Extended Data Table 1.
Cryo-EM data collection, refinement and validation statistics,
#1 DNMT-NCP167 | #2 NCP167 focused (-DNMT) | #3 DNMT focused (-NCP167) | #4 DNMT-CD-NCP combined map* (EMD-20281) (PDB 6PA7) | #5 DNMT-NCP (K36cMe3) | #6 DNMT (K36cMe3) focused (-NCP) |
#7 DNMT-NCP (K36cMe3) combined map* (EMD-21689) | |
---|---|---|---|---|---|---|---|
Data collection and processing | |||||||
Magnification | 130000 | 130000 | 130000 | 130000 | 130000 | 130000 | 130000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e−/Å2) | 65 | 65 | 65 | 65 | 65 | 65 | 65 |
Defocus range (μm) | −1.0 ~ −2.5 | −1.0 ~ −2.5 | −1.0 ~ −2.5 | −1.0 ~ −2.5 | −1.0 ~ −2.5 | −1.0 ~ −2.5 | −1.0 ~ −2.5 |
Pixel size (Å) | 1.029 | 1.029 | 1.029 | 1.029 | 1.029 | 1.029 | 1.029 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 2190114 | 180264 | |||||
Final particle images (no.) | 599344 | 406908 | 290055 | 42997 | 42997 | ||
Map resolution (Å) | 2.94 | 2.78 | 3.4 | 4.26 | 7.56 | ||
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | ||
Map resolution range (Å) | 7.0 ~ 2.94 | 5.0 ~ 2.78 | 7.0 ~ 3.40 | ||||
Refinement | |||||||
Initial model used (PDB code) | 1KX5, 4U7P, 4QLC | ||||||
Model resolution (Å) | |||||||
FSC threshold | |||||||
Model resolution range (Å) | 40–2.78 | ||||||
Map sharpening B factor (Å2) | −91 | −81 | −107 | −120 | −300 | ||
Model composition | |||||||
Non-hydrogen atoms | 21026 | ||||||
Protein residues | 1770 | ||||||
DNA base pairs | 332 | ||||||
Ligands | 2 | ||||||
C1 atoms | 3 | ||||||
B factors (Å2) | |||||||
Protein | 93.3 | ||||||
Ligand | 55.5 | ||||||
R.m.s. deviations | |||||||
Bond lengths (Å) | 0.005 | ||||||
Bond angles (°) | 0.99 | ||||||
Validation | |||||||
MolProbity score | 1.44 | ||||||
Clashscore | 4.23 | ||||||
Poor rotamers (%) | |||||||
Ramachandran plot | |||||||
Favored (%) | 96.77 | ||||||
Allowed (%) | 3.23 | ||||||
Disallowed (%) | 0 |
Combined map from focused refinement of NCP and DNMT.