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) | |||
|---|---|---|---|---|---|
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 |