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Crystal Structure of tomato Methylketone Synthase I complexed with 2-tridecanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1M PIPES-Na+, 17% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, overnight soak in 1mM
2-tridecanone, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.66 53.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.532 α = 90 b = 106.915 β = 96.52 c = 60.097 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2007-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.31 20 99.6 0.11 13.52 4.6 30189 26600 -3 27.452
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 7YAS 2.31 20 30189 26600 1321 99.6 0.218 0.22 0.1981 0.2 0.2453 0.2021 RANDOM 24.82
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] 5.436 5.221 -11.386 5.95
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 4.359 c_scbond_it 3.094 c_mcangle_it 2.927 c_mcbond_it 1.95
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3969 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 28
Software Software Software Name Purpose XSCALE data scaling CNS refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction XDS data scaling CNS phasing