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Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.0
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 6 293 100 mM cacodylate, pH 6.0, 200 mM sodium chloride, 2 M ammonium sulfate, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 4.1 70.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.537 α = 90 b = 108.537 β = 90 c = 419.79 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 2.11 30 99.4 0.063 0.999 14.59 6.44 55355
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 2.11 2.22 96.9 0.819 0.884 2.04 6.22
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 2.11 29.44 51861 2763 98.08 0.20933 0.20689 0.2132 0.25547 0.2607 RANDOM 62.093
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] 1.72 0.86 1.72 -5.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.406 r_dihedral_angle_4_deg 19.135 r_dihedral_angle_3_deg 18.039 r_long_range_B_other 12.583 r_long_range_B_refined 12.577 r_scangle_other 9.221 r_dihedral_angle_1_deg 7.273 r_mcangle_it 6.608 r_mcangle_other 6.607 r_scbond_it 6.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.406 r_dihedral_angle_4_deg 19.135 r_dihedral_angle_3_deg 18.039 r_long_range_B_other 12.583 r_long_range_B_refined 12.577 r_scangle_other 9.221 r_dihedral_angle_1_deg 7.273 r_mcangle_it 6.608 r_mcangle_other 6.607 r_scbond_it 6.484 r_scbond_other 6.483 r_mcbond_it 4.699 r_mcbond_other 4.699 r_angle_refined_deg 1.542 r_angle_other_deg 1.323 r_chiral_restr 0.062 r_bond_refined_d 0.004 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3932 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing Coot model building