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Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 13)
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, 0.1M Bis-Tris propane pH 8 and 1% (w/v) protamine sulphate
Crystal Properties Matthews coefficient Solvent content 2.19 43.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.996 α = 90 b = 82.871 β = 90 c = 88.735 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) 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 1.79 60.57 94.9 0.07 0.025 0.999 16.7 9.1 35335
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 1.79 1.966 65.1 1.544 0.46 0.67 12
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 1.79 60.566 35335 1675 72.612 0.2 0.1969 0.2044 0.2567 0.2528 44.944
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] 0.325 -0.118 -0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.824 r_dihedral_angle_4_deg 20.419 r_dihedral_angle_3_deg 16.049 r_lrange_it 7.945 r_lrange_other 7.912 r_dihedral_angle_1_deg 7.045 r_scangle_it 5.499 r_scangle_other 5.498 r_mcangle_it 5.325 r_mcangle_other 5.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.824 r_dihedral_angle_4_deg 20.419 r_dihedral_angle_3_deg 16.049 r_lrange_it 7.945 r_lrange_other 7.912 r_dihedral_angle_1_deg 7.045 r_scangle_it 5.499 r_scangle_other 5.498 r_mcangle_it 5.325 r_mcangle_other 5.324 r_mcbond_it 3.513 r_mcbond_other 3.512 r_scbond_it 3.47 r_scbond_other 3.469 r_angle_refined_deg 1.485 r_angle_other_deg 1.241 r_nbd_refined 0.215 r_nbd_other 0.209 r_symmetry_xyhbond_nbd_refined 0.194 r_symmetry_nbd_other 0.184 r_symmetry_nbd_refined 0.173 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.157 r_symmetry_xyhbond_nbd_other 0.113 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_bond_refined_d 0.007 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 3735 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 27
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PHENIX refinement STARANISO data processing PDB_EXTRACT data extraction