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Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and COVOX-278 Fabs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M amino acids (Glu, Ala, Gly, Lys, Ser), 0.1 M MES/imidazole pH 6.5, 10% (w/v) PEG 20000 and 20% (v/v) PEG MME 550.
Crystal Properties Matthews coefficient Solvent content 3.06 59.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.73 α = 90 b = 114.47 β = 90 c = 177.93 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2021-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.34 70 86.2 0.1 0.03 0.999 16.8 11.6 53251 52.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.38 0.348 0.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7NX6 2.34 57.23 1.34 53154 2653 86.07 0.1953 0.1935 0.2296 0.2062 61.39
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.494 f_angle_d 0.5406 f_chiral_restr 0.0425 f_plane_restr 0.0045 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8047 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement GDA data collection xia2 data reduction xia2 data scaling PHASER phasing