5T8F | pdb_00005t8f

p110delta/p85alpha with taselisib (GDC-0032)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DXU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG
Crystal Properties
Matthews coefficientSolvent content
2.6453.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.096α = 90
b = 108.604β = 90
c = 142.223γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.99988SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.9186.3799.90.06320.48.131603
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)
12.913.1699.90.0445.68.1

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 REPLACEMENTTHROUGHOUT5DXU2.9186.373093666799.90.2430.2420.240.3040.3RANDOM77.62
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]
2.654.72-7.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.333
r_dihedral_angle_4_deg14.4
r_dihedral_angle_3_deg13.109
r_dihedral_angle_1_deg5.205
r_angle_other_deg2.591
r_long_range_B_refined1.278
r_long_range_B_other1.278
r_angle_refined_deg1.121
r_scangle_other0.921
r_mcangle_it0.867
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.333
r_dihedral_angle_4_deg14.4
r_dihedral_angle_3_deg13.109
r_dihedral_angle_1_deg5.205
r_angle_other_deg2.591
r_long_range_B_refined1.278
r_long_range_B_other1.278
r_angle_refined_deg1.121
r_scangle_other0.921
r_mcangle_it0.867
r_mcangle_other0.867
r_scbond_it0.58
r_scbond_other0.58
r_mcbond_it0.554
r_mcbond_other0.553
r_chiral_restr0.058
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms8502
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing