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Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FK0 PDB entry 2FK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 100 mM cacodylate, pH 6.5, 200 mM sodium chloride, 2 M ammonium sulfate, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 3.94 68.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.056 α = 90 b = 108.056 β = 90 c = 419.819 γ = 120
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 2016-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.39 30 99.5 0.163 0.997 12.29 9.14 37825
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.52 98.6 1.764 0.857 2.57 8.65
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 entry 2FK0 2.39 29.35 35486 1828 98.18 0.2156 0.2132 0.2168 0.2607 0.2587 RANDOM 58.252
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] 0.07 0.04 0.07 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.116 r_dihedral_angle_4_deg 21.393 r_dihedral_angle_3_deg 19.729 r_dihedral_angle_1_deg 8.713 r_angle_refined_deg 1.716 r_angle_other_deg 1.266 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.116 r_dihedral_angle_4_deg 21.393 r_dihedral_angle_3_deg 19.729 r_dihedral_angle_1_deg 8.713 r_angle_refined_deg 1.716 r_angle_other_deg 1.266 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3932 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building PDB_EXTRACT data extraction