7VPY
Crystal structure of the neutralizing nanobody P86 against SARS-CoV-2
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SPRING-8 BEAMLINE BL44XU |
| Synchrotron site | SPring-8 |
| Beamline | BL44XU |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-06-23 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.9 |
| Spacegroup name | C 1 2 1 |
| Unit cell lengths | 105.078, 43.166, 56.027 |
| Unit cell angles | 90.00, 110.76, 90.00 |
Refinement procedure
| Resolution | 30.800 - 1.600 |
| R-factor | 0.1787 |
| Rwork | 0.177 |
| R-free | 0.21310 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5ivo |
| RMSD bond length | 0.006 |
| RMSD bond angle | 0.872 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | MOLREP |
| Refinement software | PHENIX (1.19.2_4158) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 49.130 | 1.630 |
| High resolution limit [Å] | 1.600 | 1.600 |
| Rmeas | 0.067 | 0.668 |
| Number of reflections | 30851 | 1493 |
| <I/σ(I)> | 11.9 | 2.8 |
| Completeness [%] | 99.1 | |
| Redundancy | 3.4 | |
| CC(1/2) | 0.998 | 0.835 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 51 mg/mL protein, 0.2 M Ammonium sulfate, and 30% w/v polyethylene glycol 4,000 |
