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Crystal structure of the SARS-CoV-2 S RBD in complex with pT1511 scFV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KGJ 7KGJ, 4QF1 experimental model PDB 4QF1 7KGJ, 4QF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 pT1511-RBD at 9.5 mg/ml using 16% PEG 3350, 200 mM sodium malonate, 100 mM Bis-tris propane pH 7.5 as reservoir
Crystal Properties Matthews coefficient Solvent content 3.38 63.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 345.27 α = 90 b = 54.37 β = 105.88 c = 214.69 γ = 90
Symmetry Space Group C 1 2 1
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 2021-09-01 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 2.88 48.83 96.95 0.1365 0.1484 0.05722 0.997 9.38 6.5 85773 95.53
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 2.88 2.983 1.604 1.75 0.6858 0.535 0.95
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 7KGJ, 4QF1 2.88 48.83 1.33 85642 8259 96.97 0.2043 0.2021 0.2171 0.2444 0.2582 105.21
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 5.1619 f_angle_d 0.7722 f_chiral_restr 0.0466 f_plane_restr 0.0064 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19547 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 94
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing