1UU7

Structure of human PDK1 kinase domain in complex with BIM-2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52.3 M AMMONIUM SULPHATE 0.1 M TRIS-HCL PH 8.25
Crystal Properties
Matthews coefficientSolvent content
358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.947α = 90
b = 121.947β = 90
c = 48.071γ = 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
11.93099.90.076103.744644
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)
11.91.9799.80.5922.73.5

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 1H1W1.9303179466999.80.2350.2340.279RANDOM18.42
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]
0.460.230.46-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.434
r_scangle_it3.539
r_scbond_it2.268
r_angle_refined_deg1.602
r_mcangle_it1.473
r_angle_other_deg0.871
r_mcbond_it0.826
r_symmetry_hbond_refined0.263
r_nbd_other0.243
r_symmetry_vdw_refined0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.434
r_scangle_it3.539
r_scbond_it2.268
r_angle_refined_deg1.602
r_mcangle_it1.473
r_angle_other_deg0.871
r_mcbond_it0.826
r_symmetry_hbond_refined0.263
r_nbd_other0.243
r_symmetry_vdw_refined0.221
r_symmetry_vdw_other0.217
r_nbd_refined0.211
r_xyhbond_nbd_refined0.197
r_chiral_restr0.094
r_nbtor_other0.087
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.005
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 Atoms2297
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing