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Crystal structure of human 1G04 Fab in complex with influenza virus neuraminidase from A/Hunan/02650/2016 (H7N9)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L14 5L14, 5ITB, 4FQL experimental model PDB 5ITB 5L14, 5ITB, 4FQL experimental model PDB 4FQL 5L14, 5ITB, 4FQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, pH 7.5, 5%(w/v) PEG3000, 30% (w/v) PEG400, 10%(v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.28 62.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.242 α = 90 b = 180.242 β = 90 c = 148.125 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03309 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 3.446 47.4 99.1 0.09 0.05 0.997 14.6 4.4 30994 126
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.45 3.51 0.87 0.87 0.48 0.844 1 4.1
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 5L14, 5ITB, 4FQL 3.446 47.365 1.39 30967 1493 98.94 0.1995 0.1971 0.2097 0.2472 0.2567
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 4.595 f_angle_d 1.265 f_chiral_restr 0.065 f_bond_d 0.01 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12874 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 362
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing