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Crystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XDG 6XDG, 7JMW experimental model PDB 7JMW 6XDG, 7JMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.05 M HEPES pH 7.0
20%(w/v) PEG3350
1%(w/v) Tryptone
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.007 α = 90 b = 80.414 β = 106.23 c = 72.746 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 PILATUS 6M 2021-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.97852 NFPSS BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.4 107.06 100 0.08 0.088 0.981 22.4 6.3 48529
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 99.7 0.719 0.795 0.751 2.2 5.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6XDG, 7JMW 2.4 50 44351 2243 95.81 0.1935 0.191 0.1954 0.2446 0.248 RANDOM 40.402
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] 0.53 0.26 -0.71 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.442 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 15.186 r_dihedral_angle_1_deg 6.424 r_angle_other_deg 3.853 r_angle_refined_deg 1.389 r_chiral_restr 0.258 r_gen_planes_other 0.025 r_gen_planes_refined 0.012 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.442 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 15.186 r_dihedral_angle_1_deg 6.424 r_angle_other_deg 3.853 r_angle_refined_deg 1.389 r_chiral_restr 0.258 r_gen_planes_other 0.025 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8170 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction