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Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 4)
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 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 8
Crystal Properties Matthews coefficient Solvent content 2.21 44.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.916 α = 90 b = 83.029 β = 90 c = 89.531 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 1.795 60.879 95.5 0.052 0.021 0.999 16.4 7.3 44743
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 1.796 1.879 52.2 1.568 0.605 0.457 1.2 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 THROUGHOUT 6HZR 1.795 60.879 44743 2165 91.884 0.211 0.2088 0.2153 0.2645 0.2659 50.678
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] 0.441 -0.07 -0.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.681 r_dihedral_angle_4_deg 19.274 r_dihedral_angle_3_deg 15.729 r_lrange_other 9.29 r_lrange_it 9.287 r_dihedral_angle_1_deg 7.104 r_scangle_it 6.993 r_scangle_other 6.991 r_mcangle_it 5.932 r_mcangle_other 5.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.681 r_dihedral_angle_4_deg 19.274 r_dihedral_angle_3_deg 15.729 r_lrange_other 9.29 r_lrange_it 9.287 r_dihedral_angle_1_deg 7.104 r_scangle_it 6.993 r_scangle_other 6.991 r_mcangle_it 5.932 r_mcangle_other 5.931 r_scbond_it 4.51 r_scbond_other 4.509 r_mcbond_it 4.452 r_mcbond_other 4.451 r_angle_refined_deg 1.571 r_angle_other_deg 1.291 r_nbd_refined 0.204 r_symmetry_nbd_other 0.181 r_nbd_other 0.172 r_symmetry_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.16 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3790 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing PDB_EXTRACT data extraction