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Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase (T2): the importance of potassium and chloride for its structure and function
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WL4 PDB entry 1WL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 18% PEG 5000 monomethylether, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.44 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.749 α = 90 b = 107.44 β = 103.06 c = 102.326 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 MAR CCD 165 mm mirrors 2006-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.4022 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 73.72 99.9 0.073 0.073 16.3 4.1 100031 99949 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.15 99.9 0.357 0.357 3.9 4.1 13221
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 (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 PDB entry 1WL4 2.05 73.72 99951 94953 4998 100 0.15817 0.15601 0.1604 0.1992 0.203 RANDOM 31.835
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] -0.28 -0.34 0.34 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.621 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_4_deg 12.35 r_dihedral_angle_1_deg 5.604 r_scangle_it 2.142 r_mcangle_it 1.956 r_scbond_it 1.519 r_mcbond_it 1.302 r_angle_refined_deg 1.265 r_nbtor_refined 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.621 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_4_deg 12.35 r_dihedral_angle_1_deg 5.604 r_scangle_it 2.142 r_mcangle_it 1.956 r_scbond_it 1.519 r_mcbond_it 1.302 r_angle_refined_deg 1.265 r_nbtor_refined 0.291 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.088 r_metal_ion_refined 0.053 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11512 Nucleic Acid Atoms Solvent Atoms 938 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection XDS data reduction XDS data scaling MOLREP phasing