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Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa in Complex with Covalently Bound Clavulanic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 Protein: 8.0 mg/ml, 0.01M Tris pH 8.3;
Screen - AmSO4 (F6): 0.1M Bicine pH 9.0, 2.4M Ammonium sulfate;
Soak & Cryo: 50mM Clavulanic acid, 2M Lithium sulfate, 10 min
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.94 α = 90 b = 95.451 β = 90 c = 125.974 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 CCD MARMOSAIC 300 mm CCD Be 2020-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.88 30 100 0.071 0.071 0.077 0.031 0.998 25.3 6.2 48753 -3 25.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 100 0.841 0.841 0.916 0.36 0.848 2.8 6.3
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 1E3U 1.88 29.91 46232 2457 99.83 0.1687 0.1672 0.1764 0.196 0.2057 RANDOM 31.172
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] 0.31 2.16 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.311 r_dihedral_angle_4_deg 11.927 r_dihedral_angle_3_deg 9.87 r_dihedral_angle_1_deg 3.753 r_angle_refined_deg 1.321 r_angle_other_deg 0.373 r_chiral_restr 0.066 r_gen_planes_refined 0.055 r_gen_planes_other 0.05 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.311 r_dihedral_angle_4_deg 11.927 r_dihedral_angle_3_deg 9.87 r_dihedral_angle_1_deg 3.753 r_angle_refined_deg 1.321 r_angle_other_deg 0.373 r_chiral_restr 0.066 r_gen_planes_refined 0.055 r_gen_planes_other 0.05 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3902 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing