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Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/Viet Nam/1203/2004 (H5N1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GBM PDB ENTRIES 3GBM, 2VL5, AND 1P7K experimental model PDB 2VL5 PDB ENTRIES 3GBM, 2VL5, AND 1P7K experimental model PDB 1P7K PDB ENTRIES 3GBM, 2VL5, AND 1P7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1 M HEPES, pH 7.5, 2% PEG4000, 2.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 6.15 80
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.007 α = 90 b = 251.423 β = 107.01 c = 230.811 γ = 90
Symmetry Space Group C 1 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 100 CCD MARMOSAIC 300 mm CCD 2009-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.564 50 94.9 85101 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.564 3.83 84.3 0.94 1.2 2.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 3GBM, 2VL5, AND 1P7K 3.564 47.3 1.33 84244 4209 91.46 0.203 0.2012 0.2037 0.238 0.2367 RANDOM
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 21.102 f_angle_d 1.557 f_chiral_restr 0.072 f_bond_d 0.012 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22098 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 686
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling