Table 1A.

Cryo-EM data collection, refinement and validation statistics

	KmAgoapo (EMD-38354) (PDB: 8XHS)	KmAgogDNA (EMD-38355) (PDB: 8XHV)	pre1-KmAgo-DMgDtD (EMD-38409) (PDB: 8XJX)	KmAgo-DMgDtR (EMD-38408) (PDB: 8XJW)
Data collection and processing
Magnification	105 000	105 000	105 000	105 000
Voltage (kV)	300	300	300	300
Electron exposure (e−/Å2)	54	54	54	54
Defocus range (μm)	−1.0 ∼ −1.5	−1.0 ∼ −1.5	−1.0 ∼ −1.5	−1.0 ∼ −1.5
Pixel size (Å)	0.851	0.851	0.851	0.851
Symmetry imposed	C1	C1	C1	C1
Initial particle images (no.)	2 644 446	10 959 937	13 369 141	11 662 653
Final particle images (no.)	386 173	439 341	556 763	439 557
Map resolution (Å)	2.85	2.66	2.68	2.84
FSC threshold	0.143	0.143	0.143	0.143
Map resolution range (Å)	2.44–42.73	2.30–39.22	2.48–41.04	2.43–44.28
Refinement
Initial model used	AlphaFold2	KmAgoapo	KmAgoapo	KmAgoapo
Model resolution (Å)	2.82	2.63	2.64	2.82
FSC threshold	0.143	0.143	0.143	0.143
Model resolution range (Å)	n/a	n/a	n/a	n/a
Map sharpening B factor (Å2)	−132.9	−112.1	−129.4	−130.2
Model composition
Non-hydrogen atoms	5076	6205	6310	6247
Protein residues	618	721	693	690
Ligand	0	1	1	1
B-factors (Å2)
Protein	11.35/100.10/43.16	35.94/120.37/55.79	29.99/111.22/57.56	19.94/51.65/33.65
Nucleotide	—	27.27/122.98/60.44	29.83/71.22/43.37	21.23/56.87/34.33
Ligand	—	29.16/29.16/29.16	66.88/66.88/66.88	28.24/28.24/28.24
Water	9.05/33.39/18.20	15.27/33.84/24.58	19.99/77.57/32.76	15.05/28.27/23.57
R.m.s. deviations
Bond lengths(Å)	0.003	0.003	0.003	0.002
Bond angles (o)	0.548	0.583	0.567	0.579
Validation
MolProbity score	1.63	1.66	1.76	1.79
Clashscore	4.66	5.96	7.80	9.16
Poor rotamer (%)	0.00	0.00	0.00	0.00
Ramachandran plot
Favored (%)	95.72	95.24	95.20	95.76
Allowed (%)	4.28	4.76	4.80	4.24
Disallowed (%)	0.00	0.00	0.00	0.00