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Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q8F pdb entry 2Q8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 soudium citrate, sodium potassium phosphate, sodium chrolide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.04 69.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.872 α = 90 b = 120.872 β = 90 c = 239.637 γ = 120
Symmetry Space Group P 65 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 SBC-3 mirror 2006-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98 APS 19-BM
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 2.6 50 100 0.054 10.2 7.7 32612
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 2.6 2.64 100 0.694 7.1 1597
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdb entry 2Q8F 2.6 50 32534 1647 99.95 0.206 0.205 0.2485 0.238 0.2698 RANDOM 55.257
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.817 r_dihedral_angle_3_deg 19.589 r_dihedral_angle_4_deg 17.913 r_dihedral_angle_1_deg 6.671 r_scangle_it 4.193 r_scbond_it 2.696 r_angle_refined_deg 1.82 r_mcangle_it 1.693 r_mcbond_it 0.897 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.817 r_dihedral_angle_3_deg 19.589 r_dihedral_angle_4_deg 17.913 r_dihedral_angle_1_deg 6.671 r_scangle_it 4.193 r_scbond_it 2.696 r_angle_refined_deg 1.82 r_mcangle_it 1.693 r_mcbond_it 0.897 r_nbtor_refined 0.323 r_nbd_refined 0.234 r_metal_ion_refined 0.193 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.172 r_chiral_restr 0.124 r_xyhbond_nbd_refined 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3727 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing