Table 2. X-ray diffraction data processing and crystal structure refinement.
Nanobody | 5E | 7E | 8C | 8D | 10E |
---|---|---|---|---|---|
Data processing | |||||
Space group | P312 | P1 | P21 | P1 | P212121 |
Unit cell parameters | 110.8, 110.8, 83.3 Å; 90, 90, 120 ° | 37.2, 79.0, 117.6 Å; 77.7, 87.7, 84.3 ° | 39.86, 54.17, 80.4 Å; 90, 96.36, 90 ° | 42.30, 46.54, 91.99 Å; 95.65, 100.11, 90.08 ° | 101.7, 118.3, 122.5 Å; 90, 90, 90 ° |
Resolution range (Å) | 50–2.75 (3.15–2.75) | 50–2.50 (2.56–2.50) | 50–1.73 (1.77–1.73) | 50–1.50 (1.59–1.50) | 50–2.55 (2.62–2.55) |
⟨I/σI⟩ | 10.3 (1.6) | 5.5 (0.6) | 11.8 (1.0) | 6.9 (0.5) | 11.6 (0.5) |
Completeness (%) | Spherical 70.0 (18.0) [ellipsoidal 99.6(66.7)] | 91.7 (91.3) | 99.1 (98.7) | 89.7 (89.4) | 99.8 (99.8) |
Redundancy | 5.6 (6.3) | 3.8 (3.8) | 5.6 (6.3) | 2.7 (2.7) | 7.5 (7.4) |
Rmeas (%) | 14.2 (136.3) | 20.5 (291.4) | 8.0 (225.6) | 9.1 (236.8) | 11.2 (349.6) |
CC½ (%) | 99.6 (58.0) | 99.2 (33.5) | 99.8 (35.9) | 99.7 (22.4) | 99.9 (33.5) |
Structure refinement | |||||
Rcryst/Rfree (%) | 28.9/32.3 | 25.4/29.9 | 19.0/21.5 | 17.9/22.9 | 28.0/30.3 |
RMSD bond lengths (Å)/angles (°) | 0.002/0.6 | 0.004/0.7 | 0.011/1.1 | 0.011/1.0 | 0.005/0.7 |
Ramachandran favoured/outliers (%) | 89.5/2.1 | 95.1/0.8 | 97.2/0.6 | 98.1/0.0 | 94.4/0.9 |
MolProbity score/percentile | 2.86/68th | 2.22/89th | 1.74/77th | 1.24/96th | 2.48/80th |
Protein chains in asymmetric unit | 2 | 8 | 2 | 4 | 8 |
PDB entry | 9ERT | 9ERU | 9ERW | 9ETL | 9ETJ |