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Crystal structure of H5N1 influenza virus hemagglutinin, clade 2.3.4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JUM PDB ENTRY 4JUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 19% PEG 6000, 0.2M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.16 61.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.584 α = 83.94 b = 71.557 β = 85.46 c = 247.054 γ = 60.68
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 2010-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7927 50 81.8 0.092 9.6 2.6 105080 85955 -3 56.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7927 2.9 68 0.379 1.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 4JUM 2.7927 48.873 1.96 105500 85835 4347 81.36 0.1989 0.1959 0.204 0.2541 0.2567 43.1419
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 18.287 f_angle_d 1.439 f_chiral_restr 0.099 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23528 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 224
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction