Table 1:

Cryo-EM data collection, model refinement and validation statistics

Sample	DNMT3A2/3B3-10n8n10-dinucleosome						3A2/3B3 10n5n10	10n5n10 alone	3A2/3B3 10n6n10	3A2/3B3 10n8n10 H3 peptide	3A2/3B3 ΔPWWP 10n8n10	3A2/3B3 10n25n10	10n8n10 alone
Data Statistics
Microscope	Titan Krios						Talos Arctica	Talos Arctica	Titan Krios	Talos Arctica	Talos Arctica	Talos Arctica	Talos Arctica
Voltage (kV)	300						200	200	300	200	200	200	200
Electron exposure (e−/Å2)	60						50	50	60	50	50	50	50
Pixel size (Å)	0.828						0.96	0.96	0.828	0.96	0.96	0.96	0.96
Symmetry imposed	C1						C1	C1	C1	C1	C1	C1	C1
FSC threshold	0.143						0.143	0.143	0.143	0.143	0.143	0.143	0.143
Map resolution range (Å)	3-10						15-5	10-3	10-3	15-5	15-5	15-5	10-3
Initial particle projections	2584528						96074	367292	2887646	170287	430957	331789	430957
Focus Region	Composite	Upper DNMT	Lower DNMT	Upper Nuc.	Lower Nuc.	Consen-sus	Consen-sus	Consen-sus	Consen-sus	Consen-sus	Consen-sus	Consen-sus	Consen-sus
EMD code	47344	47354	47355	47367	47353	47349	47448	47450	47461	47462	47495	47496	47499
Final particle projections	478167						40908	61854	356421	44359	37292	59084	75131
Map resolution (Å)	3.75						6.08	5.93	3.14	6.08	6.92	4.85	4.24
Model Refinement
PDB code	9E00	9E0F	9E0G	9E0R	9E09	9E05	9E2D	9E2F	9E2Q	9E2R	9E3R	9E3U	9E49
Model composition:
Non-hydrogen atoms	43875	12187	12152	12305	12355	49286	48657	24620	46712	49043	46691	24818	24442
Protein residues	3865	1510	1543	749	752	4499	4444	1459	4188	4822	4183	2248	1458
DNA base pairs	321	0	0	155	156	321	316	318	319	319	319	164	314
Ligands	4	2	2	0	0	4	4	n/a	4	4	4	2	0
Zn ions	18	9	9	0	0	9	18	n/a	18	18	18	9	0
B factors (Å2):
Overall	133.9	156.7	187.6	139.3	147.8	165.7	708.5	494.0	456.5	770.6	883.2	478.7	322.8
Protein/DNA	133.9	156.6	187.6	139.3	147.8	165.5	708.4	494.0	456.4	770.6	883.2	478.5	322.8
Ligands and Zn	310.1	283.5	287.1	n/a	n/a	363.3	912.7	n/a	672.3	770.6	1000	879.7	n/a
Validation:
Bond lengths (RMSD Å)	0.0106	0.0134	0.0117	0.0054	0.0047	0.0054	0.0118	0.0083	0.0123	0.0113	0.0116	0.0116	0.0097
Bond angles (RMSD °)	1.27	1.42	1.44	0.89	0.86	1.04	1.37	1.02	1.33	1.32	1.35	1.36	1.00
MolProbity score	1.45	1.61	1.73	1.07	1.08	1.33	1.49	1.15	1.54	1.53	1.55	1.45	1.09
Clashscore	5.16	4.46	4.29	2.81	2.31	4.15	4.66	3.21	5.67	5.44	5.68	4.51	2.98
Rotamer outliers (%)	0.0	0.0	0.0	0.0	0.0	0.0	0.03	0.00	0.00	0.03	0.00	0.00	0.00
Ramachandran plot
Favored (%)	96.95	96.62	95.53	98.35	97.68	97.32	96.26	97.83	96.47	96.44	96.42	96.59	98.11
Allowed (%)	3.05	3.38	4.47	1.65	2.32	2.68	3.74	2.17	3.53	3.56	3.58	3.41	1.89
Disallowed (%)	0	0	0	0	0	0	0	0	0	0	0	0	0