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Crystal structure of meropenem bound to OXA-57
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.12 M Monosaccharides (0.2 M D-Glucose, 0.2 M D-Mannose, 0.2 M D-Galactose, 0.2 M L-Fucose, 0.2 M D-Xylose, 0.2 M N-Acetyl-D-Glucosamine), 0.1 M Tris; BICINE pH 8.5, 37.5 % (v/v) Precipitant mix (25 % (v/v) MPD, 25 % (w/v) PEG 1000, 35 % (w/v) PEG 3350)
1hr soak in 10mM meropenem.
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.931 α = 90 b = 109.865 β = 90 c = 66.357 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 XE 9M 2020-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.912 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.42 56.53 99.7 0.997 11.7 12.8 9482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.51 0.667 1.2
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 2.42 56.53 1.35 9432 482 99.05 0.2004 0.1971 0.2096 0.2601 0.2684 80.34
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 21.7708 f_angle_d 0.8833 f_chiral_restr 0.0457 f_bond_d 0.0073 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1800 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing