2Q8I

Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q8Fpdb entry 2Q8F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6293soudium citrate, sodium potassium phosphate, sodium chrolide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.0469.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.872α = 90
b = 120.872β = 90
c = 239.637γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3mirror2006-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.98APS19-BM

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
12.6501000.05410.27.732612
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)
12.62.641000.6947.11597

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 2Q8F2.65032534164799.950.2060.2050.238RANDOM55.257
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]
0.050.030.05-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.817
r_dihedral_angle_3_deg19.589
r_dihedral_angle_4_deg17.913
r_dihedral_angle_1_deg6.671
r_scangle_it4.193
r_scbond_it2.696
r_angle_refined_deg1.82
r_mcangle_it1.693
r_mcbond_it0.897
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.817
r_dihedral_angle_3_deg19.589
r_dihedral_angle_4_deg17.913
r_dihedral_angle_1_deg6.671
r_scangle_it4.193
r_scbond_it2.696
r_angle_refined_deg1.82
r_mcangle_it1.693
r_mcbond_it0.897
r_nbtor_refined0.323
r_nbd_refined0.234
r_metal_ion_refined0.193
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.172
r_chiral_restr0.124
r_xyhbond_nbd_refined0.116
r_bond_refined_d0.02
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3727
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms43

Software

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