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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 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.143 α = 90 b = 107.577 β = 102.89 c = 101.954 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 2005-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.141 MAX II I711
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 1.9 48.22 99.9 0.083 0.083 12.7 4.2 125924 125843 23
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 1.9 2 99.9 0.294 0.294 4.8 4.1 17859
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 1.9 48.22 125843 119551 6292 100 0.15532 0.15327 0.1539 0.1945 0.1948 RANDOM 19.505
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] 0.19 0.13 0.06 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.396 r_dihedral_angle_4_deg 13.673 r_dihedral_angle_3_deg 13.139 r_dihedral_angle_1_deg 8.076 r_scangle_it 2.146 r_mcangle_it 1.905 r_scbond_it 1.525 r_angle_refined_deg 1.302 r_mcbond_it 1.266 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.396 r_dihedral_angle_4_deg 13.673 r_dihedral_angle_3_deg 13.139 r_dihedral_angle_1_deg 8.076 r_scangle_it 2.146 r_mcangle_it 1.905 r_scbond_it 1.525 r_angle_refined_deg 1.302 r_mcbond_it 1.266 r_nbtor_refined 0.29 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.088 r_metal_ion_refined 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11522 Nucleic Acid Atoms Solvent Atoms 1100 Heterogen Atoms 218
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection XDS data reduction XDS data scaling MOLREP phasing