2WXP

The crystal structure of the murine class IA PI 3-kinase p110delta in complex with GDC-0941.


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
2.4449.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.72α = 90
b = 64.04β = 103.62
c = 117.74γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.366.6799.60.0711.473.5445958-3.748.641
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)
12.32.321000.621.763.58

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 2RD02.358.1244533142299.50.221750.219910.27926RANDOM23.471
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]
-0.17-0.211.64-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.752
r_dihedral_angle_4_deg22.402
r_dihedral_angle_3_deg17.961
r_dihedral_angle_1_deg5.818
r_scangle_it3.103
r_scbond_it2.046
r_angle_refined_deg1.44
r_mcangle_it1.184
r_mcbond_it0.637
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.752
r_dihedral_angle_4_deg22.402
r_dihedral_angle_3_deg17.961
r_dihedral_angle_1_deg5.818
r_scangle_it3.103
r_scbond_it2.046
r_angle_refined_deg1.44
r_mcangle_it1.184
r_mcbond_it0.637
r_nbtor_refined0.307
r_symmetry_vdw_refined0.286
r_nbd_refined0.217
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.126
r_chiral_restr0.094
r_bond_refined_d0.014
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 Atoms43
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing