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

From: Structural and mechanistic insights into Streptococcus pneumoniae NADPH oxidase

 

Substrate-free

(EMD-18644), (PDB 8QT6)

NADPH-bound

(EMD-18645), (PDB 8QT7)

NADH-bound

(EMD-18646), (PDB 8QT9)

F397A

(EMD-18647), (PDB 8QTA)

Data collection and processing

Magnification

×215,000

×215,000

×215,000

×215,000

Voltage (kV)

300

300

300

300

Electron exposure (e– per Å2)

70

70

70

70

Defocus range (μm)

−0.7 to −2.1

−0.7 to −2.1

−0.7 to −2.1

−0.7 to −2.1

Pixel size (Ã…)

0.573

0.573

0.573

0.573

Symmetry imposed

C1

C1

C1

C1

Initial particle images (no.)

3,376,347 (Topaz)

3,115,826 (Topaz)

2,273,739 (crYOLO)

6,641,288 (Topaz)

4,948,429 (Topaz)

2,868,991 (crYOLO)

5,571,895 (Topaz)

5,183,375 (Topaz)

3,583,885 (crYOLO)

5,003,252 (Topaz)

4,668,309 (Topaz)

4,145,972 (crYOLO)

Final particle images (no.)

397,972

591,137

697,211

546,234

Map resolution (Ã…)

2.29

2.20

2.36

2.64

  FSC threshold

0.143

0.143

0.143

0.143

Map resolution range (Ã…)

2.25–26.65

2.05–32.20

2.11–36.46

2.50–9.30

Refinement

Initial model used

AF model (AF-Q8CZ28)

Substrate-free model

Substrate-free model

NADPH-bound model

Model resolution (Ã…)

2.44

2.33

2.44

2.75

  FSC threshold

0.5

0.5

0.5

0.5

Map sharpening B factor (Ã…2)

−80.1

−74.8

−79.9

−105.4

Model composition

  Nonhydrogen atoms

3,466

3,516

3,511

3,472

  Protein residues

399

399

399

399

  Ligands

   HEM

2

2

2

2

   FAD

1

1

1

1

   NDP

–

1

–

1

   NAI

–

–

1

–

  Waters

63

65

64

27

B factors (Ã…2)

  Protein

34.55

41.92

37.17

49.30

  Ligand

22.74

34.50

28.78

46.19

  Water

31.09

40.97

35.05

40.24

Root-mean-square deviations

  Bond lengths (Å)

0.004

0.009

0.003

0.009

  Bond angles (°)

0.940

0.931

0.578

0.940

Validation

 MolProbity score

1.76

1.27

1.26

1.56

  Clashscore

4.72

4.96

5.55

7.45

  Poor rotamers (%)

0.86

0.86

0.58

1.16

Ramachandran plot

  Favored (%)

98.24

98.24

98.74

97.48

  Allowed (%)

1.76

1.76

1.26

2.52

  Disallowed (%)

0

0

0

0

Q-score

0.82

0.83

0.82

0.77

  1. PDB, Protein Data Bank; FSC, Fourier shell correlation; HEM, heme group; NDP, NADPH; NAI, NADH.
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