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Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin in complex with 3'-SLNLN
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 3.43 64.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.462 α = 90 b = 101.462 β = 90 c = 388.077 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 CCD ADSC QUANTUM 315r 2017-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9765 ALS 5.0.3
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 99.7 0.11 0.04 1 33.5 7.5 56657 28
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 2.02 99.4 0.99 0.38 0.86 7.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4O5N 1.95 50 53635 2840 99.62 0.18084 0.17942 0.20757 0.2021 RANDOM 42.319
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] 1.1 0.55 1.1 -3.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.954 r_dihedral_angle_4_deg 17.264 r_dihedral_angle_3_deg 14.133 r_long_range_B_refined 6.259 r_dihedral_angle_1_deg 6.2 r_long_range_B_other 6.034 r_scangle_other 3.025 r_scbond_it 1.719 r_scbond_other 1.716 r_angle_refined_deg 1.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.954 r_dihedral_angle_4_deg 17.264 r_dihedral_angle_3_deg 14.133 r_long_range_B_refined 6.259 r_dihedral_angle_1_deg 6.2 r_long_range_B_other 6.034 r_scangle_other 3.025 r_scbond_it 1.719 r_scbond_other 1.716 r_angle_refined_deg 1.515 r_mcangle_it 1.502 r_mcangle_other 1.501 r_angle_other_deg 0.955 r_mcbond_other 0.898 r_mcbond_it 0.897 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 3852 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 316
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing