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Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NB8 PDB entry 6NB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.16 M magnesium chloride, 0.08 M Tris-HCl, pH 8.5, 24% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.11 41.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.51 α = 90 b = 56.51 β = 90 c = 252.18 γ = 90
Symmetry Space Group P 43 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 80 PIXEL DECTRIS PILATUS 6M 2020-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.043 63.045 99.5 0.162 0.166 0.035 13.1 20.9 27080 27080 32.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.043 2.15 97 1.742 1.742 1.787 0.389 0.4 18.6
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 THROUGHOUT PDB entry 6NB8 2.043 63.045 1.34 26591 1315 98.06 0.2014 0.1989 0.2034 0.2509 0.2535 42.8507
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 12.352 f_angle_d 0.549 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3307 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction