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Crystallographic structure of neutralizing antibody P14-44 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 7JMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 0.1 M Sodium citrate pH 5.6
20%(w/v) PEG4000
20%(V/V) Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.91 57.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.321 α = 90 b = 68.443 β = 115.85 c = 94.206 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 1.89 84.78 100 0.078 0.084 0.997 23.9 6.6 60097
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 1.89 1.93 100 0.778 0.846 0.814 2.5 6.4
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 7JMW 1.89 45.07 56727 2931 98.57 0.1664 0.1647 0.1742 0.2006 0.2071 RANDOM 25.594
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] -0.06 -0.13 -0.05 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.507 r_dihedral_angle_4_deg 14.105 r_dihedral_angle_3_deg 13.018 r_dihedral_angle_1_deg 6.587 r_angle_other_deg 2.405 r_angle_refined_deg 1.907 r_chiral_restr 0.115 r_bond_other_d 0.036 r_bond_refined_d 0.018 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.507 r_dihedral_angle_4_deg 14.105 r_dihedral_angle_3_deg 13.018 r_dihedral_angle_1_deg 6.587 r_angle_other_deg 2.405 r_angle_refined_deg 1.907 r_chiral_restr 0.115 r_bond_other_d 0.036 r_bond_refined_d 0.018 r_gen_planes_other 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4893 Nucleic Acid Atoms Solvent Atoms 657 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PDB_EXTRACT data extraction PHASER phasing