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Structure of the SARS-CoV receptor binding domain in complex with the human neutralizing antibody Fab fragment, C118
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2M sodium fluoride, 20% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.55 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.923 α = 90 b = 89.993 β = 113.334 c = 93.865 γ = 90
Symmetry Space Group P 1 21 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 2020-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 46.61 95.7 0.0622 0.0396 0.998 13.14 3.4 72486 59.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 79.5 0.401 0.28 0.918 2.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7K8M 2.7 46.61 1.37 72486 3606 94.68 0.1972 0.1946 0.195 0.2467 0.2468 62.79
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.1688 f_angle_d 1.166 f_chiral_restr 0.0604 f_plane_restr 0.0097 f_bond_d 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9516 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing XDS data reduction Coot model building