5M4K

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 2BU8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.82770.1 M SODIUM ACETATE PH 5.8 0.125 M MAGNESIUM CHLORIDE 6% ISOPROPANOL
Crystal Properties
Matthews coefficientSolvent content
3.0860.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.092α = 90
b = 108.092β = 90
c = 84.441γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++OSMIC BLUE MIRRORS2009-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5412

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
12.624.9695.30.15.42.0616529
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)
12.62.6994.10.5021.31.94

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 REPLACEMENTTHROUGHOUT2BU82.624.821567984195.140.21540.212330.27289RANDOM65.354
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]
-0.14-0.07-0.140.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.998
r_dihedral_angle_4_deg22.494
r_dihedral_angle_3_deg18.711
r_long_range_B_other10.775
r_long_range_B_refined10.77
r_scangle_other6.603
r_mcangle_other6.026
r_mcangle_it6.024
r_dihedral_angle_1_deg5.872
r_scbond_it4.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.998
r_dihedral_angle_4_deg22.494
r_dihedral_angle_3_deg18.711
r_long_range_B_other10.775
r_long_range_B_refined10.77
r_scangle_other6.603
r_mcangle_other6.026
r_mcangle_it6.024
r_dihedral_angle_1_deg5.872
r_scbond_it4.048
r_scbond_other4.048
r_mcbond_it3.829
r_mcbond_other3.817
r_angle_refined_deg1.664
r_angle_other_deg1.058
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms2708
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing