1UU3

Structure of human PDK1 kinase domain in complex with LY333531


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 = 121.623α = 90
b = 121.623β = 90
c = 47.875γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.72599.90.04422.14.944644
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)
11.71.7698.60.2784.73.7

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 1H1W1.7254265766196.90.1740.1730.202RANDOM17.71
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]
0.570.280.57-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.943
r_scangle_it4.225
r_scbond_it2.653
r_mcangle_it1.826
r_angle_refined_deg1.65
r_mcbond_it1.035
r_angle_other_deg0.877
r_symmetry_vdw_other0.257
r_nbd_other0.244
r_symmetry_vdw_refined0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.943
r_scangle_it4.225
r_scbond_it2.653
r_mcangle_it1.826
r_angle_refined_deg1.65
r_mcbond_it1.035
r_angle_other_deg0.877
r_symmetry_vdw_other0.257
r_nbd_other0.244
r_symmetry_vdw_refined0.223
r_nbd_refined0.22
r_symmetry_hbond_refined0.155
r_xyhbond_nbd_refined0.142
r_chiral_restr0.116
r_nbtor_other0.081
r_bond_refined_d0.015
r_gen_planes_other0.015
r_gen_planes_refined0.012
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 Atoms2249
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing