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Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to Inositol (1,3,4,5)-tetrakisphosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.08 M MAGNESIUM ACETATE, 0.05M SODIUM CACODYLATE PH 6.5, 30 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.1 0.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.399 α = 90 b = 58.922 β = 101.48 c = 36.578 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 CCD ADSC CCD 2003-05-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.861,1.040 ESRF BM14
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 1.5 25 98.6 0.08 17.7 3.7 23341 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 1.5 1.58 99.5 0.44 3.2 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.5 25 22641 617 98.2 0.147 0.145 0.1568 0.2 0.2057 RANDOM 13.01
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 -0.44 -0.64 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.717 r_scangle_it 4.62 r_scbond_it 3.225 r_mcangle_it 2.383 r_angle_refined_deg 1.785 r_mcbond_it 1.657 r_angle_other_deg 0.958 r_symmetry_vdw_other 0.273 r_nbd_other 0.264 r_nbd_refined 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.717 r_scangle_it 4.62 r_scbond_it 3.225 r_mcangle_it 2.383 r_angle_refined_deg 1.785 r_mcbond_it 1.657 r_angle_other_deg 0.958 r_symmetry_vdw_other 0.273 r_nbd_other 0.264 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.162 r_symmetry_vdw_refined 0.148 r_chiral_restr 0.131 r_nbtor_other 0.091 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.009 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 1195 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling RSPS phasing MLPHARE phasing DM phasing