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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 6M0J PDB entry 6M0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 16.2% w/v PEG4000, 0.09 M sodium citrate, pH 6.0, 0.18 M ammonium acetate, 0.02 M potassium acetate, 0.01 MES, pH 6, 1.5% v/v pentaerythritol ethoxylate (15/4 EO/OH)
Crystal Properties Matthews coefficient Solvent content 2.94 58.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.54 α = 90 b = 127.78 β = 96.66 c = 192.28 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 CMOS RDI CMOS_8M 2020-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.97625 ALS 4.2.2
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 2.65 47.75 99.6 0.199 0.215 0.079 0.996 8.7 7.4 55237
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 2.65 2.73 99.9 2.418 2.619 0.999 0.39 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 6M0J 2.65 47.5 52027 2586 98.46 0.2591 0.2578 0.2881 0.2538 RANDOM 66.749
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] 0.69 1.38 -1.91 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.603 r_dihedral_angle_4_deg 22.273 r_dihedral_angle_3_deg 12.949 r_dihedral_angle_1_deg 8.101 r_angle_refined_deg 1.398 r_angle_other_deg 1.223 r_chiral_restr 0.06 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.603 r_dihedral_angle_4_deg 22.273 r_dihedral_angle_3_deg 12.949 r_dihedral_angle_1_deg 8.101 r_angle_refined_deg 1.398 r_angle_other_deg 1.223 r_chiral_restr 0.06 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11484 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 14
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction