Table 1 Cryo-EM data collection, refinement and validation statistics
From: The GET insertase exhibits conformational plasticity and induces membrane thinning
H. sapiens Get2ΔN/Δα3’-Get1/Get3 in PMAL-C8 (EMDB-16802) (PDB 8CR2) | H. sapiens Get2ΔN-Get1/Get3 in PMAL-C8 (EMDB-16801) (PDB 8CR1) | C. thermophilum Get2ΔN-Get1/ Get3 in A835 (EMDB-16817) (PDB 8ODU) | C. thermophilum Get2ΔN-Get1/ Get3 in nanodisc (EMDB-16819) (PDB 8ODV) | |
|---|---|---|---|---|
Data collection and processing | ||||
Detector | K3 | K2 | K3 | K3 |
Magnification | 81,000 | 165,000 | 64,000 | 81,000 |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 53.2 | 46 | 55 | 60.8 |
Defocus range (μm) | 1.2-2.4 | 0.8–2.0 | 1.5–3.5 | 1.2–2.4 |
Pixel size (Å) | 1.11 | 0.81 | 1.375 | 1.11 |
Symmetry imposed | C1 | C2 | C1 | C2 |
Initial particle images (no.) | 1,995,680 | 1,561,837 | 4,337,300 | 5,218,800 |
Final particle images (no.) | 224,354 | 189,844 | 796,684 | 259,692 |
Map resolution (Å) | 4.2 | 3.2 | 5.0 | 4.7 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 4.0-7.7 | 3.1–5.4 | 4.7–9.0 | 4.1–8.5 |
Refinement | ||||
Initial model used (PDB code) | 6SO5 | 6SO5 | 3IQW, 3SJA | (this paper) |
Model resolution (Å) | 4.0 | 3.2 | 4.8 | 4.5 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map sharpening B factor (Å2) | -202 | -58 | -512 | -285 |
Model composition | ||||
Non-hydrogen atoms | 6838 | 9205 | 8420 | 8233 |
Protein residues | 855 | 1158 | 1044 | 1022 |
Ligands | ZN:1 | ZN:1 | ZN:1 | ZN:1 |
B factors (Å2) | ||||
Protein | 65 | 121 | 191 | 212 |
Ligand | 97 | 189 | 186 | 195 |
R.m.s. deviations | ||||
Bond lengths (Å) | 0.004 | 0.003 | 0.003 | 0.007 |
Bond angles (°) | 1.075 | 0.726 | 0.793 | 1.098 |
Validation | ||||
MolProbity score | 2.18 | 1.73 | 1.91 | 2.22 |
Clashscore | 19.83 | 10.58 | 14.05 | 25.51 |
Poor rotamers (%) | 0.00 | 0.00 | 0.00 | 0.00 |
Ramachandran plot | ||||
Favoured (%) | 94.24 | 96.85 | 96.18 | 95.39 |
Allowed (%) | 5.76 | 3.15 | 3.82 | 4.61 |
Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 |
