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Crystal structure of avibactam 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)
Overnight soak in 2mM avibactam.
Crystal Properties Matthews coefficient Solvent content 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.782 α = 90 b = 110.836 β = 90 c = 66.157 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 2.48 55.42 100 0.999 9 12.3 8900
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 2.48 2.58 0.59 0.8
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 2.48 55.42 1.34 8825 422 99.29 0.1953 0.1925 0.1974 0.2451 0.2526 76.31
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 22.0442 f_angle_d 1.011 f_chiral_restr 0.0496 f_bond_d 0.0079 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1812 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing