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Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 5.5
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 5.5 298 100 mM cacodylate, pH 5.5, 200 mM sodium chloride, 2 M ammonium sulfate, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 3.95 68.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.383 α = 90 b = 109.383 β = 90 c = 421.035 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 2.3 30 99.1 0.087 0.998 11.78 6.02 43303
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 2.3 2.43 94.7 0.785 0.884 2.09 5.76
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2FK0 2.3 29.79 40483 2121 97.44 0.20014 0.19858 0.22887 0.2388 RANDOM 63.67
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] 1.96 0.98 1.96 -6.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.178 r_dihedral_angle_4_deg 21.335 r_dihedral_angle_3_deg 18.61 r_long_range_B_refined 13.671 r_long_range_B_other 13.669 r_scangle_other 10.715 r_dihedral_angle_1_deg 8.172 r_mcangle_it 7.694 r_mcangle_other 7.693 r_scbond_it 7.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.178 r_dihedral_angle_4_deg 21.335 r_dihedral_angle_3_deg 18.61 r_long_range_B_refined 13.671 r_long_range_B_other 13.669 r_scangle_other 10.715 r_dihedral_angle_1_deg 8.172 r_mcangle_it 7.694 r_mcangle_other 7.693 r_scbond_it 7.251 r_scbond_other 7.251 r_mcbond_it 5.205 r_mcbond_other 5.205 r_angle_refined_deg 1.544 r_angle_other_deg 1.224 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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 122 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