5M4H

Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UYL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1M Na Cacodylate pH 6.5 25% PEG 2K MME 0.2M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.3547.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.011α = 90
b = 86.552β = 90
c = 96.957γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSBRUKER PHOTON 1002016-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.51484

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
1264.5792.30.13787.842.917134
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)
122.0394.40.51652.52.55

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1uyl264.571631881592.280.22820.223810.31703RANDOM27.303
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]
-1.020.710.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.771
r_dihedral_angle_4_deg26.24
r_dihedral_angle_3_deg16.364
r_long_range_B_refined6.998
r_long_range_B_other6.773
r_dihedral_angle_1_deg6.714
r_scangle_other4.407
r_mcangle_it3.425
r_mcangle_other3.425
r_scbond_it2.828
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.771
r_dihedral_angle_4_deg26.24
r_dihedral_angle_3_deg16.364
r_long_range_B_refined6.998
r_long_range_B_other6.773
r_dihedral_angle_1_deg6.714
r_scangle_other4.407
r_mcangle_it3.425
r_mcangle_other3.425
r_scbond_it2.828
r_scbond_other2.804
r_mcbond_it2.288
r_mcbond_other2.274
r_angle_refined_deg1.919
r_angle_other_deg1.036
r_chiral_restr0.1
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1617
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing