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Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC25.106 isolated from a vaccinated COVID-19 convalescent
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JMW 7JMW; 7KN4 experimental model PDB 7KN4 7JMW; 7KN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293.15 19% (v/v) Isopropanol, 19% (w/v) PEG 4000, 5% (v/v) Glycerol, 0.095 M Sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.934 α = 90 b = 70.719 β = 95.31 c = 76.551 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 PILATUS3 6M 2021-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03320 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 98.2 0.091 0.103 0.046 7.2 4.5 33702 18.64
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 1.9 1.93 83.1 0.717 0.891 0.516 0.518 2.6
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 7JMW; 7KN4 1.89 40.76 1.36 31201 1545 88.97 0.2159 0.2144 0.2144 0.2451 0.2463 25.4309
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 3306 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing