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Structure of pyruvate dehydrogenase kinase isoform 1 in complex with glucose-lowering drug AZD7545
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 AZD75445 was generously supplied by Dr. Rachel Mayers at AstraZeneca, 0.42 M NaK tartrate, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.979 α = 90 b = 96.979 β = 90 c = 111.352 γ = 90
Symmetry Space Group P 41 21 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 1.9 50 99.3 0.063 6.8 9.1 42222
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 1.9 1.97 100 0.434 8.7 4151
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 1.9 50 40553 2058 95.52 0.214 0.212 0.2183 0.249 0.2518 RANDOM 31.434
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] 0.69 0.69 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.547 r_dihedral_angle_4_deg 20.552 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_1_deg 6.177 r_scangle_it 4.626 r_scbond_it 3.166 r_mcangle_it 1.956 r_angle_refined_deg 1.696 r_mcbond_it 1.098 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.547 r_dihedral_angle_4_deg 20.552 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_1_deg 6.177 r_scangle_it 4.626 r_scbond_it 3.166 r_mcangle_it 1.956 r_angle_refined_deg 1.696 r_mcbond_it 1.098 r_nbtor_refined 0.312 r_metal_ion_refined 0.256 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.201 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 32
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