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Crystal structure of Pseudomonas aeruginosa PBP3 in complex with vaborbactam
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 1.99 38.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.095 α = 90 b = 83.502 β = 90 c = 88.419 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 EIGER X 9M 2021-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
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 2.2 29.49 99.8 0.112 0.997 15.2 13.2 26281
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 2.2 2.25 97.4 0.836 0.801 11.6
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 2.2 27.81 24839 1393 99.68 0.201 0.1986 0.2037 0.2412 0.2388 RANDOM 48.795
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.464 r_dihedral_angle_4_deg 19.167 r_dihedral_angle_3_deg 14.731 r_dihedral_angle_1_deg 6.673 r_angle_refined_deg 1.307 r_angle_other_deg 1.159 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.464 r_dihedral_angle_4_deg 19.167 r_dihedral_angle_3_deg 14.731 r_dihedral_angle_1_deg 6.673 r_angle_refined_deg 1.307 r_angle_other_deg 1.159 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3593 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing