☰ Navigation Tabs
Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 7)
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 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.575 α = 90 b = 82.676 β = 90 c = 88.616 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 2019-01-29 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 2.17 60.45 99.9 0.189 0.066 0.996 8.2 8.8 27129
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 2.174 2.212 99.9 2.652 0.931 0.452 8.6
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 2.17 60.45 27116 1274 99.838 0.201 0.1985 0.2038 0.2619 0.2618 50.686
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] 0.966 0.29 -1.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.046 r_dihedral_angle_4_deg 19.814 r_dihedral_angle_3_deg 16.584 r_lrange_other 10.062 r_lrange_it 10.061 r_dihedral_angle_1_deg 7.677 r_scangle_it 7.448 r_scangle_other 7.447 r_mcangle_other 6.921 r_mcangle_it 6.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.046 r_dihedral_angle_4_deg 19.814 r_dihedral_angle_3_deg 16.584 r_lrange_other 10.062 r_lrange_it 10.061 r_dihedral_angle_1_deg 7.677 r_scangle_it 7.448 r_scangle_other 7.447 r_mcangle_other 6.921 r_mcangle_it 6.918 r_scbond_it 4.893 r_scbond_other 4.892 r_mcbond_it 4.809 r_mcbond_other 4.804 r_angle_refined_deg 1.639 r_angle_other_deg 1.283 r_nbd_other 0.235 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.165 r_xyhbond_nbd_other 0.108 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.071 r_bond_refined_d 0.01 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 3665 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 23
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement