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Crystal structure of the A/Michigan/15/2014 (H3N2) influenza virus hemagglutinin apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, and 40% PEG 300
Crystal Properties Matthews coefficient Solvent content 3.41 63.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.326 α = 90 b = 100.326 β = 90 c = 394.081 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 2017-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.05 50 100 0.15 0.04 1 44.3 17.4 48747 38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 100 0.92 0.24 0.91 3.1 16
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 4O5N 2.05 50 46272 2425 99.67 0.19339 0.19193 0.2042 0.22183 0.2317 RANDOM 52.354
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] 1.14 0.57 1.14 -3.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_4_deg 14.984 r_dihedral_angle_3_deg 14.541 r_dihedral_angle_1_deg 6.398 r_long_range_B_refined 5.754 r_long_range_B_other 5.653 r_scangle_other 2.842 r_mcangle_it 1.676 r_mcangle_other 1.676 r_scbond_it 1.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_4_deg 14.984 r_dihedral_angle_3_deg 14.541 r_dihedral_angle_1_deg 6.398 r_long_range_B_refined 5.754 r_long_range_B_other 5.653 r_scangle_other 2.842 r_mcangle_it 1.676 r_mcangle_other 1.676 r_scbond_it 1.653 r_scbond_other 1.652 r_angle_refined_deg 1.476 r_mcbond_other 1.029 r_mcbond_it 1.028 r_angle_other_deg 0.929 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 3870 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling PHASER phasing