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Crystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin D190E mutant 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 9 293 0.1 M bicine pH 9 and 42% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 3.33 63.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.41 α = 90 b = 100.41 β = 90 c = 384.444 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 2017-02-12 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 1.85 50 100 0.08 0.02 1 36.7 18 64323 22
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 1.85 1.91 99.6 0.65 0.17 0.91 2.2 14
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 1.85 50 61142 3058 99.88 0.16601 0.16491 0.1769 0.18784 0.1977 RANDOM 33.271
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] 0.5 0.25 0.5 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 19.257 r_dihedral_angle_3_deg 14.297 r_dihedral_angle_1_deg 6.172 r_long_range_B_refined 6.145 r_long_range_B_other 5.627 r_scangle_other 2.696 r_angle_refined_deg 1.557 r_scbond_it 1.552 r_scbond_other 1.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 19.257 r_dihedral_angle_3_deg 14.297 r_dihedral_angle_1_deg 6.172 r_long_range_B_refined 6.145 r_long_range_B_other 5.627 r_scangle_other 2.696 r_angle_refined_deg 1.557 r_scbond_it 1.552 r_scbond_other 1.552 r_mcangle_it 1.29 r_mcangle_other 1.29 r_angle_other_deg 0.959 r_mcbond_it 0.771 r_mcbond_other 0.771 r_chiral_restr 0.09 r_bond_refined_d 0.012 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 478 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling PHASER phasing