2II3

Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component in the branched-chain alpha-ketoacid dehydrogenase complex (BCKDC), Oxidized Coenzyme A-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IHWPDB entry 2IHW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62920.1 M Na-acetate (pH 4.6), 28% PEG 4000, 0.15 M NH4-acetate, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.7355.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 194.915α = 90
b = 194.915β = 90
c = 171.997γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.98000APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.175097.80.04813.23.1126277
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.172.2591.90.392.411855

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2IHW2.1750123658624395.710.2050.2020.259RANDOM39.03
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]
-0.81-0.4-0.811.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.078
r_dihedral_angle_3_deg17.851
r_dihedral_angle_4_deg17.707
r_dihedral_angle_1_deg6.74
r_scangle_it3.751
r_scbond_it2.585
r_angle_refined_deg1.849
r_mcangle_it1.576
r_mcbond_it0.996
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.078
r_dihedral_angle_3_deg17.851
r_dihedral_angle_4_deg17.707
r_dihedral_angle_1_deg6.74
r_scangle_it3.751
r_scbond_it2.585
r_angle_refined_deg1.849
r_mcangle_it1.576
r_mcbond_it0.996
r_nbtor_refined0.309
r_symmetry_vdw_refined0.231
r_nbd_refined0.206
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.156
r_chiral_restr0.133
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14424
Nucleic Acid Atoms
Solvent Atoms742
Heterogen Atoms439

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling