2V4L

complex of human phosphoinositide 3-kinase catalytic subunit gamma (p110 gamma) with PIK-284


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CHXPDB ENTRY 2CHX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5RESERVOIR: 16-17% PEG 4000, 250 MM (NH4)2SO4 AND 100MM TRIS PH 7.5 PROTEIN: 4 MG/ML IN A BUFFER CONTAINING 0.5 MM (NH4)2SO4, 20 MM TRIS PH 7.2, 1% ETHYLENE GLYCOL, 0.02% CHAPS AND 5 MM DTT DROPS WERE 1MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
2.4950

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.353α = 90
b = 68.44β = 95.33
c = 106.619γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTORROIDAL MIRROR2005-01-05MSINGLE 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
12.554.499.70.05103.733672-3.7
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)
12.52.6497.40.321.73.8

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 2CHX2.554.3933672144097.20.250.2480.296RANDOM21.03
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]
-1.331.062.93-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.157
r_scangle_it2.349
r_angle_refined_deg1.457
r_scbond_it1.447
r_mcangle_it0.934
r_angle_other_deg0.867
r_mcbond_it0.512
r_symmetry_hbond_refined0.489
r_symmetry_vdw_refined0.426
r_symmetry_vdw_other0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.157
r_scangle_it2.349
r_angle_refined_deg1.457
r_scbond_it1.447
r_mcangle_it0.934
r_angle_other_deg0.867
r_mcbond_it0.512
r_symmetry_hbond_refined0.489
r_symmetry_vdw_refined0.426
r_symmetry_vdw_other0.303
r_nbd_other0.226
r_nbd_refined0.22
r_xyhbond_nbd_refined0.198
r_nbtor_other0.088
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms6850
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing