2WXK

The crystal structure of the murine class IA PI 3-kinase p110delta in complex with INK666.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RD0PDB ENTRY 2RD0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.820% (V/V) GLYCEROL, 10% (W/V) PEG 4K, 30 MM NANO3, 30 MM NA2HPO4, 30 MM (NH4)2SO4, 100 MM IMIDAZOLE PH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.4149

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.362α = 90
b = 143.669β = 90
c = 223.121γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.974.331000.1718.1412.0823471-3.771.323
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)
12.92.921000.742.412.36

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 2RD02.968.362270073399.990.215310.213050.28719RANDOM23.007
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]
1.88-1.970.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.818
r_dihedral_angle_4_deg22.929
r_dihedral_angle_3_deg21.415
r_angle_other_deg7.48
r_dihedral_angle_1_deg6.771
r_scangle_it3.002
r_scbond_it1.811
r_angle_refined_deg1.693
r_mcangle_it1.175
r_mcbond_it0.585
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.818
r_dihedral_angle_4_deg22.929
r_dihedral_angle_3_deg21.415
r_angle_other_deg7.48
r_dihedral_angle_1_deg6.771
r_scangle_it3.002
r_scbond_it1.811
r_angle_refined_deg1.693
r_mcangle_it1.175
r_mcbond_it0.585
r_nbd_other0.337
r_nbtor_refined0.329
r_symmetry_vdw_refined0.312
r_symmetry_hbond_refined0.267
r_nbd_refined0.264
r_xyhbond_nbd_refined0.185
r_chiral_restr0.109
r_bond_other_d0.107
r_nbtor_other0.063
r_bond_refined_d0.015
r_gen_planes_other0.008
r_gen_planes_refined0.007
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 Atoms6739
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing