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Crystal structure of the IVR-165 (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 277 44% 2-methyl-2,4-pentanediol, 0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.31 62.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.4 α = 90 b = 100.4 β = 90 c = 382.058 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 EIGER X 16M 2017-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 1.95 50 100 0.15 0.04 1 26 18.1 54947 25
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 1.95 2.01 100 0.9 0.22 0.92 2.8 17.4
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 1.95 50 51993 2670 99.97 0.16792 0.16665 0.174 0.19319 0.201 RANDOM 44.227
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] 0.9 0.45 0.9 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.82 r_dihedral_angle_4_deg 18.671 r_dihedral_angle_3_deg 14.27 r_long_range_B_refined 6.216 r_long_range_B_other 6.043 r_dihedral_angle_1_deg 5.912 r_scangle_other 2.905 r_scbond_it 1.64 r_scbond_other 1.64 r_angle_refined_deg 1.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.82 r_dihedral_angle_4_deg 18.671 r_dihedral_angle_3_deg 14.27 r_long_range_B_refined 6.216 r_long_range_B_other 6.043 r_dihedral_angle_1_deg 5.912 r_scangle_other 2.905 r_scbond_it 1.64 r_scbond_other 1.64 r_angle_refined_deg 1.487 r_mcangle_it 1.475 r_mcangle_other 1.474 r_angle_other_deg 0.921 r_mcbond_it 0.885 r_mcbond_other 0.885 r_chiral_restr 0.081 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 3879 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 201
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing