8DW9
Crystal structure of neutralizing antibody D29 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 21 21 21 |
Unit cell lengths | 80.171, 106.707, 207.650 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 95.090 - 4.000 |
R-factor | 0.3522 |
Rwork | 0.300 |
R-free | 0.38070 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7sd5 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (Refine) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 146.180 | 146.180 | 3.340 |
High resolution limit [Å] | 3.250 | 13.790 | 3.250 |
Rmerge | 0.957 | 0.904 | 2.608 |
Rmeas | 1.029 | 0.973 | 2.798 |
Rpim | 0.374 | 0.354 | 1.006 |
Total number of observations | 416989 | 5258 | 34867 |
Number of reflections | 15675 | 759 | 4606 |
<I/σ(I)> | 2.9 | 5.5 | 0.8 |
Completeness [%] | 99.8 | 98.4 | 99.9 |
Redundancy | 7.4 | 6.9 | 7.6 |
CC(1/2) | 0.879 | 0.945 | 0.293 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 2 M ammonium sulfate, 0.05 M MES, pH 6.0, 5 mM magnesium acetate tetrahydrate |