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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 2.39 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.257 α = 90 b = 106.493 β = 102.95 c = 101.734 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 2005-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8125 EMBL/DESY, HAMBURG X11
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 73.32 99.9 0.078 0.078 14.8 4.2 98026 97946 25
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 2.16 99.9 0.3 0.3 5.2 4.2 14142
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 73.32 97945 93047 4898 100 0.15948 0.15743 0.159 0.19803 0.1995 RANDOM 23.507
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] -0.34 -0.05 0.34 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.273 r_dihedral_angle_4_deg 13.682 r_dihedral_angle_3_deg 13.531 r_dihedral_angle_1_deg 5.699 r_scangle_it 2.237 r_mcangle_it 2.091 r_scbond_it 1.614 r_mcbond_it 1.496 r_angle_refined_deg 1.307 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.273 r_dihedral_angle_4_deg 13.682 r_dihedral_angle_3_deg 13.531 r_dihedral_angle_1_deg 5.699 r_scangle_it 2.237 r_mcangle_it 2.091 r_scbond_it 1.614 r_mcbond_it 1.496 r_angle_refined_deg 1.307 r_nbtor_refined 0.296 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.189 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11512 Nucleic Acid Atoms Solvent Atoms 904 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection XDS data reduction XDS data scaling MOLREP phasing