3APD

Crystal structure of human PI3K-gamma in complex with CH5108134


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E8YPDB ENTRY 1E8Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229320% PEG3350, 0.2M (NH4)2SO4, 0.1M Tris-HCl, streak seeding, pH 7.2, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.95α = 90
b = 67.46β = 95.68
c = 106.28γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315mirrors2006-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.54860.95399.70.0460.04617.73.73308433084
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)
2.552.6199.410.683.762419

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 1E8Y2.5560.953308416751000.25320.24980.3162RANDOM59.4382
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]
-0.881.22.6-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.638
r_dihedral_angle_3_deg16.247
r_dihedral_angle_4_deg13.451
r_dihedral_angle_1_deg6.21
r_scangle_it6.181
r_scbond_it4.191
r_mcangle_it3.074
r_mcbond_it1.74
r_angle_refined_deg1.08
r_angle_other_deg0.801
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.638
r_dihedral_angle_3_deg16.247
r_dihedral_angle_4_deg13.451
r_dihedral_angle_1_deg6.21
r_scangle_it6.181
r_scbond_it4.191
r_mcangle_it3.074
r_mcbond_it1.74
r_angle_refined_deg1.08
r_angle_other_deg0.801
r_mcbond_other0.355
r_chiral_restr0.06
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6562
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms38

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
MOLREPphasing