5XGJ | pdb_00005xgj

Crystal structure of PI3K complex with an inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.150.15M Lithium sulfate, 0.1M Tris-HCl pH 8.5, 28%(W/V) PEG2000MME
Crystal Properties
Matthews coefficientSolvent content
2.448.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.877α = 90
b = 136.368β = 90
c = 149.028γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSDECTRIS PILATUS3 S 6M2016-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U11SSRFBL19U1

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
12.9750990.15710.64629684
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.983.0998.22.255.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.975028231140098.580.233410.23110.230.279170.28RANDOM98.564
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]
1.3-5.44.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.101
r_dihedral_angle_3_deg13.047
r_dihedral_angle_4_deg12.706
r_dihedral_angle_1_deg5.171
r_long_range_B_refined4.729
r_long_range_B_other4.729
r_mcangle_it2.905
r_mcangle_other2.904
r_scangle_other2.31
r_mcbond_it1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.101
r_dihedral_angle_3_deg13.047
r_dihedral_angle_4_deg12.706
r_dihedral_angle_1_deg5.171
r_long_range_B_refined4.729
r_long_range_B_other4.729
r_mcangle_it2.905
r_mcangle_other2.904
r_scangle_other2.31
r_mcbond_it1.64
r_mcbond_other1.64
r_scbond_it1.259
r_scbond_other1.258
r_angle_refined_deg0.96
r_angle_other_deg0.814
r_chiral_restr0.053
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10371
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing