2IBY

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
2.448.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.349α = 90
b = 106.746β = 103.06
c = 101.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.07225ESRFID23-1

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
11.8573.3299.90.0690.06913.74.113349013336526
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)
11.851.951000.3240.3244.64.119414

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 1WL41.8573.3213336512669766681000.166070.164110.20312RANDOM25.388
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]
0.07-0.210.02-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.298
r_dihedral_angle_4_deg14.075
r_dihedral_angle_3_deg12.462
r_dihedral_angle_1_deg8.07
r_scangle_it2.227
r_mcangle_it1.995
r_scbond_it1.595
r_mcbond_it1.341
r_angle_refined_deg1.305
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.298
r_dihedral_angle_4_deg14.075
r_dihedral_angle_3_deg12.462
r_dihedral_angle_1_deg8.07
r_scangle_it2.227
r_mcangle_it1.995
r_scbond_it1.595
r_mcbond_it1.341
r_angle_refined_deg1.305
r_nbtor_refined0.297
r_nbd_refined0.208
r_symmetry_vdw_refined0.205
r_symmetry_hbond_refined0.128
r_xyhbond_nbd_refined0.126
r_chiral_restr0.087
r_metal_ion_refined0.058
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 Atoms1162
Heterogen Atoms224

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing