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Structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with Compound 6
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 7.8 293 25% (w/v) polyethylene glycol 3 350, 0.1 M Bis-Tris propane pH 7.8 and 1% (w/v) protamine sulphate
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.568 α = 90 b = 83.128 β = 90 c = 90.063 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 2018-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9793 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 1.55 61.09 95.5 0.051 0.02 0.999 17.5 7.9 56715
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 1.55 1.69 64.7 1.179 0.448 0.705 1.6 7.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6HZR 1.55 61.09 53940 2775 75.57 0.16 0.1567 0.1699 0.229 0.2391 RANDOM 38.566
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] -9.38 5.94 3.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.795 r_rigid_bond_restr 18.828 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 14.911 r_dihedral_angle_1_deg 7.106 r_angle_refined_deg 1.674 r_angle_other_deg 1.389 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.795 r_rigid_bond_restr 18.828 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 14.911 r_dihedral_angle_1_deg 7.106 r_angle_refined_deg 1.674 r_angle_other_deg 1.389 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3763 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction STARANISO data processing