2WXF

The crystal structure of the murine class IA PI 3-kinase p110delta in complex with PIK-39.


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
2.4549.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.42α = 90
b = 65.01β = 103.53
c = 116.69γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-07-20MSINGLE 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
11.938.9598.50.0716.316.7980511-3.731.476
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)
11.91.9296.30.841.786.77

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 2RD01.938.9578074243698.420.210520.20960.23986RANDOM19.363
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]
0.570.130.57-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.981
r_dihedral_angle_4_deg20.848
r_dihedral_angle_3_deg15.926
r_dihedral_angle_1_deg5.189
r_scangle_it3.206
r_scbond_it2.046
r_angle_refined_deg1.253
r_mcangle_it1.229
r_mcbond_it0.66
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.981
r_dihedral_angle_4_deg20.848
r_dihedral_angle_3_deg15.926
r_dihedral_angle_1_deg5.189
r_scangle_it3.206
r_scbond_it2.046
r_angle_refined_deg1.253
r_mcangle_it1.229
r_mcbond_it0.66
r_nbtor_refined0.302
r_symmetry_vdw_refined0.238
r_nbd_refined0.201
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.095
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms6633
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing