Table 1 Data collection and processing information
From: Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer
Parameter | Intasome-NCP | NCP-D02-strep | 601 nucleosome |
|---|---|---|---|
Data Collection | |||
Microscope | FEI Titan Krios | FEI Titan Krios | FEI Titan Krios |
Detector | FEI Falcon II | FEI Falcon III | FEI Falcon III |
Acceleration voltage (kV) | 300 | 300 | 300 |
Number of micrographs | 4916 | 4182 | 1300 |
Frames per micrographs | 7 | 30 | 30 |
Frame rate (/s) | 4.3 | 60 | 60 |
Dose per frame (e-/pixel) | 9.86 | 1.12 | 1.24 |
Accumulated dose (e-/Å2) | 56 | 28.3 | 31.3 |
defocus range (μm) | 1.5–3.5 | 1.5–3.5 | 1.5–3.5 |
Frames | |||
Alignment software | MotionCorr | MotionCor2 | MotionCor2 |
Frames used in final reconstruction | 1–7 | 1–30 | 2–30 |
Dose weighting | No | yes | yes |
CTF | |||
Fitting software | CTFFIND3 | Gctf | Gctf |
Correction | full | full | full |
Particles | |||
Picking software | Xmipp & Relion 1.3 | Relion 2.1 | Relion 2.1 |
Picked | 989177 | 1131653 | 205680 |
Used in final reconstruction | 177155 | 62196 | 123123 |
Alignment | |||
Alignment software | Relion 1.3 | Relion 2.1 | Relion 2.1 |
Initial reference map | EMD-2992 | CryoSPARC ab initio | CryoSPARC ab initio |
low pass filter limit (Å) | 50 | 50 | 50 |
number of iterations | 25 | 25 | 25 |
local frame drift correction | yes | no | no |
Reconstruction | |||
Reconstruction software | Relion 1.3 | Relion 2.1 | Relion 2.1 |
Box Size | 240 × 240 × 240 | 256 × 256 × 256 | 256 × 256 × 256 |
Voxel size (Å) | 1.11 | 1.09 | 1.09 |
Symmetry | C1 | C1 | C2 |
Resolution limit (Å) | 2.22 | 2.18 Å | 2.18 Å |
Resolution estimate (Å) | 3.9 | 4.2 | 3.5 |
Masking | Yes | Yes | Yes |
Sharpening (Å2) | Bfactor: -146 | Bfactor: -150 | Bfactor: -110 |
EMDB ID | EMD-4960 | EMD-4692 | EMD-4693 |
Model building | |||
Number of protein residues | 1742 | 747 | |
Number of DNA residues | 358 | 284 | |
Bond length outliers | 0.00% | 0.00% | |
Bond angle outliers | 0.02% | 0.00% | |
Bonds (R.M.S.D) | 0.010 | 0.008 | |
Angles (R.M.S.D) | 1.183 | 0.856 | |
Ramachandaran favoured/outlier | 94.3%/0.00% | 96.85%/0% | |
Rotamer favoured/outlier | 98.5%/0% | 99.51/0% | |
Clashscore | 10.55 | 4.91 | |
Model vs Data CC (mask) | 0.71 | 0.85 | |
Molprobity score | 1.91 | 1.45 | |
PDB ID | PDB: 6RNY | PDB: 6R0C | |
