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Structure of P. aeruginosa PBP3 in complex with vaborbactam
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 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 8
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.175 α = 90 b = 83.659 β = 90 c = 89.53 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-F 2018-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 2.012 61.126 94 0.074 0.027 0.999 15.5 8.5 25128
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 2.012 2.215 62.9 1.041 0.429 0.679 6.7
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 (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 2.012 61.126 25128 1161 72.476 0.211 0.2077 0.2149 0.2809 0.2848 48.485
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] 0.48 -0.171 -0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.01 r_dihedral_angle_4_deg 20.085 r_dihedral_angle_3_deg 16.147 r_lrange_other 9.199 r_lrange_it 9.198 r_dihedral_angle_1_deg 7.685 r_scangle_it 6.658 r_scangle_other 6.656 r_mcangle_it 6.418 r_mcangle_other 6.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.01 r_dihedral_angle_4_deg 20.085 r_dihedral_angle_3_deg 16.147 r_lrange_other 9.199 r_lrange_it 9.198 r_dihedral_angle_1_deg 7.685 r_scangle_it 6.658 r_scangle_other 6.656 r_mcangle_it 6.418 r_mcangle_other 6.417 r_mcbond_other 4.413 r_mcbond_it 4.412 r_scbond_it 4.375 r_scbond_other 4.374 r_angle_refined_deg 1.622 r_angle_other_deg 1.247 r_symmetry_xyhbond_nbd_refined 0.235 r_nbd_refined 0.217 r_nbd_other 0.205 r_xyhbond_nbd_refined 0.189 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.148 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.009 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 3841 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling STARANISO data processing PDB_EXTRACT data extraction PHASER phasing