Table S1.
DWV structure quality indicators
| Parameter | Cryo-EM structure of native DWV virion | Cryo-EM structure of DWV virion incubated in crystallization buffer and cross-linked with 1% glutaraldehyde | Cryo-EM structure of DWV virion incubated in crystallization buffer | Cryo-EM structure of DWV virion at pH 5.0 | Crystal structure of DWV virion | Crystal structure of P domain |
| EMDB accession no. | EMD-4014 | EMD-3574 | EMD-3570 | EMD-3575 | NA | NA |
| PDB ID code | 5L8Q | 5MV5 | 5MUP | 5MV6 | 5G52 | 5G51 |
| Space group | NA | NA | NA | NA | I23 | C222 |
| a, b, c, Å | NA | NA | NA | NA | 360.13, 360.13, 360.13 | 63.97, 104.92, 57.95 |
| α, β, γ, ° | NA | NA | NA | NA | 90, 90, 90 | 90, 90, 90 |
| Resolution, Å | 3.5 | 3.1 | 3.8 | 4.1 | 29.8–3.8 (3.9–3.8)* | 39.8–1.45 (1.47–1.45)* |
| Rmerge† | NA | NA | NA | NA | 0.37 (0.81)* | 0.06 (0.54)* |
| 〈I〉/〈σI〉 | NA | NA | NA | NA | 2.0 (0.9)* | 14.2 (2.1)* |
| Completeness, % | NA | NA | NA | NA | 75.7 (76.1)* | 99.9 (98.4)* |
| Redundancy | NA | NA | NA | NA | 1.8 | 6.1 |
| No. of reflections | NA | NA | NA | NA | 102,129 | 212,754 |
| Rwork/Rfree | 0.296/0.336 | 0.310/0.312 | 0.362/0.379 | 0.337/0.381 | 0.301/0.337 | 0.189/0.212 |
| No. of atoms | 7,111‡ | 7,005‡ | 6,673‡ | 6,857‡ | 7,047‡ | 1,457 protein, 242 water |
| rmsd bond lengths, Å | 0.01 | 0.013 | 0.010 | 0.009 | 0.006 | 0.006 |
| rmsd bond angles, ° | 1.151 | 1.376 | 1.318 | 1.324 | 1.284 | 1.047 |
| Ramachandran favored, %§ | 90.9. | 92.4 | 92.9 | 92.4 | 81.6 | 97.2 |
| Ramachandran allowed, %§ | 8.3 | 7.6 | 7.1 | 7.6 | 16.2 | 2.8 |
| Ramachandran outliers, %§ | 0.8 | 0 | 0 | 0 | 2.2 | 0 |
| Poor rotamers, %§ | 0 | 0.5 | 0.6 | 0.1 | 8.1 | 2 |
| Clashscore (percentile) | 15.99 (95) | 7.83 (82) | 9.82 (72) | 13.16 (57) | 23.07 (89) | 7.05 (80) |
| MolProbity score (percentile) | 2.23 (99) | 1.90 (81) | 1.97 (77) | 2.10 (70) | 3.24 (81) | 1.76 (63) |
| Cβ deviations, %§ | 0 | 0 | 0 | 0 | 0.05 | 0 |
| CC¶ | NA | NA | NA | NA | 0.807 (0.618) | NA |
| Average B-factor of protein atoms, Å2 | 122.8 | 85.8 | 110.3 | 149.1 | 45.7 | 24.2 |
NA, not applicable.
*
Statistics for the highest resolution shell are shown in parentheses.
†
Rmerge = ΣhΣj|lhj − 〈lh〉|/ΣΣ|lhj|.
‡
Statistics are given for one icosahedral asymmetric unit.
§
According to the criterion of Molprobity (46).
¶
Correlation coefficient of observed structure factor amplitudes and structure factor amplitudes calculated from NCS-averaged map.