,000 |
Final particle images (no.) | 400,925 | 189,991 | 223,081 | 136,130 |
Map resolution (Å) | 2.84 | 3.34 | 3.8 | 4.19 |
FSC threshold 0.143 | ||||
Map resolution range (Å) | 2–3.5 | 3–4.5 | 3.5–6 | 3.5–6.5 |
Refinement | ||||
Initial model used (PDB code) | IST2 AlphaFold | IST2716GDN (9HHE) | IST2716GDN (9HHE) | IST2716GDN (9HHE) |
Model resolution (Å) | 2.8 | 3.5 | 4.1 | 4.4 |
FSC threshold 0.5 | ||||
Map sharpening B factor (Å2) | −50 | DeepEMhancer | DeepEMhancer | DeepEMhancer |
Model composition | ||||
Nonhydrogen atoms | 9,248 | 8,152 | 7,849 | 7,862 |
Protein residues | 1,130 | 990 | 951 | 958 |
Ligands | - | - | - | - |
B factors (Å2) | ||||
Protein | 85.57 | 82.44 | 96.5 | 89.42 |
Ligand | - | - | - | - |
Root-mean-square deviations | ||||
Bond lengths (Å) | 0.002 | 0.002 | 0.003 | 0.003 |
Bond angles (°) | 0.549 | 0.508 | 0.669 | 0.554 |
Validation | ||||
MolProbity score | 1.93 | 2.15 | 2.45 | 1.64 |
Clashscore | 7.58 | 7.02 | 11.36 | 10.00 |
Poor rotamers (%) | 2.01 | 4.62 | 6.29 | 0.23 |
Ramachandran plot | ||||
Favored (%) | 95.87 | 96.17 | 95.97 | 97.4 |
Allowed (%) | 3.95 | 3.83 | 4.03 | 2.60 |
Disallowed (%) | 0.18 | 0.00 | 0.00 | 0.00 |
