7FBJ
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRF BEAMLINE BL18U1 |
| Synchrotron site | SSRF |
| Beamline | BL18U1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-05-08 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 0.97915 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 82.020, 73.753, 270.717 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 90.400 - 2.850 |
| R-factor | 0.2559 |
| Rwork | 0.254 |
| R-free | 0.30040 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2i26 7eam |
| RMSD bond length | 0.012 |
| RMSD bond angle | 1.794 |
| Data reduction software | DIALS |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 135.360 | 135.360 | 2.910 |
| High resolution limit [Å] | 2.850 | 14.250 | 2.850 |
| Rmerge | 0.129 | 0.075 | 0.646 |
| Rmeas | 0.145 | 0.089 | 0.717 |
| Rpim | 0.064 | 0.046 | 0.306 |
| Total number of observations | 390964 | 2530 | 23633 |
| Number of reflections | 76077 | 661 | 4462 |
| <I/σ(I)> | 7.2 | 10.7 | 1.8 |
| Completeness [%] | 99.8 | 96.6 | 99.2 |
| Redundancy | 5.1 | 3.8 | 5.3 |
| CC(1/2) | 0.961 | 0.929 | 0.877 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION | 7.5 | 293 | 0.22M Sodium citrate tribasic dihydrate 23% PEG 3350 |
