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Crystal Structure of Acetylornithine Aminotransferase from Elizabethkingia anophelis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 ElanA.01026.a.B1.PW37983 at 19.6 mg/ml, incubated with 3 mM ornithine and alpha-ketoglutaric acid and mixed 1:1 with an equal volume JCSG+(a3): 20% (w/v) PEG-3350, 200 mM ammonium citrate dibasic, cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.33 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.6 α = 90 b = 77.47 β = 129.46 c = 104.96 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 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2017-03-22 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) Rrim 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 42.354 99.4 0.037 0.043 0.999 20.68 3.792 101355 -3 20.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 99.5 0.514 0.601 0.862 2.52 3.761
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 FREE R-VALUE 2OAT 1.65 42.354 1.34 101344 1923 99.78 0.1558 0.1553 0.1568 0.1801 0.1805 30.2083
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 15.21 f_angle_d 0.806 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5911 Nucleic Acid Atoms Solvent Atoms 723 Heterogen Atoms 67
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MoRDa phasing