8DWA
Crystal structure of neutralizing antibody P1D9 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 24-ID-C |
| Synchrotron site | APS |
| Beamline | 24-ID-C |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2022-03-03 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 0.979180 |
| Spacegroup name | P 42 21 2 |
| Unit cell lengths | 147.136, 147.136, 80.108 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 63.550 - 3.200 |
| R-factor | 0.23788 |
| Rwork | 0.235 |
| R-free | 0.29747 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 7sd5 |
| RMSD bond length | 0.009 |
| RMSD bond angle | 1.539 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.5.32) |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 144.150 | 144.150 | 3.340 |
| High resolution limit [Å] | 3.120 | 8.820 | 3.120 |
| Rmerge | 0.516 | 0.168 | 4.520 |
| Rmeas | 0.527 | 0.172 | 4.607 |
| Rpim | 0.104 | 0.038 | 0.887 |
| Total number of observations | 392913 | 16536 | 72125 |
| Number of reflections | 15333 | 785 | 2704 |
| <I/σ(I)> | 6.9 | 22.1 | 0.9 |
| Completeness [%] | 100.0 | 100 | 100 |
| Redundancy | 25.6 | 21.1 | 26.7 |
| CC(1/2) | 0.991 | 0.990 | 0.437 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 18% w/v PEG5000 MME |
