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Structure of P. aeruginosa PBP3 in complex with an aryl boronic acid (Compound 2)
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 8 293 25% (w/v) polyethylene glycol 3 350, 0.1 M Bis-Tris propane pH 8 and 1% (w/v) protamine sulphate
Crystal Properties Matthews coefficient Solvent content 2.12 41.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.25 α = 90 b = 83.158 β = 90 c = 90.115 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 PILATUS 6M Mirrors 2018-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97934 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 1.587 61.113 95.5 0.059 0.024 0.999 15.8 7.4 53748
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 1.587 1.706 65.4 1.329 0.512 0.599 7.6
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 1.587 61.113 53748 2603 76.782 0.154 0.1498 0.1642 0.2343 0.2423 41.788
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] -2.566 2.039 0.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.189 r_dihedral_angle_4_deg 17.971 r_dihedral_angle_3_deg 15.57 r_lrange_it 11.587 r_lrange_other 11.572 r_scangle_it 11.564 r_scangle_other 11.563 r_scbond_it 9.559 r_scbond_other 9.558 r_mcangle_it 9.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.189 r_dihedral_angle_4_deg 17.971 r_dihedral_angle_3_deg 15.57 r_lrange_it 11.587 r_lrange_other 11.572 r_scangle_it 11.564 r_scangle_other 11.563 r_scbond_it 9.559 r_scbond_other 9.558 r_mcangle_it 9.135 r_mcangle_other 9.135 r_mcbond_it 8.024 r_mcbond_other 8.022 r_dihedral_angle_1_deg 7.207 r_rigid_bond_restr 4.848 r_angle_refined_deg 1.748 r_angle_other_deg 1.382 r_nbd_other 0.216 r_nbd_refined 0.211 r_symmetry_nbd_other 0.195 r_symmetry_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.135 r_symmetry_xyhbond_nbd_other 0.089 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3839 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling STARANISO data processing PHASER phasing PDB_EXTRACT data extraction