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Crystal structure of Pseudomonas aeruginosa PBP3 in complex with gamma-lactam YU253911
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.765 α = 90 b = 82.661 β = 90 c = 88.799 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 2020-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 99.8 0.158 0.165 0.046 6.4 12.5 34157
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 99.8 1.159 1.207 0.334 0.934 12.6
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 (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 3PBO 2 33.91 32335 1770 99.27 0.1778 0.1752 0.185 0.2266 0.2303 RANDOM 31.247
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.214 r_dihedral_angle_4_deg 21.494 r_dihedral_angle_3_deg 15.685 r_dihedral_angle_1_deg 6.92 r_angle_refined_deg 1.656 r_angle_other_deg 1.353 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.214 r_dihedral_angle_4_deg 21.494 r_dihedral_angle_3_deg 15.685 r_dihedral_angle_1_deg 6.92 r_angle_refined_deg 1.656 r_angle_other_deg 1.353 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3578 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction PHASER phasing