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Crystal Structure of the Haemagglutinin (with Asn-133 Glycosylation) from an H7N9 Influenza Virus Isolated from Humans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TI8 PDB ENTRY 1TI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 291 291 K, 0.1 M PIPES PH 7.0, 2.2 M AMMONIUM SULFATE, 1% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.55 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.13 α = 90 b = 116.13 β = 90 c = 295.51 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 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.3 58.13 99.6 0.08 10.92 5.7 34364 2.28
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 2.3 2.38 99.5 0.69 2.28 5.9
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 1TI8 2.3 58.13 32404 1725 98.9 0.25183 0.24953 0.2511 0.29557 0.2975 RANDOM 56.815
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] 0.27 0.27 0.27 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.06 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 16.051 r_dihedral_angle_1_deg 5.885 r_scbond_it 1.24 r_angle_refined_deg 1.037 r_angle_other_deg 0.699 r_mcangle_it 0.659 r_mcbond_it 0.365 r_mcbond_other 0.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.06 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 16.051 r_dihedral_angle_1_deg 5.885 r_scbond_it 1.24 r_angle_refined_deg 1.037 r_angle_other_deg 0.699 r_mcangle_it 0.659 r_mcbond_it 0.365 r_mcbond_other 0.365 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3795 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing