2IBU

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
2.3948.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.249α = 90
b = 106.569β = 102.9
c = 101.497γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2004-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8115EMBL/DESY, HAMBURGX11

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
11.919.4699.90.0680.068164.312280112261625
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)
11.921000.3470.3474.34.217454

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 1WL41.919.4612261511648461311000.167190.165590.19772RANDOM26.242
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]
-0.180.090.38-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.158
r_dihedral_angle_4_deg14.565
r_dihedral_angle_3_deg12.932
r_dihedral_angle_1_deg8.071
r_scangle_it2.197
r_mcangle_it1.995
r_scbond_it1.558
r_mcbond_it1.428
r_angle_refined_deg1.332
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.158
r_dihedral_angle_4_deg14.565
r_dihedral_angle_3_deg12.932
r_dihedral_angle_1_deg8.071
r_scangle_it2.197
r_mcangle_it1.995
r_scbond_it1.558
r_mcbond_it1.428
r_angle_refined_deg1.332
r_nbtor_refined0.297
r_nbd_refined0.202
r_symmetry_vdw_refined0.185
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.124
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11522
Nucleic Acid Atoms
Solvent Atoms1171
Heterogen Atoms202

Software

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