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Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 3B4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YM0 6YM0,4HGK experimental model PDB 4HGK 6YM0,4HGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Sodium acetate trihydrate, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.85 56.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.144 α = 90 b = 90.74 β = 90 c = 122.692 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 2020-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.92 81.14 99.9 0.046 0.049 0.019 0.999 19.6 6.7 69770 47.87
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 1.92 1.96 99.9 1.981 2.14 0.804 0.529 6.9
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 6YM0,4HGK 1.92 72.96 1.34 69667 3510 99.79 0.1921 0.1904 0.1908 0.2263 0.2256 62.22
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 12.6436 f_angle_d 0.9111 f_chiral_restr 0.0606 f_bond_d 0.0103 f_plane_restr 0.0085
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4900 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 104
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing