Table 2 cryo-EM data collection, map, and model refinement statistics

From: Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage

 

(DH270.4-CH848.10.17)

(DH270.5-CH848.10.17)

(DH270.6-CH848.10.17)

(VRC01-CH848.0526.25)

(VRC01-CH848.10.17)

(DH270.6-CH848.0526.25)

(VRC01-CH848.0836.10)

(VRC01-CH848.0358.80)

Data Collection

Microscope

FEI Titan Krios

Detector

Gatan K3

Magnification

105000

Voltage (kV)

300

Electron dose (e-/Ã…2)

60

60

53.15

69.98

60

60

60

60

Pixel Size (Ã…)

1.066

1.066

1.066

1.066

1.066

1.066

1.066

1.066

Defocus Range (µm)

~0.8–4.3

~0.7–4.1

~0.5–4.1

~0.5–3.1

~0.5–3.5

~0.5–3.5

~0.5–3.5

~0.5–3.5

Reconstruction Software cryoSPARC

Symmetry

C3

C3

C3

C3

C3

C3

C3

C3

Particles

107890

76211

106823

252873

35839

119542

28746

46336

Box size (pix)

384

384

384

384

384

384

384

384

Resolution (Ã…) (FSC0.143)a

3.3

4.0

3.82

4.0

4.5

3.9

4.6

4.9

Coordinate Refinement (Phenix)b

Protein residues

2490

2496

2490

2514

2457

2574

2505

2523

R.m.s. deviations

Bond lengths (Ã…)

0.006

0.008

0.006

0.004

0.005

0.006

0.004

0.006

Bond angles (°)

0.915

1.100

1.055

0.845

0.894

1.041

0.949

0.997

Validation

Molprobity score

1.57

1.71

1.71

1.53

1.80

1.76

1.71

1.90

Clash score

3.13

4.02

4.37

2.96

5.01

4.26

4.65

6.60

Favored rotamers (%)

99.72

99.68

99.30

99.77

99.81

99.73

99.59

100

EMRinger Score

1.95

0.36

1.74

1.66

1.65

1.49

1.31

0.56

Ramachandran plot

Favored regions (%)

92.46

90.94

91.93

93.14

90.56

89.78

92.51

90.15

Disallowed regions (%)

0.32

0.44

0.41

0.24

0.41

0.35

0.12

0.24

  1. a Resolutions are reported according to the FSC 0.143 gold-standard criterion.
  2. b Statistics are reported for the protein residues within the complex excluding the antibody constant domains.