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Crystal structure of pyruvate dehydrogenase kinase isoform 4 in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZKJ PDB entry 2ZKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.9M ammonium sulfate, 4% polyethylene glycol 400, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.595 α = 90 b = 69.374 β = 99.26 c = 82.328 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2008-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.03 50 99.5 0.038 30 3.6 50510 34
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 2.03 2.07 99.4 0.255 4.7 3.3 2483
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 2ZKJ 2.03 50 47925 2564 99.25 0.18536 0.18295 0.1815 0.23016 0.2303 RANDOM 38.294
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] -0.09 -0.61 0.84 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.978 r_dihedral_angle_4_deg 19.908 r_dihedral_angle_3_deg 16.829 r_dihedral_angle_1_deg 6.056 r_scangle_it 4.738 r_scbond_it 3.062 r_mcangle_it 1.819 r_angle_refined_deg 1.817 r_mcbond_it 1.059 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.978 r_dihedral_angle_4_deg 19.908 r_dihedral_angle_3_deg 16.829 r_dihedral_angle_1_deg 6.056 r_scangle_it 4.738 r_scbond_it 3.062 r_mcangle_it 1.819 r_angle_refined_deg 1.817 r_mcbond_it 1.059 r_chiral_restr 0.136 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5756 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing