1OKY

Structure of human PDK1 kinase domain in complex with staurosporine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H1WPDB ENTRY 1H1W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52.1 M AMMONIUM SULPHATE 0.1 M TRIS-HCL PH 7.2
Crystal Properties
Matthews coefficientSolvent content
358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.172α = 90
b = 124.172β = 90
c = 47.314γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2002-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.32595.80.0967.51.81801828.1
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)
12.32.3895.80.5051.81.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1H1W2.324.671801275395.70.2190.2190.255RANDOM33.1
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]
4.522.014.52-9.05
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22
c_scangle_it3.22
c_mcangle_it2.58
c_scbond_it2.15
c_angle_deg1.7
c_mcbond_it1.54
c_improper_angle_d0.77
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22
c_scangle_it3.22
c_mcangle_it2.58
c_scbond_it2.15
c_angle_deg1.7
c_mcbond_it1.54
c_improper_angle_d0.77
c_bond_d0.007
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 Atoms2288
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms78

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing