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Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.024 α = 90 b = 192.024 β = 90 c = 57.058 γ = 120
Symmetry Space Group P 31 1 2
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 X 9M 2019-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.127 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.943 49.05 99.5 0.174 0.092 0.997 4.2 8.5 87426
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.943 1.977 93 1.599 0.925 0.745 7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1OAT 1.95 49.05 1.34 82532 4075 94.42 0.2452 0.2434 0.2784 0.3 40.4095
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 9510 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction PHENIX phasing