2PE0

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 5-Hydroxy-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-1,3-dihydro-indol-2-one 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 = 123.951α = 90
b = 123.951β = 90
c = 47.217γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray96.2CCDADSC QUANTUM 3152003-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.2ALS8.2.2

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
12.352097.40.10447.442.6217172-323.4
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)
12.352.49990.39741.612.7

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 REFINEMENTTHROUGHOUT2.3519.712171511478861383.90.2020.20.24RANDOM25.9
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]
-0.648.68-0.641.28
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.4
c_scangle_it4.48
c_scbond_it3.08
c_mcangle_it2.9
c_mcbond_it1.86
c_angle_deg0.9
c_improper_angle_d0.62
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.4
c_scangle_it4.48
c_scbond_it3.08
c_mcangle_it2.9
c_mcbond_it1.86
c_angle_deg0.9
c_improper_angle_d0.62
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 Atoms49
Heterogen Atoms46

Software

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