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Structure of sybody SR4 in complex with the SARS-CoV-2 S Receptor Binding domain (RBD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M0J 6M0J, 5M13 experimental model PDB 5M13 6M0J, 5M13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (w/v) PEG 3000, 100mM HEPES pH 7.5, 200mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.69 54.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.553 α = 90 b = 65.553 β = 90 c = 344.526 γ = 120
Symmetry Space Group P 65 2 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 PSI PILATUS 6M 2020-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
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 2.15 47.4 100 0.163 0.055 0.997 10.2 9.5 25170 33.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.22 100 1.333 0.437 0.889 1.9 9.9
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 6M0J, 5M13 2.15 47.4 1.33 25148 1213 99.83 0.1856 0.1836 0.1877 0.2239 0.2244 35.13
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 23.9803 f_angle_d 0.8453 f_chiral_restr 0.0514 f_bond_d 0.0073 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2460 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing