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Crystal Structure of tomato Methylketone Synthase I complexed with 3-hydroxyoctanoate
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+, 22% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, 4 hr soak in 1mM
3-hydroxyoctanoate, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 46.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.038 α = 90 b = 92.38 β = 97.56 c = 60.596 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 315 2006-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 0.97944 SSRL BL1-5
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 2.2 19.6 99.1 0.14 8.85 3.1 26450 26450 -3 27.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 99.1 0.517 2.49 3.1 932
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 2.2 19.6 26450 26450 1319 99.1 0.22 0.222 0.2022 0.2041 0.2357 0.1969 RANDOM 25.5093
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] 0.795 -0.505 -1.548 0.753
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 4.278 c_scbond_it 3.053 c_mcangle_it 2.994 c_mcbond_it 1.984
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3975 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling CNS refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction CNS phasing