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Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 0.9 M ammonium tartrate, 0.1 M sodium acetate pH 4.6, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.87 68.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.622 α = 90 b = 110.622 β = 90 c = 228.742 γ = 90
Symmetry Space Group I 41 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 CCD ADSC QUANTUM 315r 2013-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97921 APS 19-ID
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 1.75 50 99.9 0.05 53.3 14.1 71388 71273 -3
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 1.75 1.78 100 0.756 2.5 14.2 3526
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.752 33.588 1.34 118277 3317 86.71 0.1877 0.1873 0.2014 0.2057
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] -0.2658 -0.2658 0.5316
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.798 f_angle_d 1.056 f_chiral_restr 0.071 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2921 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 32
Software Software Software Name Purpose HKL-3000 data collection PHENIX model building PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing