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Crystal structure of the SARS-CoV-2 S RBD in complex with pT1611 scFV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KGJ 7KGJ, 2GHW experimental model PDB 2GHW 7KGJ, 2GHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 pT1611-RBD at 18.7 mg/ml using 1.6 M ammonium-sulfate, 2 % PEG 1000, 100 mM HEPES pH 8 as reservoir
Crystal Properties Matthews coefficient Solvent content 3.2 61.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.294 α = 90 b = 90.946 β = 90 c = 154.602 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 EIGER X 16M 2021-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
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 1.6 49 99.9 0.09057 0.09415 0.02549 1 21.14 13.6 164051 22.35
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 1.6 1.657 99.98 1.872 1.944 0.5198 0.699 1.67 13.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7KGJ, 2GHW 1.6 49 1.34 163954 2460 99.56 0.1947 0.1945 0.2077 0.2123 28.55
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 6.1205 f_angle_d 0.8643 f_chiral_restr 0.0576 f_plane_restr 0.0081 f_bond_d 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6455 Nucleic Acid Atoms Solvent Atoms 756 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing