2Q8H

Structure of pyruvate dehydrogenase kinase isoform 1 in complex with dichloroacetate (DCA)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62930.42 M NaK tartrate, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8857.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.323α = 90
b = 98.323β = 90
c = 110.559γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

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

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125099.437074
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)
122.071000.561

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISpdb entry 2Q8F25036097180296.80.2320.230.27744.04
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]
0.440.44-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.332
r_dihedral_angle_4_deg19.573
r_dihedral_angle_3_deg14.755
r_dihedral_angle_1_deg6.042
r_scangle_it3.174
r_scbond_it2.171
r_mcangle_it1.473
r_angle_refined_deg1.378
r_mcbond_it0.82
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.332
r_dihedral_angle_4_deg19.573
r_dihedral_angle_3_deg14.755
r_dihedral_angle_1_deg6.042
r_scangle_it3.174
r_scbond_it2.171
r_mcangle_it1.473
r_angle_refined_deg1.378
r_mcbond_it0.82
r_nbtor_refined0.304
r_metal_ion_refined0.275
r_nbd_refined0.21
r_symmetry_vdw_refined0.151
r_xyhbond_nbd_refined0.145
r_symmetry_hbond_refined0.111
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2952
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms7

Software

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