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SARS-CoV-2 Receptor Binding Domain in Complex with Ab17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M0J 6M0J, 4L5F, 4HCl experimental model PDB 4L5F 6M0J, 4L5F, 4HCl experimental model PDB 4HCL 6M0J, 4L5F, 4HCl
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.15 0.1 M HEPES pH 7.0 and 30% v/v Jeffamine ED-2001 pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.29 62.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.931 α = 90 b = 207.931 β = 90 c = 86.662 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 EIGER X 16M 2021-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-E 0.9792 APS 21-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.5 79.99 99.98 0.395 0.405 0.088 10.1 21.1 24539 104.62
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 3.5 3.55 100 0.235
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, 4L5F, 4HCl 3.5 79.99 1.36 24538 1206 99.99 0.2989 0.2965 0.2959 0.3442 0.3436 95.58
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 5.0848 f_angle_d 0.8015 f_chiral_restr 0.0491 f_plane_restr 0.0051 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9099 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction PDB_EXTRACT data extraction XDS data scaling