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Crystal structure of the SARS-CoV-2 RBD in complex with the ultrapotent antibody CV2.1169 and CR3022
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M0J 6M0J, 7K3Q, 6YLA experimental model PDB 7K3Q 6M0J, 7K3Q, 6YLA experimental model PDB 6YLA 6M0J, 7K3Q, 6YLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 15% PEG 8000, 0.5 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.29 62.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.751 α = 90 b = 97.751 β = 90 c = 164.474 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS EIGER X 9M 2021-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.88 48.88 99.4 0.261 0.271 0.072 0.995 10.2 14 34600
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 3.02 96 3.509 3.643 0.971 0.214 13.9
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 6M0J, 7K3Q, 6YLA 2.89 48.88 1.33 34364 1785 99.77 0.2409 0.2386 0.2473 0.281 0.2919 91.2269
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 6613 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing