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Crystal structure of Human PDK1 kinase domain in complex with an allosteric activator bound to the PIF-pocket
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 1.4M SODIUM CITRATE, 0.1M SODIUM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.15 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.55 α = 90 b = 44 β = 100.42 c = 47.24 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2007-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97915 ESRF ID23-1
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 46.47 99.8 0.094 3.3 23875 23875 16.22
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 2 100 0.368 3.9 3.3 3464
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 MOLECULAR REPLACEMENT THROUGHOUT 3HRC 1.9 46.47 23490 384 99.78 0.16511 0.1649 0.1694 0.1768 0.1839 RANDOM 13.846
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] -0.36 -0.45 -0.19 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.923 r_dihedral_angle_4_deg 23.452 r_dihedral_angle_3_deg 12.28 r_dihedral_angle_1_deg 5.704 r_scangle_it 3.922 r_scbond_it 2.4 r_angle_refined_deg 1.463 r_mcangle_it 1.318 r_mcbond_it 0.69 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.923 r_dihedral_angle_4_deg 23.452 r_dihedral_angle_3_deg 12.28 r_dihedral_angle_1_deg 5.704 r_scangle_it 3.922 r_scbond_it 2.4 r_angle_refined_deg 1.463 r_mcangle_it 1.318 r_mcbond_it 0.69 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 2242 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction SCALA data scaling PHASER phasing