Table 1 Cryo-EM data collection and refinement statistics
Cryo-EM (EMDB-23027) (PDB 7KTR) | Negative stain (EMDB-23028) (PDB 7KTS) | |
|---|---|---|
Data collection and processing | ||
Microscope | FEI Titan Krios G2 | FEI Technai F20 |
Camera | Gatan K3 Summit (super resolution) | Gatan UltraScan4000 |
Voltage (keV) | 300 | 120 |
Magnification | 64,000 | 80,000 |
Defocus range (μm) | 0.9–3.4 | 0.4–3.9 |
Micrographs/videos | 10,224 | 1 |
Frames per video | 50 | NA |
Pixel size (Å) | 1.187 | 1.4 |
Total dose (e−/Å−2) | 50 | 35 |
Symmetry imposed | C1 | C1 |
Particles initial/final | 3,167,367/357,441 | 47,790/3,157 |
Map resolution (Å) | 2.9 | 19 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.5–9.0 | NA |
Model refinements | ||
Initial model used (PDB code) | 6F3T, de novo | |
Method | real space, adp | rigid bodya |
Model resolution (Å) | 3.0 | NA |
FSC threshold | 0.5 | NA |
Model resolution range (Å) | 2.3–25.4 | NA |
Map-to-model cross-correlation | 0.80 | 0.52 |
Map sharpening B factor (Å2) | NAb | −1,200 |
Model composition | ||
Nonhydrogen atoms | 40,337 | 51,173 |
Protein residues | 5,169 | 6,632 |
Ligands | 1 | 0 |
Mean model B factors (Å2) | ||
Protein | 73.6 | not refined |
Ligand | 66.6 | not refined |
R.m.s. deviations | ||
Bond lengths (Å) | 0.004 | 0.005 |
Bond angles (°) | 0.62 | 0.99 |
Validation | ||
MolProbity score | 1.50 | 1.62 |
All-atom clashscore | 3.42 | 4.79 |
Rotamer outliers (%) | 0.02 | 0.02 |
C-beta deviations | 0 | 0 |
Ramachandran plot | ||
Favored (%) | 94.72 | 94.57 |
Allowed (%) | 5.24 | 5.38 |
Disallowed (%) | 0.04 | 0.05 |
Rama-Z score, whole (r.m.s.) | 0.16 (0.12) | −0.35 (0.11) |
