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Human antibody S1V2-51 in complex with the influenza hemagglutinin head domain of A/Aichi/2/1968 (X-31)(H3N2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E56 6E56, 5I18, 6E4X experimental model PDB 5I18 6E56, 5I18, 6E4X experimental model PDB 6E4X 6E56, 5I18, 6E4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 291.15 0.3 M Magnesium chloride, 25% (w/v) PEG 2000, 15% (w/v) Glycerol, 0.1 M BICINE, pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.19 61.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.42 α = 90 b = 101.56 β = 108.01 c = 77.41 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 80 PIXEL DECTRIS EIGER X 16M 2019-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 2.598 42.65 98.84 0.06237 0.07237 0.03622 0.998 12.78 3.8 30757
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 2.598 2.691 96.86 0.7997 0.931 0.4695 0.583 1.35 3.8
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 6E56, 5I18, 6E4X 2.598 42.646 1.35 30752 1579 98.86 0.187 0.1853 0.1928 0.2154 0.2194 80.1681
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 6.596 f_angle_d 1.406 f_chiral_restr 0.07 f_bond_d 0.014 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5372 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 147
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHENIX phasing