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C. rodentium YcbB - ertapenem complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298.15 C. rodentium YcbB was crystallized at 20C by sitting drop vapour diffusion using 0.2 uL protein solution (8.8 mg/mL purified protein in Buffer A) and 0.1 uL of mother liquor (0.16 M calcium acetate, 0.08 M Sodium Cacodylate pH 6.5, 14% (v/v) PEG 8k, 20% (v/v) glycerol) with the addition of 1mM ertapenem.
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.997 α = 90 b = 117.705 β = 90 c = 125.185 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 CCD RAYONIX MX300HE 2019-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.0332 CLSI 08B1-1
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 2.6 42.876 99 0.43 0.98 3.57 6.6 20707 52.68
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 2.6 2.67 0.308
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 6NTW 2.6 35.97 1.33 20707 1029 99.48 0.228 0.2256 0.2104 0.2738 0.2576 61.6049
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4014 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing