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Structure of human PDK1 kinase domain in complex with LY333531
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H1W PDB ENTRY 1H1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 2.1 M AMMONIUM SULPHATE 0.1 M TRIS-HCL PH 7.2
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.623 α = 90 b = 121.623 β = 90 c = 47.875 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 CCD 2003-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.7 25 99.9 0.044 22.1 4.9 44644
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 1.7 1.76 98.6 0.278 4.7 3.7
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 PDB ENTRY 1H1W 1.7 25 42657 661 96.9 0.174 0.173 0.1803 0.202 0.2156 RANDOM 17.71
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] 0.57 0.28 0.57 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.943 r_scangle_it 4.225 r_scbond_it 2.653 r_mcangle_it 1.826 r_angle_refined_deg 1.65 r_mcbond_it 1.035 r_angle_other_deg 0.877 r_symmetry_vdw_other 0.257 r_nbd_other 0.244 r_symmetry_vdw_refined 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.943 r_scangle_it 4.225 r_scbond_it 2.653 r_mcangle_it 1.826 r_angle_refined_deg 1.65 r_mcbond_it 1.035 r_angle_other_deg 0.877 r_symmetry_vdw_other 0.257 r_nbd_other 0.244 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.116 r_nbtor_other 0.081 r_bond_refined_d 0.015 r_gen_planes_other 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2249 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing