2XCK

Crystal structure of PDK1 in complex with a pyrazoloquinazoline inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12.0 M AMMONIUM SULFATE, 0.1 M TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.957.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.115α = 90
b = 123.115β = 90
c = 47.24γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.3301000.18.16.518571
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)
12.32.41000.516.5

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 1H1W2.3301760494899.950.194950.192610.23969RANDOM28.563
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]
0.990.50.99-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.223
r_dihedral_angle_4_deg19.05
r_dihedral_angle_3_deg16.823
r_dihedral_angle_1_deg7.161
r_scangle_it4.283
r_scbond_it2.842
r_mcangle_it1.989
r_angle_refined_deg1.701
r_mcbond_it1.129
r_symmetry_vdw_refined0.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.223
r_dihedral_angle_4_deg19.05
r_dihedral_angle_3_deg16.823
r_dihedral_angle_1_deg7.161
r_scangle_it4.283
r_scbond_it2.842
r_mcangle_it1.989
r_angle_refined_deg1.701
r_mcbond_it1.129
r_symmetry_vdw_refined0.513
r_nbtor_refined0.312
r_nbd_refined0.225
r_symmetry_hbond_refined0.206
r_xyhbond_nbd_refined0.191
r_chiral_restr0.117
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms2251
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling