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Discovery of a Novel, Potent and Selective Inhibitor of 3-Phosphoinositide Dependent Kinase (PDK1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.2M Ammonium Sulfate, 10mM EDTA, 5-10% glycerol, 0.1M HEPES, pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.91 57.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.982 α = 90 b = 122.982 β = 90 c = 47.505 γ = 120
Symmetry Space Group P 32 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 93 CCD ADSC QUANTUM 4 2009-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.92 50 99.6 0.077 15 3.3 31671 31671 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.98 99.9 0.52 2.1 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.92 50 30059 30059 1600 99.54 0.17376 0.17376 0.17167 0.1717 0.21289 0.2135 RANDOM 24.159
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] 0.6 0.3 0.6 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_4_deg 20.692 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_1_deg 6.604 r_scangle_it 5.99 r_scbond_it 3.833 r_mcangle_it 2.571 r_angle_refined_deg 2.226 r_mcbond_it 1.506 r_chiral_restr 0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_4_deg 20.692 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_1_deg 6.604 r_scangle_it 5.99 r_scbond_it 3.833 r_mcangle_it 2.571 r_angle_refined_deg 2.226 r_mcbond_it 1.506 r_chiral_restr 0.171 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 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 2269 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 88
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement ARP model building WARP model building HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing