Table 2.
Data collection, model refinement and validation for averaged nucleosome structure analysis. Related to Figure 3, 6
| Micrograph name | Interphase mono lot 1 |
Interphase di lot 1 |
Interphase oligo lot 1 |
Metaphase mono lot 1 |
Metaphase di lot 1 |
Metaphase oligo lot 1 |
Interphase, 'Freed' (Crosslinked after MNase) lot 2 |
Interphase oligo lot 2 |
Metaphase oligo lot 2 |
GUB-closed nucleosome |
GUB-open nucleosome |
|||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Deta collection and prosessing | ||||||||||||||
| Microscope | FEI Titan Krios | FEI Titan Krios | FEI Talos Arctica | FEI Titan Krios | FEI Titan Krios | FEI Talos Arctica | FEI Talos Arctica | FEI Talos Arctica | FEI Talos Arctica | FEI Talos Arctica | FEI Talos Arctica | |||
| Magnification | 25,000 | 20,000 | 28,000 | 25,000 | 20,000 | 28,000 | 28,000 | 28,000 | 28,000 | 28,000 | 28,000 | |||
| Voltage (kV) | 300 | 300 | 200 | 300 | 300 | 200 | 200 | 200 | 200 | 200 | 200 | |||
| Camera | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | Gatan K2 Summit | |||
| Electron exposure (e−/Å) | 45.0 | 55.5 | 33.1 | 44.7 | 54.0 | 38.3 | 35.3 | 37.3 | 31.1 | 34.2 | 34.2 | |||
| Defocus range (μm) | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | −1 ~ −3 | |||
| Pixel size (Å) | 1.33 | 1.6 | 1.5 | 1.33 | 1.6 | 1.5 | 1.5 | 1.5 | 1.5 | 1.5 | 1.5 | |||
| Micrographs | 1,622 | 1,270 | 1,325 | 1,637 | 1,347 | 2,676 | 2,049 | 1,375 | 1,044 | |||||
| EMPIAR ID of raw micrographs | EMPIAR-10742 | EMPIAR-10744 | EMPIAR-10692 | EMPIAR-10743 | EMPIAR-10745 | EMPIAR-10691 | EMPIAR-10750 | EMPIAR-10747 | EMPIAR-10746 | EMPIAR-10749 | EMPIAR-10748 | |||
| EM 3D map. Name | Nucleosome | Nucleosome | Nucleosome | Nucleosome | Nucleosome | Nucleosome | Nucleosome + H1.8 |
"Free" nucleosome |
Nucleosome | Nucleosome | Nucleosome + H1.8 |
GUB-closed nucleosome |
GUB-open nucleosome |
|
| Initial particle images (no.) | 147,921 | 213,608 | 571,558 | 116,669 | 167,734 | 898,553 | 259,060 | 178,949 | 194,837 | 203,052 | 199,125 | |||
| Particles for nucleosome ab-initio reconstruction (no.) | 13,434 | 21,650 | 85,994 | 11,325 | 9,515 | 154,208 | 25,123 | 61,931 | 50,002 | 86,720 | 75,171 | |||
| Particles for 'decoy' ab-initio reconstruction (no.) | 134,487 | 100,946 | 485,564 | 105,344 | 102,722 | 744,345 | 133,700 | 117,018 | 144,835 | 116,332 | 123,954 | |||
| particle for 3D clasification (no.) | 147,921 | 122,596 | 571,558 | 116,669 | 112,237 | 898,553 | 158,823 | 178,949 | 194,837 | 203,052 | 199,125 | |||
| Particle images (no.) | 13,798 | 15,653 | 89,191 | 13,350 | 6,027 | 155,413 | 27,383 | 20,835 | 52,163 | 52,941 | 6,399 | 76,391 | 62,823 | |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | |
| Map resolution (FSC=0.143) | 5.12 | 4.74 | 3.38 | 5.64 | 8.1 | 3.5 | 4.42 | 5.44 | 3.54 | 3.77 | 5.6 | 3.77 | 4.52 | |
| CTF rifinement | ✓ (Relion 3.1) | ✓
(Relion 3.1) |
✓ (Relion 3.1) | ✓ (Relion 3.1) | ✓ (Relion 3.1) | ✓ (Relion 3.1) | - | ✓ (Relion 3.1) | ✓ (Relion 3.1) | ✓ (Relion 3.1) | - | ✓ (Relion 3.1) | ✓ (Relion 3.1) | |
| Particle polishing | ✓ (Relion 3.1) | ✓
(Relion 3.1) |
✓ (Relion 3.1) | ✓ (Relion 3.1) | ✓ (Relion 3.1) | ✓ (Relion 3.1) | - | ✓ (Relion 3.1) | ✓ (Relion 3.1) | ✓ (Relion 3.1) | - | ✓ (Relion 3.1) | ✓ (Relion 3.1) | |
| Postprocess Pixel size | 1.3 | 1.66 | 1.47 | 1.3 | 1.66 | 1.47 | - | 1.47 | 1.47 | 1.47 | - | 1.47 | 1.47 | |
| EM data resource ID | EMD-22797 | EMD-22798 | EMD-22790 | EMD-22800 | EMD-22801 | EMD-22791 | EMD-22792 | EMD-23826 | EMD-23819 | EMD-23821 | - | EMD-23823 | EMD-23824 | |
| Atomic coordinate name | - | - | Nucleosome | - | - | Nucleosome | Nucleosome + H1.8 | - | - | - | - | - | - | - |
| Pixel size | 1.47 | 1.47 | 1.47 | |||||||||||
| Model resolution (Å) | 3.38 | 3.5 | 4.4 | |||||||||||
| Initial model used (code) | 6DZT, 5NL0 | 6DZT, 5NL0 | 5NL0 | |||||||||||
| Map sharpening | RELION 3.1 (Postprocess) | RELION 3.1 (Postprocess) | CryoSPARC, bsoft (blocres/blocafilt) | |||||||||||
| Map sharpening B factor (Å2) | −60.3386 | −30.7959 | - | |||||||||||
| Model composition | ||||||||||||||
| Non-hydrogen atoms | 12,169 | 12,408 | 13,710 | |||||||||||
| Protein residues | 755 | 760 | 842 | |||||||||||
| Nucleotide | 302 | 312 | 344 | |||||||||||
| Model vs. Data | ||||||||||||||
| CC (mask) | 0.81 | 0.8 | 0.73 | |||||||||||
| CC (box) | 0.74 | 0.73 | 0.83 | |||||||||||
| CC (peak) | 0.7 | 0.69 | 0.72 | |||||||||||
| CC (volume) | 0.79 | 0.78 | 0.76 | |||||||||||
| R.m.s. deviations | ||||||||||||||
| Bond lengths (Å) | 0.008 | 0.008 | 0.008 | |||||||||||
| BoBond angles (°) | 0.691 | 0.753 | 0.867 | |||||||||||
| Validation | ||||||||||||||
| MolProbity score | 2.42 | 2.56 | 2.96 | |||||||||||
| Clashscore | 6.86 | 9.71 | 30.6 | |||||||||||
| Ramachandran plot | ||||||||||||||
| Favored (%) | 94.99 | 95.3 | 93.93 | |||||||||||
| Allowed (%) | 5.01 | 4.57 | 6.07 | |||||||||||
| Disallowed (%) | 0 | 0.13 | 0 | |||||||||||
| Protein data bank ID | 7KBD | 7KBE | 7KBF | |||||||||||