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crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BTZ PDB ENTRY 2BTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.8 277 100MM MES PH5.8-6, 10% ISOPROPANOL, 200MM CALCIUM ACETATE, 10MG/ML PROTEIN 4 DEGREES, pH 5.80
Crystal Properties Matthews coefficient Solvent content 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.703 α = 90 b = 108.703 β = 90 c = 83.855 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 CCD ADSC CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 30 98.5 0.05 21.2 3.44 21971
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 96.2 0.31 3.91 3.16
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BTZ 2.4 30 21888 1067 0.238 0.2465 RANDOM
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] -4.976 -5.98 -4.976 9.953
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.635 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.635 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2883 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 59
Software Software Software Name Purpose CNX refinement HKL data reduction SCALEPACK data scaling CNX phasing