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Crystal structure of H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BGZ PDB ENTRY 4BGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BIS-TRIS PROPANE PH 7.5, 0.05 - 0.15 M K/NAPO4 (PH 7.0), 15-18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.25 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.407 α = 90 b = 117.251 β = 92.52 c = 101.003 γ = 90
Symmetry Space Group P 1 21 1
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.86 70.03 98.3 0.08 8.8 3 46268 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 3.01 99 0.52 2 3
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 PDB ENTRY 4BGZ 2.86 70.13 43919 2341 98.15 0.19778 0.19529 0.1964 0.24444 0.2411 RANDOM 79.448
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] 5.45 -4.35 -2.81 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_4_deg 11.846 r_dihedral_angle_1_deg 5.37 r_mcangle_it 2.256 r_scbond_it 1.714 r_mcbond_it 1.315 r_mcbond_other 1.315 r_angle_refined_deg 1.17 r_angle_other_deg 0.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_4_deg 11.846 r_dihedral_angle_1_deg 5.37 r_mcangle_it 2.256 r_scbond_it 1.714 r_mcbond_it 1.315 r_mcbond_other 1.315 r_angle_refined_deg 1.17 r_angle_other_deg 0.764 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11610 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling PHASER phasing