Table 1 Cryo-EM structures data collection, refinement and validation statistics
Sample | A/H7N9 polymerase with Pol II pS5 CTD mimic bound in site 1 A/2 A | |||
|---|---|---|---|---|
Structure | Pre-initiation state in replicase (R)-like conformation PB2-C(R), ENDO(T) | Pre-initiation state core ENDO(T) | Pre-initiation state in intermediate (I)-conformation PB2-C(I), ENDO(T) | Elongation state stalled with UpNHpp ENDO(T) |
PDB ID | PDB ID 8PM0 | PDB ID 8PNP | PDB ID 8R3L | PDB ID 8PNQ |
EMDB ID | EMD-17755 | EMD-17782 | EMD-18872 | EMD-17783 |
Data collection and processing | ||||
Microscope | ThermoFisher Krios TEM | |||
Voltage (kV) | 300 | |||
Camera | Gatan K3 direct electron detector mounted on a Gatan Bioquantum LS/967 energy filter | |||
Magnification | 105000 | |||
Nominal defocus range (μm) | −0.8/−2.0 | |||
Electron exposure (e–/Å2) | 40 | |||
Number of frames collected (no.) | 40 | |||
Number of frames processed (no.) | 40 | |||
Pixel size (Å) | 0.84 | |||
Initial micrographs (no.) | 6000 | |||
Final micrographs (no.) | 5883 | |||
Refinement | ||||
Particles per class (no.) | 33395 | 260565 | 17121 | 14878 |
Map resolution (Å), 0.143 FSC | 2.9 | 2.5 | 3.25 | 2.9 |
Model resolution (Å), 0.5 FSC | 3.0 | 2.5 | 3.3 | 2.9 |
Map sharpening B factor (Å2) | −20 | −30 | −20 | −20 |
Map versus model cross-correlation (CCmask) | 0.8428 | 0.8901 | 0.8179 | 0.8826 |
Model composition | ||||
Non-hydrogen atoms | 16673 | 14464 | 17878 | 14917 |
Protein residues | 1997 | 1716 | 2149 | 1727 |
Nucleotide residues | 31 | 29 | 31 | 45 |
Water | - | 43 | - | - |
Ligands | 1 Mg | - | - | 2 Mg, 1 UpNHpp |
B factors (Å2) | ||||
Protein | 74.00 | 67.24 | 89.19 | 70.02 |
Nucleotide | 72.82 | 60.96 | 90.96 | 83.39 |
Ligand | 48.38 | - | - | 68.99 |
Water | - | 33.97 | - | - |
RMS deviations | ||||
Bond lengths (Å) | 0.003 | 0.003 | 0.002 | 0.005 |
Bond angles (°) | 0.475 | 0.499 | 0.478 | 0.465 |
Validation | ||||
MolProbity score | 1.53 | 1.35 | 1.53 | 1.40 |
All-atom clash score | 4.79 | 4.32 | 6.41 | 3.86 |
Poor rotamers (%) | 2.03 | 1.24 | 0.21 | 2.01 |
Ramachandran plot | ||||
Favoured (%) | 97.77 | 97.70 | 97.00 | 98.24 |
Allowed (%) | 2.23 | 2.24 | 3.00 | 1.76 |
Outliers (%) | 0.00 | 0.06 | - | 0.00 |
