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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 2BU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.8 277 0.1 M SODIUM ACETATE PH 5.8
0.125 M MAGNESIUM CHLORIDE
6% ISOPROPANOL
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.249 α = 90 b = 108.249 β = 90 c = 85.221 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC BLUE MIRRORS 2010-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5412
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 2.6 93.75 95.4 0.093 6.1 2.3 16626
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 2.6 2.69 95.9 0.642 1.6 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2BU8 2.6 93.75 15759 843 94.51 0.20552 0.20269 0.25958 0.2568 RANDOM 76.632
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] 1.69 0.84 1.69 -5.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.461 r_dihedral_angle_4_deg 20.138 r_dihedral_angle_3_deg 19.667 r_long_range_B_other 12.047 r_long_range_B_refined 12.036 r_scangle_other 8.58 r_mcangle_other 7.763 r_mcangle_it 7.762 r_dihedral_angle_1_deg 6.38 r_scbond_other 5.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.461 r_dihedral_angle_4_deg 20.138 r_dihedral_angle_3_deg 19.667 r_long_range_B_other 12.047 r_long_range_B_refined 12.036 r_scangle_other 8.58 r_mcangle_other 7.763 r_mcangle_it 7.762 r_dihedral_angle_1_deg 6.38 r_scbond_other 5.7 r_scbond_it 5.698 r_mcbond_it 5.374 r_mcbond_other 5.344 r_angle_refined_deg 1.748 r_angle_other_deg 1.068 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 2685 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing