Table 1 Cryo-EM data collection, refinement, and validation statistics of MuV Lintegral–P and Lbody–P
From: Structures of the mumps virus polymerase complex via cryo-electron microscopy
Lintegral–P | RdRp-PRNTase of Lintegral–P | CD-MTase-CTD of Lintegral–P | P of Lintegral–P | Lbody–P | P of Lbody–P | |
|---|---|---|---|---|---|---|
Data collection and processing | ||||||
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 50 | 50 | 50 | 50 | 50 | 50 |
Defocus range (μm) | –1.5 to –2.5 | –1.5 to –2.5 | –1.5 to –2.5 | –1.5 to –2.5 | –1.5 to –2.5 | –1.5 to –2.5 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images(no.) | 2,087,570 | 2,087,570 | 2,087,570 | 2,087,570 | 2,087,570 | 2,087,570 |
Final particle images (no.) | 438,014 | 438,014 | 438,014 | 88,107 | 477,568 | 41,168 |
Pixel size (Å) | 0.53 | 0.53 | 0.53 | 1.06 | 0.53 | 1.06 |
Map resolution (Å) | 3.02 | 2.93 | 3.13 | 3.49 | 3.01 | 3.63 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map sharpening B factor (Å2) | 136.8 | 133.6 | 156.1 | 132.3 | 143.6 | 123.1 |
EMDB code | 37957 | 37959 | 37958 | 37960 | 37961 | 37962 |
Composite map EMD-35864 | Composite map EMD-37964 | |||||
Model building and refinement | ||||||
Initial model used (PDB code) | / | 6V85 | / | 4EIJ | 6V85 | 4EIJ |
Model composition | ||||||
Non-hydrogen atoms | / | 11,632 | 5,588 | 2,096 | 10,784 | 1,958 |
Protein residues | / | 1,464 | 699 | 278 | 1,350 | 258 |
Ligands | / | 2 | 0 | 0 | 2 | 0 |
B factors (Å2) | ||||||
Protein | / | 61.76 | 76.74 | 115.85 | 58.08 | 130.10 |
Ligand | / | 147.46 | / | / | 142.51 | / |
R.m.s deviations | ||||||
Bond lengths (Å) | / | 0.005 | 0.005 | 0.008 | 0.004 | 0.007 |
Bond angles (°) | / | 0.757 | 0.777 | 1.234 | 0.605 | 1.108 |
Validation | ||||||
MolProbity score | / | 1.73 | 1.66 | 1.91 | 1.42 | 1.80 |
Clashscore | / | 10.29 | 14.27 | 17.23 | 7.74 | 16.46 |
Poor rotamer (%) | / | 1.22 | 0.64 | 1.67 | 0.33 | 0.45 |
Ramachandran plot | ||||||
Favored (%) | / | 97.31 | 98.09 | 98.52 | 98.21 | 97.60 |
Allowed (%) | / | 2.69 | 1.91 | 1.48 | 1.79 | 2.40 |
Disallowed (%) | / | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
PDB code | / | 8YXM | 8YXL | 8YXO | 8YXP | 8YXR |
Composite model PDB ID 8IZL | Composite model PDB ID 8X01 | |||||
