Table 2 X-ray crystallography data collection and refinement statistics

From: Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2

 

H11-D4–RBD (PDB 6YZ5)

H11-H4–RBD (PDB 6ZBP)

H11-H4–RBD–CR3022 (PDB 6ZH9)

H11-D4–RBD–CR3022 (PDB 6Z2M) (PDB 6YZ7)

Data collection

Space group

P3121

P3121

P 42212

P21212

P 4122

Cell dimensions

     

a, b, c (Å)

78.3, 78.3, 127.1

73.2, 73.2, 131.7

156.4, 154.4, 116.3

149.7, 150.4, 119.5

154.6, 154.6, 229.3

α, β, γ (°)

90, 90, 120

90, 90, 120

90, 90, 90

90, 90, 90

90, 90, 90

Resolution (Å)a

46–1.80 (1.85–1.80)

57–1.85 (1.90–1.85)

60–3.31 (3.37–3.31)

105–2.72 (2.96–2.72)

128–3.29 (3.35–3.29)

Rmerge

0.109 (1.7)

0.086 (2.05)

0.091 (3.9)

0.168 (1.6)

0.82 (–)

Rpim

0.036 (0.54)

0.028 (0.46)

0.018 (0.77)

0.047 (0.46)

0.094 (4.1)

I/σ (I)

20.6 (1.9)

18.2 (1.7)

21.9 (0.5)

11.2 (1.6)

4.9 (0.2)

CC1/2

1.0 (0.7)

1.0 (0.7)

1.0 (0.3)

1.0 (0.5)

1.0 (0.4)

Completeness (%)

99.7 (99.7)

99.8 (99.5)

100 (100)

65 (14)

100 (93)

Completeness (%) (ellipsoidal)b

   

95.6 (82.1)

 

Redundancy

19.7 (20.1)

19.7 (20.9)

25.6 (26.5)

13.7 (12.4)

78.4 (77.9)

Refinement

Resolution (Å)

46.3–1.80 (1.85–1.80)

57.2–1.85 (1.90–1.85)

128–3.31 (3.4–3.31)

78–2.71 (2.96–2.71)

128–3.29 (3.4–3.29)

No. reflections

40,120 (3,066)

35,506 (2,585)

20,977 (1,538)

47,412 (2,371)

39,015 (1,538)

Rwork/Rfree

16.6/19.3 (30.5/29.2)

18.5/21.7 (30.0/33.3)

26.3/30.5 (40.5/41.6)

19.8/24.1 (28.8/29.9)

23.7/26.8 (41.5/37.9)

No. atoms

     

Protein

2,571

2,591

5,906

11,731

11,718

Ions/buffer

64

19

Water

241

103

Residual B factors

     

Protein

38

28

118

65

157

Ligand/ion

55

71

Water

45

53

R.m.s. deviations

     

Bond lengths (Å)

0.010

0.012

0.008

0.004

0.004

Bond angles (°)

1.4

1.68

1.63

0.74

1.39

  1. Data were collected from a single crystal for each structure.
  2. aValues in parentheses are for the highest-resolution shell.
  3. bThese data showed significant anisotropy and were truncated accordingly.