Table 1. Summary of image reconstruction and model building.
Sample prepared @ | DHBc 2 weeks |
DHBc 10 months |
DHBcR124EΔ 2 weeks |
DHBc+FkpA 2 weeks |
DHBcR124E 3 months |
|
---|---|---|---|---|---|---|
Magnification | 75,000 | |||||
Acquisition mode | integrating mode | counting mode | Counting mode | Counting mode | Integrating mode | Integrating mode |
Total exposure | 39 e-/Å2 | 77 e-/Å2 | 60 e-/Å2 | 60 e-/Å2 | 40 e-/Å2 | 40 e-/Å2 |
Exposure time | 3.5 s | 75 s | 54 s | 56.6 s | 2.4 s | 2.3 s |
Pixel size | 1.0635 Å | |||||
Beam diameter | 1 µm | |||||
C2 aperture | 70 µm | |||||
Objective aperture | 100 µm | |||||
Spot size | 5 | 9 | 9 | 9 | 5 | 5 |
Number of movies per hole | 2 | 3 | 2 | 3 | 3 | 2 |
Number of fractions | 20 | 47 | 40 | 40 | 40 | 20 |
Number of movies | 3541 | 2473 | 1496 | 2425 | 4339 | 1226 |
Defocus range | 700–2200 nm | 500–2100 nm | 500–1300 nm | 500–1600 nm | 600–1900 nm | 500–2000 nm |
Acquisition software | EPU | |||||
Frame alignment and dose weighting | MotionCor2 | |||||
CTF estimation | CtfFind4.1 | |||||
Processing software | RELION3 | |||||
Number of selected capsids | 91,445 | 89,241 | 74,760 | 129,522 | 161,596 | 35,820 |
Capsids in final map | 41,117 | 20,251 | 44,498 | 24,854 | 44,374 | 23,384 |
Resolution capsid | 6.1 Å | 3.7 Å | 3.0 Å | 4.2 Å | 4.0 Å | 6.0 Å |
EMDB | 10800 | 10803 | 10801 | 10802 | ||
extracted asymmetric units | 2,428,920 | 1,215,060 | 2,669,880 | 1,210,560 | 2,662,440 | n/a |
Extracted units in final map | 561,731 | 919,612 | 516,257 | n/a | 383,200 | n/a |
Resolution asymmetric unit | 5.4 Å | 3.0 Å | 3.0 Å | n/a | 3.9 Å | n/a |
Model building, refinement and validation | - | Coot, Phenix, Chimera | Coot, Phenix, Chimera | - | - | - |