☰ Navigation Tabs
Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to DiC4-phosphatidylinositol (3,4,5)-trisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other PDK1PH INSP4 MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 25 % PEG 4000, 0.1 M SODIUM ACETATE [PH 4.2], 0.3 M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.1 0.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.264 α = 90 b = 58.943 β = 102.33 c = 36.44 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS 4 MIRRORS 2003-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.45 30 99.7 0.05 8.8 2.9 25810 2
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 1.45 1.5 100 0.37 2.5 2.7
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 PDK1PH INSP4 MODEL 1.45 25 25241 545 99.7 0.183 0.182 0.2002 0.236 0.2514 RANDOM 26.94
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] 1.58 0.06 -0.83 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_4_deg 17.708 r_dihedral_angle_3_deg 13.71 r_dihedral_angle_1_deg 6.622 r_scangle_it 4.923 r_scbond_it 3.614 r_mcangle_it 2.305 r_mcbond_it 1.727 r_angle_refined_deg 1.703 r_angle_other_deg 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_4_deg 17.708 r_dihedral_angle_3_deg 13.71 r_dihedral_angle_1_deg 6.622 r_scangle_it 4.923 r_scbond_it 3.614 r_mcangle_it 2.305 r_mcbond_it 1.727 r_angle_refined_deg 1.703 r_angle_other_deg 0.86 r_mcbond_other 0.745 r_symmetry_hbond_refined 0.274 r_symmetry_vdw_other 0.24 r_nbd_refined 0.221 r_nbd_other 0.2 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.109 r_nbtor_other 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_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 1194 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling CNS phasing