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Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 3)
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 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 6
Crystal Properties Matthews coefficient Solvent content 2.17 43.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.301 α = 90 b = 82.24 β = 90 c = 88.521 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) 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 1.44 60.25 95.7 0.045 0.048 0.018 0.999 18 7.1 67984
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.59 67.6 0.869 0.952 0.381 0.702 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 1.44 60.25 67984 3362 73.53 0.144 0.1407 0.147 0.201 0.202 34.327
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] -0.944 -1.216 2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.48 r_dihedral_angle_4_deg 20.09 r_dihedral_angle_3_deg 14.52 r_scangle_it 8.705 r_scangle_other 8.704 r_lrange_it 8.471 r_lrange_other 8.447 r_scbond_it 7.467 r_scbond_other 7.467 r_dihedral_angle_1_deg 6.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.48 r_dihedral_angle_4_deg 20.09 r_dihedral_angle_3_deg 14.52 r_scangle_it 8.705 r_scangle_other 8.704 r_lrange_it 8.471 r_lrange_other 8.447 r_scbond_it 7.467 r_scbond_other 7.467 r_dihedral_angle_1_deg 6.667 r_rigid_bond_restr 6.535 r_mcangle_it 5.877 r_mcangle_other 5.876 r_mcbond_it 4.973 r_mcbond_other 4.956 r_angle_refined_deg 1.805 r_angle_other_deg 1.448 r_nbd_refined 0.216 r_nbd_other 0.216 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.148 r_xyhbond_nbd_refined 0.123 r_symmetry_xyhbond_nbd_refined 0.111 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3767 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 30
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PHENIX refinement STARANISO data processing PDB_EXTRACT data extraction