Table 1. Cryo-EM data collection, refinement and validation statistics.

The Table shows cryo-EM data collection, reconstruction, and model validation results and values. See also Figures S2–S4.

	Mature virion (CA16-M)	A-particle (CA16-A)	Empty particle (CA16-E)	CA16-M:18A7	CA16-M:18A7-local	CA16-A:18A7	CA16-E:18A7	CA16-M:14B10	CA16-M:NA9D7	CA16-M:18A7:14B10:NA9D7
Data collection and processing
Magnification	x93,000	x93,000	x93,000	x130,000	x130,000	x130,000	x130,000	x93,000	x93,000	x93,000
Voltage (kV)	300	300	300	300	300	300	300	300	300	300
Electron exposure (e−/Å2)	40	40	40	56	56	56	56	40	40	40
Defocus range (μm)	−0.5 to −4.2	−0.5 to −4.2	−0.4 to −5.5	−0.3 to −2.9	−0.3 to −2.9	−0.3 to −2.9	−0.3 to −2.9	−0.4 to −4.2	−0.5 to −4.7	−0.5 to −4.6
Pixel size (Å)	1.128	1.128	1.128	1.307	1.307	1.307	1.307	1.128	1.120	1.120
Symmetry imposed	I2	I2	I2	I2	C1	I2	I2	I2	I2	I2
Initial particle images (no.)	29,497	29,497	14,507	101,235	726,696	101,235	101,235	38,833	52,713	38,967
Final particle images (no.)	17,781	3,409	11,574	60,558	57,409	10,246	10,406	10,580	45,235	27,819
Map resolution (Å)	3.56	3.33	3.43	2.65	3.67	3.07	3.13	3.30	3.06	3.78
FSC threshold	0.143	0.143	0.143	0.143	0.143	0.143	0.143	0.143	0.143	0.143
Map resolution range (Å)	3.0–5.0	3.0–5.0	3.0–5.0	2.5–4.5	3.0–5.0	2.5–4.5	2.5–4.5	2.5–4.5	3–5.0	3.0–5.0
Refinement
Initial model used (PDB code)	5C4W	4JGY	5C9A	5C4W	5C4W	4JGY	5C9A	5C4W	5C4W	n/a
Model resolution (Å)	3.72	3.51	3.53	2.75	3.71	3.17	3.23	3.40	3.32	n/a
FSC threshold	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Model resolution range (Å)	3.0–5.0	3.0–5.0	3.0–5.0	2.5–4.5	3.0–5.0	2.5–4.5	2.5–4.5	2.5–4.5	3–5.0
Map sharpening B factor (Å2)	−148.4	−170.8	−204.7	−124.7	−90.0	−116.4	−126.7	−173.5	−90.0	−220.7
Model composition										n/a
Non-hydrogen atoms	6,444	5,087	4,972	6,433	10,754	5,072	49,62	8,125	8,181
Protein residues	827	648	636	826	1,329	646	635	1,045	1,055
Ligands	1	0	0	1	5	0	0	1	1
B factors (Å2)
Protein	98.01	101.06	93.84	35.93	75.63	54.81	60.51	71.06	83.62
Ligand	105.89			36.93	65.80			65.93	57.87
R.m.s. deviations
Bond lengths (Å)	0.006	0.006	0.006	0.006	0.007	0.006	0.006	0.006	0.009
Bond angles (°)	0.780	0.709	0.804	0.798	1.124	0.765	0.735	0.868	0.869
Validation
MolProbity score	1.16	1.38	1.51	1.28	2.19	1.16	1.59	1.60	1.41
Clashscore	2.98	3.27	3.24	3.15	9.36	2.29	3.86	4.18	3.28
Poor rotamers (%)	0.71	0.18	0.36	1.14	2.05	0.72	0.18	0.34	0.67
Ramachandran plot
Favored (%)	97.67	96.20	94.19	97.30	92.72	97.14	93.70	93.96	95.86
Allowed (%)	2.33	3.80	5.81	2.58	6.74	2.7	6.30	5.94	4.14
Disallowed (%)	0.00	0.00	0.00	0.12	0.54	0.16	0.00	0.10	0.00