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Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B12 Fab)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.1 M BICINE pH 8.5, 20% (w/v ) PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.97 58.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.834 α = 90 b = 113.25 β = 90 c = 268.878 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 2.1 200 98.9 0.257 0.995 8.98 7.01 149225 -3
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 2.1 2.23 94.7 0.397 1.35 6.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7BZ5 2.102 134.44 149225 7437 98.7 0.1846 0.183 0.2155 0.2056 RANDOM 47.61
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] -4.0863 7.5903 -3.504
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.58 t_omega_torsion 3.7 t_angle_deg 0.97 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 14511 Nucleic Acid Atoms Solvent Atoms 1642 Heterogen Atoms 42
Software Software Software Name Purpose BUSTER refinement PHENIX data processing O model building XDS data reduction XDS data scaling PHASER phasing