2PE1

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) {2-Oxo-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-2,3-dihydro-1H-indol-5-yl}-urea {BX-517} COMPLEX


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5298AMMONIUM SULFATE, TRIS, EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
3.262

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.234α = 90
b = 125.234β = 90
c = 47.696γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.142099.50.1155.893.36238474.58.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.142.27990.37691.73.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIER PLUS REFINEMENTTHROUGHOUT2.1419.9122383123028903960.2240.2220.282RANDOM17.7
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]
-0.111.24-0.110.22
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21
c_scangle_it3.94
c_scbond_it2.8
c_mcangle_it2.71
c_mcbond_it1.86
c_angle_deg0.9
c_improper_angle_d0.71
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21
c_scangle_it3.94
c_scbond_it2.8
c_mcangle_it2.71
c_mcbond_it1.86
c_angle_deg0.9
c_improper_angle_d0.71
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2255
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms55

Software

Software
Software NamePurpose
CNXrefinement
XTALVIEWrefinement
X-GENdata reduction
X-GENdata scaling
CNXphasing