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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-04
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 8.5% isopropanol
10% ethylene glycol
15% glycerol
0.085 M HEPES pH 7.5
17% polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.246 α = 90 b = 84.678 β = 99.58 c = 57.301 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.35 50 97.2 0.163 0.179 0.072 5.7 5.5 37264
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 88.6 0.898 1.02 0.47 0.677 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6XC4 2.359 48.624 1.36 37224 1814 96.84 0.1972 0.1951 0.2001 0.2381 0.2392 51.852
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4767 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing