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Crystal structure of influenza A virus hemagglutinin from A/Ohio/09/2015 bound to the stalk-binding CR6261 antibody Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 InvbR.18715.a.KN11.PD38335/CR6261 Fab PD38376 at 10.3 mg/mL against Morpheus screen condition C6: 10% PEG 8000, 20% ethylene glycol, 0.1 M MOPS/HEPES pH 7.5, 0.03 M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate, crystal tracking ID 311368c6, unique puck ID dai6-1
Crystal Properties Matthews coefficient Solvent content 3.48 64.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.59 α = 90 b = 205.59 β = 90 c = 205.59 γ = 90
Symmetry Space Group I 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2019-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.85 35.26 99.9 0.084 0.091 0.998 15.52 6.928 33765 73.976
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.92 100 0.89 0.962 0.74 2.17 7.055
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 3GBN 2.85 35.26 1.36 33728 1613 99.87 0.2104 0.2086 0.2151 0.2475 0.2527 94.4453
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 18.622 f_angle_d 0.702 f_chiral_restr 0.047 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5864 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction