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Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 containing 3.5 M NaCOOH pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.98 58.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.172 α = 90 b = 232.32 β = 90 c = 135.162 γ = 90
Symmetry Space Group C 2 2 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 XE 16M 2020-09-09 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 2.42 53.4 98.5 0.25 0.051 0.993 7.6 23.7 32012 53.43
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 2.42 2.46 0.363 0.4
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 FREE R-VALUE 6ZCZ 2.42 53.36 1.33 31718 1610 97.58 0.1918 0.1896 0.1905 0.2314 0.2307 57.5
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 17.3496 f_angle_d 0.6128 f_chiral_restr 0.0446 f_plane_restr 0.0038 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4774 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 68
Software Software Software Name Purpose GDA data collection PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing