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Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 15)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 25% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 6 and 1% (w/v) protamine sulphate
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.256 α = 90 b = 82.977 β = 90 c = 89.089 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M mirrors 2018-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.907 60.719 99.7 0.054 0.021 0.999 16.7 7.2 40602
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.907 1.94 98.3 1.654 0.702 0.366 0.9 6.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6HZR 1.907 60.719 40602 1968 99.674 0.201 0.1985 0.2056 0.2456 0.2481 51.936
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] 0.834 -0.872 0.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.798 r_dihedral_angle_4_deg 20.403 r_dihedral_angle_3_deg 16.364 r_lrange_other 9.881 r_lrange_it 9.874 r_scangle_it 7.326 r_scangle_other 7.324 r_dihedral_angle_1_deg 7.308 r_mcangle_it 6.473 r_mcangle_other 6.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.798 r_dihedral_angle_4_deg 20.403 r_dihedral_angle_3_deg 16.364 r_lrange_other 9.881 r_lrange_it 9.874 r_scangle_it 7.326 r_scangle_other 7.324 r_dihedral_angle_1_deg 7.308 r_mcangle_it 6.473 r_mcangle_other 6.472 r_scbond_it 4.806 r_scbond_other 4.804 r_mcbond_other 4.629 r_mcbond_it 4.628 r_angle_refined_deg 1.541 r_angle_other_deg 1.293 r_nbd_refined 0.216 r_nbd_other 0.211 r_symmetry_nbd_other 0.179 r_symmetry_nbd_refined 0.162 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3657 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 21
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction