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Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 12)
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 2.12 41.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.038 α = 90 b = 81.925 β = 90 c = 88.241 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 2019-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.36 60.039 91.7 0.072 0.077 0.026 0.999 15.1 8.1 69775
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.491 62.5 0.85 0.935 0.381 5.7
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 1.36 60.039 69775 3465 65.603 0.147 0.1445 0.1444 0.2035 0.2038 20.581
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] -1.72 -1.212 2.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.549 r_dihedral_angle_4_deg 20.404 r_dihedral_angle_3_deg 13.65 r_rigid_bond_restr 10.267 r_dihedral_angle_1_deg 6.748 r_lrange_it 5.183 r_lrange_other 5.12 r_scangle_it 4.943 r_scangle_other 4.942 r_scbond_other 4.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.549 r_dihedral_angle_4_deg 20.404 r_dihedral_angle_3_deg 13.65 r_rigid_bond_restr 10.267 r_dihedral_angle_1_deg 6.748 r_lrange_it 5.183 r_lrange_other 5.12 r_scangle_it 4.943 r_scangle_other 4.942 r_scbond_other 4.261 r_scbond_it 4.258 r_mcangle_it 3.602 r_mcangle_other 3.602 r_mcbond_other 3.094 r_mcbond_it 3.093 r_angle_refined_deg 1.924 r_angle_other_deg 1.462 r_symmetry_nbd_refined 0.33 r_nbd_other 0.288 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.219 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.167 r_xyhbond_nbd_other 0.161 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3795 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction