Extended Data Table 1 Cryo-EM data collection, refinement, and validation statistics for the HSV-1 HP complex structures presented in this study
From: Structural and mechanistic insights into herpesvirus helicase–primase and its therapeutic inhibitors
HP+AMNV | HP+PTV | HP+PTV+forked DNA+ATP-γ-S+Mg2+ | HP+forked DNA+ATP-γ-S+Mg2+ | |||||
|---|---|---|---|---|---|---|---|---|
EMDB ID | Body1 EMD-49269 | Body2 EMD-49326 | Body1 EMD-49304 | Body2 EMD-49306 | Body1 EMD-49290 | Body2 EMD-49291 | Body1 EMD-49276 | Body2 EMD-49277 |
PDB ID | ||||||||
Data collection and processing | ||||||||
Magnification | 165,000 | 165,000 | 165,000 | 165,000 | 165,000 | 165,000 | 165,000 | 165, 000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 |
Defocus range (μm) | -0.6 to -2.2 | -0.6 to -2.2 | -0.6 to -2.2 | -0.6 to -2.2 | -0.6 to -2.2 | -0.6 to -2.2 | -0.6 to -2.2 | -0.6 to -2.2 |
Pixel size (Å) | 0.729 | 0.729 | 0.729 | 0.729 | 0.729 | 0.729 | 0.729 | 0.729 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 640,335 | 640,335 | 537,060 | 537,060 | 564,777 | 564,777 | 371,973 | 371.973 |
Final particle images (no.) | 115,543 | 115,543 | 136,652 | 136,652 | 155,321 | 155,321 | 52,547 | 52,547 |
Map resolution (Å) | 2.9 | 3.2 | 2.8 | 3.2 | 3.0 | 3.4 | 3.3 | 3.8 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | ||||||||
Refinement | ||||||||
Initial model used | ||||||||
Model resolution (Å) | ||||||||
Model resolution range (Å) | ||||||||
Map sharpening B factor (Å2) | -55.41 | -96.97 | -48.71 | -77.31 | -60.25 | -96.47 | -64.62 | -112.57 |
Model composition | ||||||||
Non-hydrogen atoms | 7957 | 6695 | 7837 | 5188 | 8051 | 6695 | 7909 | 4872 |
Protein residues | 1043 | 847 | 1030 | 651 | 1058 | 847 | 1039 | 616 |
Ligands | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 |
B factors (Å2) | ||||||||
Protein | 30.63 | 48.71 | 18.70 | 34.74 | 43.32 | 53.01 | 44.75 | 72.92 |
Ligand | 43.83 | 27.33 | 37.25 | |||||
R.m.s. deviations | ||||||||
Bond lengths (Å) | 0.006 | 0.010 | 0.008 | 0.008 | 0.018 | 0.013 | 0.013 | 0.003 |
Bond angles (°) | 0.827 | 1.105 | 0.856 | 1.116 | 1.096 | 0.873 | 1.047 | 0.668 |
Validation | ||||||||
MolProbity score | 2.01 | 2.1 | 2.03 | 2.9 | 2.19 | 2.21 | 2.25 | 1.82 |
Clashscore | 11.34 | 12.50 | 13.46 | 21.80 | 13.77 | 16.79 | 17.37 | 11.64 |
Poor rotamers (%) | 0 | 1.3 | 0.0 | 5.44 | 0 | 0.29 | 0 | 0 |
Ramachandran plot | ||||||||
Favored (%) | 93.30 | 94.47 | 94.17 | 91.29 | 90.25 | 92.03 | 91.37 | 96.39 |
Allowed (%) | 6.7 | 5.16 | 5.73 | 8.71 | 9.55 | 7.97 | 8.53 | 3.61 |
Disallowed (%) | 0.0 | 0.38 | 0.1 | 0.0 | 0.19 | 0.0 | 0.10 | 0.0 |
