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Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BTZ
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 3.29 62.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.317 α = 90 b = 109.317 β = 90 c = 85.087 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 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.97 94.75 99 0.057 0.061 0.019 0.999 19.1 10.1 40079 43.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.02 98.9 1.124 0.363 0.78 10.3
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 2btz 1.97 94.67 1.34 40060 2042 97.66 0.1971 0.1965 0.2006 0.2085 0.2127 57.2
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 10.4938 f_angle_d 0.6511 f_chiral_restr 0.0427 f_plane_restr 0.0042 f_bond_d 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2734 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling MOLREP phasing