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Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M0J 6M0J, 4KMT, 5I1D, 6YM0 experimental model PDB 4KMT 6M0J, 4KMT, 5I1D, 6YM0 experimental model PDB 5I1D 6M0J, 4KMT, 5I1D, 6YM0 experimental model PDB 6YM0 6M0J, 4KMT, 5I1D, 6YM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Sodium malonate, 0.1 M Tris pH 8.0 and 30% w/v Polyethylene glycol 1,000
Crystal Properties Matthews coefficient Solvent content 4.28 71.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.124 α = 90 b = 163.124 β = 90 c = 189.076 γ = 90
Symmetry Space Group P 41 21 2
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 2020-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 58.8 100 0.303 0.034 0.997 11.6 78.7 97407 72.83
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 0.45
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 6M0J, 4KMT, 5I1D, 6YM0 2.42 55.31 1.33 94154 4837 96.77 0.2139 0.2127 0.2156 0.2367 0.242 89.23
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 17.7654 f_angle_d 0.5215 f_chiral_restr 0.0463 f_plane_restr 0.0043 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9947 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 87
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing