2IB9

Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase (T2): the importance of potassium and chloride for its structure and function


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WL4PDB entry 1WL4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527718% PEG 5000 monomethylether, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.4449.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.749α = 90
b = 107.44β = 103.06
c = 102.326γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A1.4022EMBL/DESY, HAMBURGBW7A

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0573.7299.90.0730.07316.34.11000319994927
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)RedundancyNumber Unique Reflections (All)
12.052.1599.90.3570.3573.94.113221

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1WL42.0573.72999519495349981000.158170.156010.1992RANDOM31.835
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]
-0.28-0.340.34-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.621
r_dihedral_angle_3_deg13.491
r_dihedral_angle_4_deg12.35
r_dihedral_angle_1_deg5.604
r_scangle_it2.142
r_mcangle_it1.956
r_scbond_it1.519
r_mcbond_it1.302
r_angle_refined_deg1.265
r_nbtor_refined0.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.621
r_dihedral_angle_3_deg13.491
r_dihedral_angle_4_deg12.35
r_dihedral_angle_1_deg5.604
r_scangle_it2.142
r_mcangle_it1.956
r_scbond_it1.519
r_mcbond_it1.302
r_angle_refined_deg1.265
r_nbtor_refined0.291
r_nbd_refined0.202
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.124
r_symmetry_hbond_refined0.11
r_chiral_restr0.088
r_metal_ion_refined0.053
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11512
Nucleic Acid Atoms
Solvent Atoms938
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing