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Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 14)
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 2.17 43.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.7 α = 90 b = 82.724 β = 90 c = 88.538 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 2019-01-26 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 2.137 60.446 94.1 0.121 0.044 0.999 12.9 8.6 21028
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 2.137 2.341 67.2 1.311 0.499 0.582 1.6 7.8
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 2.137 60.446 21028 960 73.499 0.196 0.1919 0.1971 0.2743 0.2752 48.565
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] 0.193 -0.313 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.65 r_dihedral_angle_4_deg 20.769 r_dihedral_angle_3_deg 17.404 r_lrange_it 9.125 r_lrange_other 9.06 r_dihedral_angle_1_deg 7.636 r_scangle_it 6.468 r_scangle_other 6.467 r_mcangle_it 5.852 r_mcangle_other 5.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.65 r_dihedral_angle_4_deg 20.769 r_dihedral_angle_3_deg 17.404 r_lrange_it 9.125 r_lrange_other 9.06 r_dihedral_angle_1_deg 7.636 r_scangle_it 6.468 r_scangle_other 6.467 r_mcangle_it 5.852 r_mcangle_other 5.848 r_scbond_it 4.179 r_scbond_other 4.178 r_mcbond_it 3.904 r_mcbond_other 3.903 r_angle_refined_deg 1.57 r_angle_other_deg 1.231 r_symmetry_xyhbond_nbd_refined 0.234 r_nbd_other 0.232 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.214 r_symmetry_nbd_other 0.19 r_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.061 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 3731 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 32
Software Software Software Name Purpose XDS data reduction Aimless data scaling STARANISO data processing PHASER phasing REFMAC refinement PDB_EXTRACT data extraction