Table 1 X-ray crystallographic data and refinement statistics (molecular replacement) for the antigen binding fragments of the CAP228 antibodies in complex with various V2 antigens
From: Common helical V1V2 conformations of HIV-1 Envelope expose the α4β7 binding site on intact virions
A CAP228-16H bound to CAP225 V1V2-1FD6 | B CAP228-3D bound to CAP45 V2 peptide | C CAP228-16H bound to CAP228 V1V2-1FD6 | |
|---|---|---|---|
Data collection | |||
Space group | P1211 | C121 | C121 |
Cell dimensions | |||
a, b, c (Å) | 110.35, 41.76, 144.52 | 208.36, 43.81, 119.91 | 81.99, 73.79, 191.03 |
α,β,γ (°) | 90, 97, 90 | 90, 94, 90 | 90, 92, 90 |
Resolution (Å) | 50.00–2.30 (2.34–2.30)a | 50.00–2.60 (2.64-2.60) | 50.00–3.21 (3.27–3.21) |
Unique reflections | 58,982 | 33,817 | 19,842 |
R pim | 0.121 (0.743) | 0.122 (0.390) | 0.098 (0.500) |
I/σI | 7.6 (4.2) | 7.5 (3.9) | 6.8 (2.0) |
CC 1/2 | 0.952 (0.560) | 0.936 (0.812) | 0.958 (0.856) |
Completeness (%) | 99.6 (99.4) | 100.0 (100.0) | 89.7 (89.4) |
Redundancy | 3.6 (3.6) | 6.0 (3.6) | 3.2 (3.2) |
Refinement | |||
Resolution (Å) | 36.10–2.30 | 42.87–2.60 | 40.98–3.21 |
No. of reflections | 58721 (4982) | 33801 (3122) | 17788 (1388) |
Rwork/Rfree | 0.19/0.22 | 0.22/0.25 | 0.22/0.27 |
No. atoms (no H) | 7237 | 6694 | 7719 |
Protein | 6792 | 6529 | 7684 |
Ligand | 39 | 0 | 0 |
Water | 406 | 168 | 0 |
B factors (no H) (Å2) | 48 | 64 | 99 |
Protein | 48 | 65 | 99 |
Ligand | 120 | 0 | 0 |
Water | 43 | 39 | 0 |
Wilson B-factor (Å2) | 33 | 40 | 82 |
RMS deviations | |||
Bond lengths (Å) | 0.002 | 0.004 | 0.004 |
Bond angles (°) | 0.615 | 0.596 | 0.681 |
Ramachandran plot (%) | |||
Favoured regions | 98.87% | 97.83% | 95.08% |
Outlier regions | 0.00% | 0.00% | 0.00% |
Rotamer outliers (%) | 0.00% | 0.00% | 0.00% |
Molprobity clash score | 0.67 | 1.56 | 3.31 |
Molprobity overall score | 0.72 | 0.94 | 1.83 |
PDB ID | 6FY2 | 6FY3 | 6FY1 |
