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Human antibody S8V1-172 in complex with the influenza hemagglutinin head domain of A/Sydney/05/1997(H3N2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XPZ 6XPZ, 6MHR, 6E4X experimental model PDB 6MHR 6XPZ, 6MHR, 6E4X experimental model PDB 6E4X 6XPZ, 6MHR, 6E4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291.15 0.1 M tris(hydroxymethyl)aminomethane pH 8.5 and 25% (w/v) poly(ethylene glycol) 3350
Crystal Properties Matthews coefficient Solvent content 4.09 69.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.7 α = 90 b = 94.7 β = 90 c = 248.84 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 80 PIXEL DECTRIS EIGER2 X 16M 2020-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97911 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.6 49.56 99.46 0.04592 0.996 12.72 2 15613 117.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.729 99.87 0.3232 0.709 2
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 FREE R-VALUE 6XPZ, 6MHR, 6E4X 3.6 49.56 1.35 15611 789 99.52 0.2347 0.2329 0.236 0.2682 0.2716 118.51
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.0764 f_angle_d 0.6051 f_chiral_restr 0.0713 f_plane_restr 0.0051 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5403 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 150
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing