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Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295.15 50 mM KHPO4 pH 7.5, 1.7 M ammonium sulfate and 4% (v/v) PEG400, 5 mM ADP
Crystal Properties Matthews coefficient Solvent content 1.99 38.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.965 α = 90 b = 67.441 β = 101.185 c = 78.605 γ = 90
Symmetry Space Group P 1 21 1
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 6M 2014-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.95 68.64 98.1 0.057 0.069 0.039 0.996 9.7 3 51337 28.9
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 1.95 2 97.1 0.354 0.436 0.251 0.815 2 2.8
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 2zkj 1.95 68.64 1.35 51289 2388 97.69 0.2034 0.2021 0.2017 0.2286 0.2274 36.21
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 11.1314 f_angle_d 0.513 f_chiral_restr 0.0397 f_plane_restr 0.0029 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5487 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling MOLREP phasing Coot model building