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Crystal Structure of tomato Methylketone Synthase I H243A variant complexed with beta-ketoheptanoate
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 7 277 0.1M MOPSO-Na+, 15% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, overnight soak in 1mM
beta-ketoheptanoate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.237 α = 90 b = 94.387 β = 97.59 c = 60.077 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 2007-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
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 2.3 19.6 88.8 0.118 11.19 4.1 21097 21096 -3 32.115
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 7YAS 2.3 19.37 21097 21093 1083 0.235 0.2086 0.2052 0.2028 0.2728 0.2684 RANDOM 28.3783
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.208 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_4_deg 13.444 r_dihedral_angle_1_deg 5.361 r_scangle_it 1.445 r_angle_refined_deg 1.111 r_scbond_it 0.885 r_mcangle_it 0.865 r_mcbond_it 0.476 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.208 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_4_deg 13.444 r_dihedral_angle_1_deg 5.361 r_scangle_it 1.445 r_angle_refined_deg 1.111 r_scbond_it 0.885 r_mcangle_it 0.865 r_mcbond_it 0.476 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3944 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 20
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction XDS data scaling CNS phasing