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Crystal structure of Pseudomonas aeruginosa PBP3 in complex with zidebactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% polyethylene glycol 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.92 35.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.372 α = 90 b = 80.025 β = 90 c = 88.115 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 S 6M 2020-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.49 25 99.9 0.182 0.997 22.3 12 17225
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.56 100 1.21 0.942 12.8
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 (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 THROUGHOUT 3PBQ 2.49 24.94 16353 836 98.63 0.2033 0.1996 0.2022 0.2719 0.276 RANDOM 46.553
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] -0.01 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.695 r_dihedral_angle_4_deg 17.606 r_dihedral_angle_3_deg 15.532 r_dihedral_angle_1_deg 6.845 r_angle_refined_deg 1.372 r_angle_other_deg 1.177 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.695 r_dihedral_angle_4_deg 17.606 r_dihedral_angle_3_deg 15.532 r_dihedral_angle_1_deg 6.845 r_angle_refined_deg 1.372 r_angle_other_deg 1.177 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3539 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction SCALEPACK data scaling PHASER phasing