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.