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Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1M Na Cacodylate pH 6.5
25% PEG 2K MME
0.2M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.011 α = 90 b = 86.552 β = 90 c = 96.957 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS BRUKER PHOTON 100 2016-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.51484
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 64.57 92.3 0.1378 7.84 2.9 17134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 94.4 0.5165 2.5 2.55
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1uyl 2 64.57 16318 815 92.28 0.2282 0.22381 0.2276 0.31703 0.3195 RANDOM 27.303
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] -1.02 0.71 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.771 r_dihedral_angle_4_deg 26.24 r_dihedral_angle_3_deg 16.364 r_long_range_B_refined 6.998 r_long_range_B_other 6.773 r_dihedral_angle_1_deg 6.714 r_scangle_other 4.407 r_mcangle_it 3.425 r_mcangle_other 3.425 r_scbond_it 2.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.771 r_dihedral_angle_4_deg 26.24 r_dihedral_angle_3_deg 16.364 r_long_range_B_refined 6.998 r_long_range_B_other 6.773 r_dihedral_angle_1_deg 6.714 r_scangle_other 4.407 r_mcangle_it 3.425 r_mcangle_other 3.425 r_scbond_it 2.828 r_scbond_other 2.804 r_mcbond_it 2.288 r_mcbond_other 2.274 r_angle_refined_deg 1.919 r_angle_other_deg 1.036 r_chiral_restr 0.1 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 1617 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing