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OXA-48: Q5 mutant in an acyl enzyme complex with piperacillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 See Frohlich et al (2024). Nature Catalysis
Crystal Properties Matthews coefficient Solvent content 2.27 45.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.895 α = 90 b = 45.34 β = 107.227 c = 64.327 γ = 90
Symmetry Space Group C 1 2 1
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 2022-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 1.5 40.3 99.81 0.08011 0.998 11.42 5.1 40625 16.42
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 1.5 1.554 0.7383 0.684
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 22.97 1.35 40621 3832 97.87 0.1659 0.1644 0.1652 0.1958 0.1974 22.2
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 f_dihedral_angle_d 19.4377 f_angle_d 1.4278 f_chiral_restr 0.0609 f_bond_d 0.0104 f_plane_restr 0.0097
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1921 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 128
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling ABS phasing