7KM5
Crystal structure of SARS-CoV-2 RBD complexed with Nanosota-1
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 24-ID-E |
| Synchrotron site | APS |
| Beamline | 24-ID-E |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2020-09-16 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.97918 |
| Spacegroup name | P 43 21 2 |
| Unit cell lengths | 60.849, 60.849, 410.701 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 48.890 - 3.190 |
| R-factor | 0.2492 |
| Rwork | 0.247 |
| R-free | 0.29410 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 7c01 |
| RMSD bond length | 0.002 |
| RMSD bond angle | 0.448 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.18.2_3874) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 48.890 | 48.890 | 3.410 |
| High resolution limit [Å] | 3.190 | 9.020 | 3.190 |
| Rmerge | 0.145 | 0.041 | 0.754 |
| Rmeas | 0.163 | 0.047 | 0.850 |
| Rpim | 0.074 | 0.022 | 0.382 |
| Total number of observations | 2802 | 11102 | |
| Number of reflections | 13567 | 691 | 2415 |
| <I/σ(I)> | 8.2 | 24.9 | 2.2 |
| Completeness [%] | 98.3 | 93.2 | 98.7 |
| Redundancy | 4.7 | 4.1 | 4.6 |
| CC(1/2) | 0.995 | 0.998 | 0.916 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 295 | 50 mM MnCl2, 50 mM MES (pH 6.0), 20% (W/V) PEG 4000 |
