Extended Data Table 1 |. Cryo-EM data collection, refinement and validation statistics.
PCFT-NB (EMDB-12140) (PDB7BC6) | PCFT-NB + pemetrexed (EMDB-12141) (PDB7BC7) | |
---|---|---|
Data collection and processing | ||
Magnification | 105,000 | 105,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e-/Å2) | 59.1 | 58.5 |
Defocus range (μm) | 0.8 – 2.5 | 0.8 – 2.5 |
Pixel size (Ă) | 0.832 | 0.832 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 5,538,959 | 9,420,673 |
Final particle images (no.) | 174,399 | 341,318 |
Map resolution (Å) | 3.2 | 3.3 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 3.2–3.6 | 3.2–4.4 |
Refinement | ||
Initial model used (PDB code) | None | 7BC6 |
Model resolution (Å) | 3.2 | 3.3 |
FSC threshold | 0.143 | 0.143 |
Model resolution range (Å) | 3.2–3.6 | 3.2–4.4 |
Map sharpening B factor (Å2) | −95.3 | −81.8 |
Model composition | ||
Non-hydrogen atoms | 4178 | 4209 |
Protein residues | 549 | 549 |
Ligands | 0 | LYA: 1 |
B factors (Å2) | ||
Protein | 39.19 | 55.49 |
Ligand | N/A | 60.24 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.008 | 0.008 |
Bond angles (°) | 0.893 | 0.870 |
Validation | ||
MolProbity score | 1.95 | 2.13 |
Clashscore | 9.52 | 12.19 |
Poor rotamers (%) | 0.92 | 0.23 |
Ramachandran plot | ||
Favored (%) | 93.03 | 90.46 |
Allowed (%) | 6.97 | 9.36 |
Disallowed (%) | 0.00 | 0.18 |