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Crystallographic structure of neutralizing antibody 10-40 in complex with SARS-CoV-2 spike receptor binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L5B PDB entry 7L5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 310 0.2 M potassium thiocyanate, 0.1 M sodium acetate, pH 5.5, 8% PEG550 MME, 8% PEG20000
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.756 α = 90 b = 79.845 β = 90 c = 118.864 γ = 90
Symmetry Space Group P 21 21 21
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 2021-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.53 59.44 97.1 0.045 1 17.5 7.4 111889 25.84
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 1.53 1.53 0.256
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 PDB entry 7L5B 1.53 59.44 106248 5520 96.77 0.17773 0.17627 0.185 0.20625 0.2145 RANDOM 29.157
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] -0.5 0.06 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.779 r_dihedral_angle_4_deg 20.777 r_dihedral_angle_3_deg 11.765 r_dihedral_angle_1_deg 7.416 r_long_range_B_refined 7.061 r_long_range_B_other 6.936 r_scangle_other 5.532 r_scbond_it 3.799 r_scbond_other 3.798 r_mcangle_it 3.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.779 r_dihedral_angle_4_deg 20.777 r_dihedral_angle_3_deg 11.765 r_dihedral_angle_1_deg 7.416 r_long_range_B_refined 7.061 r_long_range_B_other 6.936 r_scangle_other 5.532 r_scbond_it 3.799 r_scbond_other 3.798 r_mcangle_it 3.414 r_mcangle_other 3.414 r_mcbond_it 2.515 r_mcbond_other 2.515 r_angle_refined_deg 1.783 r_angle_other_deg 1.477 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4851 Nucleic Acid Atoms Solvent Atoms 678 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing