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Crystal structure of SARS-CoV-2 receptor binding domain in complex with the Fab fragments of neutralizing antibodies 298 and 52
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DN3 4DN3, 5CZX, 6XDG experimental model PDB 5CZX 4DN3, 5CZX, 6XDG experimental model PDB 6XDG 4DN3, 5CZX, 6XDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 20% (w/v) 2-propanol, 20% (w/v) PEG 4000, 0.1 M sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 3.01 59.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.617 α = 90 b = 87.617 β = 90 c = 325.096 γ = 120
Symmetry Space Group P 32 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 PILATUS3 X 6M 2020-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03317 APS 23-ID-D
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 2.95 39.66 99.9 0.168 0.043 0.998 12.3 15.7 31545 78.6
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 2.95 3.05 99.9 0.742 0.201 0.863 1.4 14.3
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 THROUGHOUT 4DN3, 5CZX, 6XDG 2.95 39.61 1.34 31422 1602 99.2 0.2625 0.2612 0.2625 0.2871 0.2779 103.9794
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8047 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 14
Software Software Software Name Purpose XPREP data reduction PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing