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CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) {2-Oxo-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-2,3-dihydro-1H-indol-5-yl}-urea {BX-517} COMPLEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 AMMONIUM SULFATE, TRIS, EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.234 α = 90 b = 125.234 β = 90 c = 47.696 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 100 CCD ADSC QUANTUM 4 2003-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 2.14 20 99.5 0.115 5.89 3.36 23847 4.5 8.1
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 2.14 2.27 99 0.3769 1.7 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 DIFFERENCE FOURIER PLUS REFINEMENT THROUGHOUT 2.14 19.91 2 23831 23028 903 96 0.224 0.222 0.2235 0.282 0.2875 RANDOM 17.7
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] -0.11 1.24 -0.11 0.22
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_scangle_it 3.94 c_scbond_it 2.8 c_mcangle_it 2.71 c_mcbond_it 1.86 c_angle_deg 0.9 c_improper_angle_d 0.71 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_scangle_it 3.94 c_scbond_it 2.8 c_mcangle_it 2.71 c_mcbond_it 1.86 c_angle_deg 0.9 c_improper_angle_d 0.71 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2255 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 55
Software Software Software Name Purpose CNX refinement XTALVIEW refinement X-GEN data reduction X-GEN data scaling CNX phasing