1W1D

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to Inositol (1,3,4,5)-tetrakisphosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.08 M MAGNESIUM ACETATE, 0.05M SODIUM CACODYLATE PH 6.5, 30 % PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.10.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.399α = 90
b = 58.922β = 101.48
c = 36.578γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-05-05MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.861,1.040ESRFBM14

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
11.52598.60.0817.73.7233412
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)
11.51.5899.50.443.23.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.5252264161798.20.1470.1450.2RANDOM13.01
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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.717
r_scangle_it4.62
r_scbond_it3.225
r_mcangle_it2.383
r_angle_refined_deg1.785
r_mcbond_it1.657
r_angle_other_deg0.958
r_symmetry_vdw_other0.273
r_nbd_other0.264
r_nbd_refined0.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.717
r_scangle_it4.62
r_scbond_it3.225
r_mcangle_it2.383
r_angle_refined_deg1.785
r_mcbond_it1.657
r_angle_other_deg0.958
r_symmetry_vdw_other0.273
r_nbd_other0.264
r_nbd_refined0.217
r_symmetry_hbond_refined0.202
r_xyhbond_nbd_refined0.162
r_symmetry_vdw_refined0.148
r_chiral_restr0.131
r_nbtor_other0.091
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.009
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms1195
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RSPSphasing
MLPHAREphasing
DMphasing