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Discovery and development of a novel inhaled antivirulence therapy for the treatment of Pseudomonas aeruginosa infections in patients with chronic respiratory disease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MOPS pH 6.5, 1.3-1.8 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.98 α = 90 b = 44.52 β = 100.61 c = 161.71 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 PIXEL DECTRIS PILATUS 6M-F 2018-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.74 41.69 97.2 0.917 3.9 3.1 44296
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.74 2.81 0.305 1.1
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 3DBK 2.74 41.73 42147 2143 97.12 0.25825 0.2561 0.2611 0.30117 0.3042 RANDOM 35.263
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] 0.39 0.23 0.83 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.655 r_dihedral_angle_4_deg 17.886 r_dihedral_angle_3_deg 16.995 r_long_range_B_refined 7.326 r_long_range_B_other 7.324 r_dihedral_angle_1_deg 7.253 r_scangle_other 3.89 r_mcangle_it 3.541 r_mcangle_other 3.541 r_scbond_it 2.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.655 r_dihedral_angle_4_deg 17.886 r_dihedral_angle_3_deg 16.995 r_long_range_B_refined 7.326 r_long_range_B_other 7.324 r_dihedral_angle_1_deg 7.253 r_scangle_other 3.89 r_mcangle_it 3.541 r_mcangle_other 3.541 r_scbond_it 2.406 r_scbond_other 2.406 r_mcbond_it 2.215 r_mcbond_other 2.215 r_angle_refined_deg 1.557 r_angle_other_deg 1.259 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 9268 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing