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Crystal structure of an equine H7 hemagglutinin from A/equine/NY/49/73 (H7N7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BSG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.1 M HEPES, pH 6.5, 2.4 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.92 74.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.404 α = 90 b = 87.404 β = 90 c = 524.848 γ = 120
Symmetry Space Group P 63 2 2
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 PILATUS3 6M 2018-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 3.3 50 99.8 0.2 0.05 0.99 8.4 15.7 19888
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.36 100 1 0.37 0.73 9.8
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 4BSG 3.3 46.24 18177 986 99.71 0.20181 0.19997 0.2067 0.23738 0.2408 RANDOM 79.832
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] -0.21 -0.1 -0.21 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.45 r_dihedral_angle_3_deg 21.185 r_long_range_B_refined 18.946 r_long_range_B_other 18.945 r_dihedral_angle_4_deg 18.866 r_mcangle_it 13.403 r_mcangle_other 13.401 r_scangle_other 12.362 r_dihedral_angle_1_deg 9.222 r_mcbond_it 8.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.45 r_dihedral_angle_3_deg 21.185 r_long_range_B_refined 18.946 r_long_range_B_other 18.945 r_dihedral_angle_4_deg 18.866 r_mcangle_it 13.403 r_mcangle_other 13.401 r_scangle_other 12.362 r_dihedral_angle_1_deg 9.222 r_mcbond_it 8.642 r_mcbond_other 8.642 r_scbond_other 7.869 r_scbond_it 7.861 r_angle_refined_deg 1.951 r_angle_other_deg 1.424 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 3838 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing