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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 3.08 60.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.092 α = 90 b = 108.092 β = 90 c = 84.441 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 2009-04-22 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 24.96 95.3 0.1 5.4 2.06 16529
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 94.1 0.502 1.3 1.94
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 2BU8 2.6 24.82 15679 841 95.14 0.2154 0.21233 0.2162 0.27289 0.2781 RANDOM 65.354
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 -0.14 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.998 r_dihedral_angle_4_deg 22.494 r_dihedral_angle_3_deg 18.711 r_long_range_B_other 10.775 r_long_range_B_refined 10.77 r_scangle_other 6.603 r_mcangle_other 6.026 r_mcangle_it 6.024 r_dihedral_angle_1_deg 5.872 r_scbond_it 4.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.998 r_dihedral_angle_4_deg 22.494 r_dihedral_angle_3_deg 18.711 r_long_range_B_other 10.775 r_long_range_B_refined 10.77 r_scangle_other 6.603 r_mcangle_other 6.026 r_mcangle_it 6.024 r_dihedral_angle_1_deg 5.872 r_scbond_it 4.048 r_scbond_other 4.048 r_mcbond_it 3.829 r_mcbond_other 3.817 r_angle_refined_deg 1.664 r_angle_other_deg 1.058 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 2708 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing