7JX3
Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 4.2.2 |
Synchrotron site | ALS |
Beamline | 4.2.2 |
Temperature [K] | 100 |
Detector technology | CMOS |
Collection date | 2020-08-07 |
Detector | RDI CMOS_8M |
Wavelength(s) | 0.97625 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 79.540, 127.780, 192.280 |
Unit cell angles | 90.00, 96.66, 90.00 |
Refinement procedure
Resolution | 47.500 - 2.650 |
R-factor | 0.2591 |
Rwork | 0.258 |
R-free | 0.28810 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6m0j |
RMSD bond length | 0.004 |
RMSD bond angle | 1.398 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER (2.8.3) |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 47.750 | 47.750 | 2.730 |
High resolution limit [Å] | 2.650 | 11.240 | 2.650 |
Rmerge | 0.199 | 0.044 | 2.418 |
Rmeas | 0.215 | 0.047 | 2.619 |
Rpim | 0.079 | 0.018 | 0.999 |
Total number of observations | 406155 | 4953 | 30682 |
Number of reflections | 55237 | 714 | 4503 |
<I/σ(I)> | 8.7 | 37.6 | 0.7 |
Completeness [%] | 99.6 | 93.4 | 99.9 |
Redundancy | 7.4 | 6.9 | 6.8 |
CC(1/2) | 0.996 | 0.997 | 0.390 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | 16.2% w/v PEG4000, 0.09 M sodium citrate, pH 6.0, 0.18 M ammonium acetate, 0.02 M potassium acetate, 0.01 MES, pH 6, 1.5% v/v pentaerythritol ethoxylate (15/4 EO/OH) |