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Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa
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 9 292 Protein: 8.0 mg/ml, 0.01M Tris pH 8.3;
Screen, AmSO4 (F6): 0.1M Bicine pH 9.0, 2.4M Ammonium sulfate;
Cryo: 2M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.813 α = 90 b = 96.346 β = 90 c = 125.137 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 1.65 30 100 0.06 0.06 0.066 0.027 0.999 27 6 71761 -3 21.1
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 1.65 1.68 100 0.841 0.841 0.919 0.365 0.8 2.4 6.1
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 1.65 29.75 68142 3543 99.74 0.1648 0.1636 0.1752 0.19 0.1991 RANDOM 25.851
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] 0.15 1.2 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.494 r_dihedral_angle_4_deg 15.855 r_dihedral_angle_3_deg 10.226 r_dihedral_angle_1_deg 4.123 r_angle_refined_deg 1.336 r_angle_other_deg 0.351 r_chiral_restr 0.067 r_gen_planes_refined 0.057 r_gen_planes_other 0.053 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.494 r_dihedral_angle_4_deg 15.855 r_dihedral_angle_3_deg 10.226 r_dihedral_angle_1_deg 4.123 r_angle_refined_deg 1.336 r_angle_other_deg 0.351 r_chiral_restr 0.067 r_gen_planes_refined 0.057 r_gen_planes_other 0.053 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3811 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing