Extended Data Table 2.

Statistics of cryo-EM data collection, refinement and validation

	PRC (intact TIR) (EMD-20452) (PDB 6PQR)	PRC (nicked TIR) (EMD-20453) (PDB 6PQU)	HFC (EMD-20455) (PDB 6PQX)	TEC (EMD-20456) (PDB 6PQY)	STC (EMD-20457) (PDB 6PR5)
Data collection and processing
Magnification	130,000	130,000	130,000	130,000	130,000
Voltage (kV)	300	300	300	300	300
Electron exposure (e−/Å2)	50.8	52.2	52.2	54.4	54.4
Defocus range (μm)	−1.5–−2.5	−1.5–−2.5	−1.5–−2.5	−1.5–−2.5	−1.5–−2.5
Pixel size (Å)	1.05	1.05	1.05	1.05	1.05
Symmetry imposed	C2	C2	C2	C2	C1
Initial particle images (no.)	243,518	300,406	262,691	228,413	228,413
Final particle images (no.)	32,984	59,333	3,997	26,397	43,661
Map resolution (Å)	3.4	3.3	4.6	4.2	3.3
FSC threshold	0.143	0.143	0.143	0.143	0.143
Map resolution range (Å)	2.4–5.2	2.4–5.6	4.0–8.0	3.7–6.8	2.5–5.6
Refinement
Initial model used (PDB code)	6PQN	6PQN	6PQN	6PQN	6PQN
Model resolution (Å)	3.7	3.6	4.8	4.7	3.5
FSC threshold	0.5	0.5	0.5	0.5	0.5
Model resolution range (Å)	2.4–5.2	2.4–5.6	4.0–8.0	3.7–6.8	2.5–5.6
Map sharpening B factor (Å2)	−90	−90	−126	−120	−90
Model composition
Non-hydrogen atoms	9266	10004	10116	8690	10194
Protein residues	936	936	960	920	960
Nucleotides	88	124	120	64	124
Ligands	6	6	4	0	6
B factors (Å2)
Protein	105.51	74.58	89.52	182.34	59.68
Nucleic acid	104.92	131.57	160.90	158.19	91.35
Ligand	109.58	93.13	81.45		69.54
R.m.s. deviations
Bond lengths (Å)	0.009	0.008	0.006	0.007	0.008
Bond angles (°)	0.830	0.890	0.984	0.980	0.768
Validation
MolProbity score	1.91	2.04	2.39	2.35	1.64
Clashscore	16.01	23.12	16.06	24.55	13.64
Poor rotamers (%)	0.24	1.21	2.35	0.49	0.71
Ramachandran plot
Favored (%)	96.74	97.39	94.14	92.51	98.33
Allowed (%)	3.26	2.39	5.23	6.83	1.36
Disallowed (%)	0	0.22	0.63	0.66	0.31