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

From: Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex

 

T. gondii CIII2

(EMDB 52621),

(PDB 9I4X)

T. gondii CIV

(EMDB 52622),

(PDB 9I4Y)

C. sabaeus CIII2

(EMDB 51939),

(PDB 9H8T)

T. gondii CIII2 ELQ-300

(EMDB 51157),

(PDB 9G9T)

Data collection and processing

Magnification

165,000

165,000

165,000

165,000

Voltage (kV)

300

300

300

300

Electron exposure (e− Å−2)

36

36

36

36

Defocus range (μm)

0.6–1.8

0.6–1.8

0.6–1.8

0.6–1.6

Pixel size (Å)

0.83

0.83

0.83

0.3

Symmetry imposed

C2

C1

C1

C2

Initial particle images (no.)

2,658,324

2,658,324

2,658,324

4,451,128

Final particle images (no.)

432,158

432,158

637,287

2,056,878

Map resolution (Å)

2.79

3.16

2.67

1.83

FSC threshold

0.143

0.143

0.134

0.143

Map resolution range (Å)

2.6–3.2

2.45–8.18

2.6–2.93

1.74–2.06

Refinement

Initial model used (PDB code)

AlphaFold + de novo

AlphaFold + de novo

7o37

AlphaFold + de novo

Model resolution (Å)

3.6

3.1

2.83

1.9

FSC threshold

0.5

0.5

0.5

0.5

Model resolution range (Å)

2.6–3.2

2.45–8.18

2.6–2.93

1.74–2.06

Map sharpening B factor (Å2)

78.7

70.4

99.5

45.6

Model composition

 Non-hydrogen atoms

83,424

60,600

67,256

82.473

 Protein residues

5,060

3,515

4,091

4,830

 Ligands

18

22

12

18

B factors (Å2)

 Protein

39.40

57.54

32.53

8.94

 Ligand

33.65

59.96

28.56

14.20

Root mean square deviations

 Bond lengths (Å)

0.003

0.014

0.002

0.003

 Bond angles (°)

0.493

1.157

0.524

0.555

Validation

 MolProbity score

1.44

1.29

1.12

1.18

 Clashscore

5.18

2.34

2.02

1.9

 Poor rotamers (%)

1.01

0.65

0.63

0.43

Ramachandran plot

 Favored (%)

97.12

96.02

97.21

96.48

 Allowed (%)

2.84

3.61

2.74

3.31

 Disallowed (%)

0.04

0.38

0.05

0.21

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