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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 60.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.651 α = 90 b = 108.651 β = 90 c = 83.657 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 2010-06-30 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 2.4 29.37 95.3 0.109 4.9 2.01 21000
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 2.4 2.49 93.5 0.57 1.1 1.97
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 2.4 27.89 19890 1083 95.1 0.21894 0.21663 0.2213 0.2617 0.261 RANDOM 59.832
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] -0.11 -0.06 -0.11 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.544 r_dihedral_angle_4_deg 22.637 r_dihedral_angle_3_deg 19.071 r_long_range_B_other 11.114 r_long_range_B_refined 11.109 r_scangle_other 7.088 r_dihedral_angle_1_deg 6.65 r_mcangle_it 6.524 r_mcangle_other 6.524 r_scbond_other 4.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.544 r_dihedral_angle_4_deg 22.637 r_dihedral_angle_3_deg 19.071 r_long_range_B_other 11.114 r_long_range_B_refined 11.109 r_scangle_other 7.088 r_dihedral_angle_1_deg 6.65 r_mcangle_it 6.524 r_mcangle_other 6.524 r_scbond_other 4.417 r_scbond_it 4.415 r_mcbond_it 4.242 r_mcbond_other 4.209 r_angle_refined_deg 1.845 r_angle_other_deg 1.116 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 2752 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing