1W1G

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to DiC4-phosphatidylinositol (3,4,5)-trisphosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.225 % PEG 4000, 0.1 M SODIUM ACETATE [PH 4.2], 0.3 M AMMONIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.10.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.264α = 90
b = 58.943β = 102.33
c = 36.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS 4MIRRORS2003-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.453099.70.058.82.9258102
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.51000.372.52.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDK1PH INSP4 MODEL1.45252524154599.70.1830.1820.236RANDOM26.94
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]
1.580.06-0.83-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.693
r_dihedral_angle_4_deg17.708
r_dihedral_angle_3_deg13.71
r_dihedral_angle_1_deg6.622
r_scangle_it4.923
r_scbond_it3.614
r_mcangle_it2.305
r_mcbond_it1.727
r_angle_refined_deg1.703
r_angle_other_deg0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.693
r_dihedral_angle_4_deg17.708
r_dihedral_angle_3_deg13.71
r_dihedral_angle_1_deg6.622
r_scangle_it4.923
r_scbond_it3.614
r_mcangle_it2.305
r_mcbond_it1.727
r_angle_refined_deg1.703
r_angle_other_deg0.86
r_mcbond_other0.745
r_symmetry_hbond_refined0.274
r_symmetry_vdw_other0.24
r_nbd_refined0.221
r_nbd_other0.2
r_nbtor_refined0.181
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.159
r_chiral_restr0.109
r_nbtor_other0.107
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1194
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing