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Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277.15 50 mM Na acetate pH 5.5, 100 mM magnesium chloride and 8% (v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 3.25 62.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.155 α = 90 b = 109.155 β = 90 c = 84.359 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 PIXEL DECTRIS PILATUS3 S 6M 2016-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 94.53 99.8 0.15 0.154 0.034 0.998 20 20.6 17660 54.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 99.5 2.002 2.05 0.439 0.796 2.8 21.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7EBH 2.6 54.58 1.34 17623 868 99.67 0.2257 0.2244 0.2241 0.251 0.254 60.42
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.5761 f_angle_d 0.3909 f_chiral_restr 0.0372 f_plane_restr 0.0023 f_bond_d 0.0014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2721 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling Coot model building PHENIX phasing