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

Data collection and processing

Magnification

81,000

81,000

81,000

81,000

81,000

81,000

Voltage (kV)

300

300

300

300

300

300

Electron exposure (e^–/Ų)

60

60

60

60

60

60

Defocus range (μm)

−0.8 to −2.2

−0.8 to −2.2

−0.8 to −2.2

−0.8 to −2.2

−0.8 to −2.2

−0.8 to −2.2

Pixel size (Å)

1.08

1.08

1.08

1.08

1.08

1.08

Symmetry imposed

C2

C2

C2

C2

C2

C1

Initial particle images (no.)

10,161,232

4,721,956

2,660,046

1,689,820

798,366

729,894

Final particle images (no.)

328,072

226,876

271,938

131,058

58,231

481,923

Map resolution (Å)

FSC threshold

2.89

0.143

2.49

0.143

2.85

0.143

3.01

0.143

3.13

0.143

3.28

0.143

Map resolution range (Å)

2.45–25.49

2.42–39.15

2.39–44.53

2.66–48.31

2.74–35.39

2.70–46.11

Refinement

Initial model used (PDB code)

de novo model, and 4JPZ⁵⁶.

Nan-Iav-CaM apo

Nan-Iav-CaM +NAM

Nan-Iav-CaM apo

Nan-Iav-CaM +NAM and 1CFD⁶⁵

Nan-Iav-CaM +AP+Ca²⁺

Map sharpening B factor (Ų)

−80

−60

−130.4

−80

−80

−184.0

Model composition

Non-hydrogen atoms

23,278

23,420

24,654

23,394

24,694

21,655

Protein residues

2902

2904

3054

2902

3054

2975

Ligands

PC: 6, PS: 2, CA: 6, PE: 12

PC: 6, PS: 2, CA: 6, PE: 14, NCA: 2

PC: 6, PS: 2, PE: 14, NCA: 2

PC: 6, PS: 2, CA: 6, PE: 12, AP:2

PC: 2, AP: 2, PS: 2, PE: 8

AP: 5

B factors (Ų)

Protein

93.05

83.35

50.70

79.34

79.53

102.60

Ligand

59.12

54.43

19.61

48.65

49.75

74.22

R.m.s. deviations

Bond lengths (Å)

0.002

0.003

0.004

0.002

0.003

0.003

Bond angles (°)

0.607

0.650

0.624

0.568

0.569

0.570

Validation

MolProbity score

1.17

1.12

1.20

1.08

1.26

1.59

Clashscore

2.98

3.04

3.28

2.86

3.26

3.48

Poor rotamers (%)

0.43

0.69

0.41

0.26

0.71

2.42

Ramachandran plot

Favored (%)

97.60

97.91

97.61

98.01

97.21

97.11

Allowed (%)

2.40

2.09

2.39

1.99

2.79

2.89

Disallowed (%)

0.00

0.00

0.00

0.00

0.00

0.00