5M4E

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 DIFFUSION6.52770.1 M Na Cacodylate pH 6.5 25% PEG 2K MME 0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.5451.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.388α = 90
b = 89.06β = 90
c = 99.505γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++OSMIC BLUE MIRRORS2009-05-01MSINGLE 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
11.924.6498.50.0629.92.722925
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)
11.91.9794.90.2593.32.43

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 REPLACEMENTTHROUGHOUT1UYL1.924.6421741118198.440.165680.162980.21791RANDOM26.981
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]
-0.140.51-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.075
r_dihedral_angle_4_deg23.986
r_dihedral_angle_3_deg13.297
r_long_range_B_refined7.76
r_long_range_B_other7.338
r_dihedral_angle_1_deg6.132
r_scangle_other5.559
r_scbond_it3.821
r_scbond_other3.777
r_mcangle_other3.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.075
r_dihedral_angle_4_deg23.986
r_dihedral_angle_3_deg13.297
r_long_range_B_refined7.76
r_long_range_B_other7.338
r_dihedral_angle_1_deg6.132
r_scangle_other5.559
r_scbond_it3.821
r_scbond_other3.777
r_mcangle_other3.101
r_mcangle_it3.1
r_mcbond_it2.191
r_mcbond_other2.19
r_angle_refined_deg1.963
r_angle_other_deg1.124
r_chiral_restr0.138
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms1628
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms30

Software

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