8SOD

Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 1


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelSwissModel1e8x 
in silico modelAlphaFold 
experimental modelPDB 6C2Y 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.236
f_angle_d0.581
f_chiral_restr0.041
f_plane_restr0.009
f_bond_d0.003
Sample
PI3K-gamma-ADP bound with two Gbetagamma subunits in State 1
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot force 2
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles167954
Reported Resolution (Å)3.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (6C2Y, 6C2Y)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Targetcorrelation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)55
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.1
IMAGE ACQUISITIONLeginon
CTF CORRECTIONcryoSPARC3.3.1
MODEL FITTINGUCSF Chimera1.15
MODEL FITTINGCoot9.6
MODEL REFINEMENTCoot9.6
MODEL REFINEMENTPHENIX1.20-4459
INITIAL EULER ASSIGNMENTcryoSPARC3.3.1
FINAL EULER ASSIGNMENTcryoSPARC3.3.1
CLASSIFICATIONcryoSPARC3.3.1
RECONSTRUCTIONcryoSPARC3.3.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION