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LY-CoV488 neutralizing antibody against SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 293 8% PEG 3350,
200 mM L-Proline,
100 mM Hepes pH 7.7
Crystal Properties Matthews coefficient Solvent content 3.32 62.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.806 α = 90 b = 260.59 β = 90 c = 94.997 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 S 6M 2020-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.72 30 98.8 0.051 0.999 13.4 13 97212
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.82 98.8 0.63 0.973 3.4 13.4
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 7KMG 1.72 29.39 92421 4791 98.52 0.1963 0.1939 0.1947 0.2423 0.2441 RANDOM 40.618
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] -24.69 -19.96 44.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.132 r_sphericity_bonded 32.816 r_sphericity_free 14.656 r_dihedral_angle_3_deg 13.768 r_dihedral_angle_4_deg 12.889 r_dihedral_angle_1_deg 7.073 r_rigid_bond_restr 1.46 r_angle_refined_deg 1.1 r_chiral_restr 0.091 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.132 r_sphericity_bonded 32.816 r_sphericity_free 14.656 r_dihedral_angle_3_deg 13.768 r_dihedral_angle_4_deg 12.889 r_dihedral_angle_1_deg 7.073 r_rigid_bond_restr 1.46 r_angle_refined_deg 1.1 r_chiral_restr 0.091 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4622 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing