Table 1.

Cryo-EM data collection, refinement, and validation statistics

	PUS3D118A; PDB: 9F9Q; EMD-16917; EMPIAR-16917	PUS3D118A_tRNAGln; PDB: 8OKD; EMD-16926; EMPIAR-11511	PUS3D118A_tRNAArg; PDB: 9ENE; EMD-19832; EMPIAR-12004	PUS3D118A_pre-tRNAArg; PDB: 9ENF; EMD-19833; EMPIAR-12005	PUS3R116A-2x tRNAGln; PDB: 9ENB; EMD-19830; EMPIAR-12003	PUS3R116A-1x tRNAGln; PDB: 9ENC; EMD-19831; EMPIAR-12003
Data collection and processing
Magnification	105,000×	105,000×	105,000×	105,000×	105,000×	105,000×
Voltage (keV)	300	300	300	300	300	300
Electron exposure (e−/Å2)	40	40	40	40	40	40
Defocus range (µM)	−3	−0.9 to −1.5	−0.9 to −1.5	−0.9 to −1.5	−0.9 to −1.5	−0.9 to −1.5
Pixel size (Å)	0.86	0.86	0.86	0.86	0.8456	0.8456
Symmetry imposed	C2	C2	C2	C2	C2	C1
Initial particle images (no.)	334,282	482,246	3,192,624	725,923	3,452,930	3,010,115
Final particle images (no.)	63,173	147,307	74,761	381,809	569,272	265,234
Map resolution (Å)	6.5	3.1	3.2	3.2	2.7	3.4
FSC threshold	0.143	0.143	0.143	0.143	0.143	0.143
Map resolution range (Å)	6.0 > 10 Å	2.5 to >10 Å	2.9 to >10 Å	2.9 to >10 Å	2.4–8.3 Å	3.0 to >10 Å
Refinement
Initial model used		AlphaFold2	AlphaFold2	AlphaFold2	AlphaFold2	AlphaFold2
Model resolution (Å)		3.3	3.1	3.1	3.1	3.9
FSC threshold		0.143	0.143	0.143	0.143	0.143
Model resolutionange (Å)		–	–	–	–	–
Model composition
Non-hydrogen atoms		7,964	8,490	8,245	8,268	6,162
Protein residues		582	658	530	636	563
Nucleotide residues		150	146	182	144	72
Ligands		–	–	–	Mg:6	–
B factors (Å2)
Protein		135.64	170.54	150.66	176.01	212.43
Nucleotide		211.14	283.81	454.72	257.95	289.89
Ligands		–	–	–	106.04	–
Root-mean-square deviations (RMSDs)
Bond lengths (Å)		0.002	0.004	0.003	0.005	0.004
Bond angles (°)		0.502	0.638	0.607	0.512	0.512
Validation
MolProbity score		1.76	1.80	2.16	1.56	1.69
Clashscore		8.12	7.49	15.33	4.96	5.41
Poor rotamers (%)		0	0.17	0	0.18	0
Ramachandran
Favored (%)		95.44	94.24	92.35	95.65	93.99
Allowed (%)		4.56	5.76	7.65	4.35	6.01
Disallowed (%)		0	0	0	0	0
CC volume		0.8	0.86	0.61	0.87	0.85