2WXH | pdb_00002wxh

The crystal structure of the murine class IA PI 3-kinase p110delta in complex with SW14.


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
2.4750.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.87α = 90
b = 65.01β = 103.58
c = 117.08γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-07-05MSINGLE 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
11.943.1199.40.0712.663.5981877-3.729.603
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)
11.91.9299.60.641.633.59

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2RD01.938.0479331248099.180.218240.21740.280.245040.3RANDOM7.734
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]
0.170.150.31-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.405
r_dihedral_angle_4_deg19.981
r_dihedral_angle_3_deg15.748
r_dihedral_angle_1_deg5.176
r_scangle_it2.82
r_scbond_it1.738
r_angle_refined_deg1.262
r_mcangle_it0.898
r_mcbond_it0.429
r_nbtor_refined0.306
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6633
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing