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Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B3 Fab)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.2 M Ammonium phosphate dibasic, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.1 60.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.174 α = 90 b = 112.843 β = 90 c = 267.846 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2020-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.77 200 98.1 0.382 0.983 5.41 6.94 63645
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.94 88.6 0.233 0.68 6.51
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 7KFV 2.792 133.92 63645 3092 99 0.1913 0.1893 0.2001 0.2293 0.2448 RANDOM 86.67
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] -11.333 11.0801 0.2529
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.18 t_omega_torsion 2.94 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14459 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 42
Software Software Software Name Purpose BUSTER refinement PHENIX data processing O model building XDS data reduction XDS data scaling PHASER phasing