6TKO

Phosphorylated turkey beta1 adrenoceptor with bound agonist formoterol coupled to arrestin-2 in lipid nanodisc.


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6IBL 
experimental modelPDB 4JQI 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.3097
f_angle_d0.4114
f_chiral_restr0.0392
f_plane_restr0.0017
f_bond_d0.0015
Sample
Formoterol-bound beta1-adrenoceptor coupled to beta-arrestin-1 stabilised by Fab30.
Sample Components
Beta-1 adrenergic receptor
Beta-arrestin-1
Fab30 heavy chain
Fab30 light chain
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlotted for 2-3 seconds before plunging. Liquid ethane maintained at 92.15 K.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles403991
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsHalf maps were locally filtered between refinement iterations using SIDESPLITTER, an adaptation of the LAFTER algorithm that maintains gold-standard s ...Half maps were locally filtered between refinement iterations using SIDESPLITTER, an adaptation of the LAFTER algorithm that maintains gold-standard separation between the two half maps.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6IBL, 4JQI, 4JQI, 4JQI, 4JQI)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetCorrelation coefficient
Overall B Value80.6
Fitting Procedure
DetailsInitial placement was done manually in Coot, followed by rigid-body refinement in PHENIX and jelly-body refinement in REFMAC5. Manual remodeling was p ...Initial placement was done manually in Coot, followed by rigid-body refinement in PHENIX and jelly-body refinement in REFMAC5. Manual remodeling was performed in Coot and iterated with real space refinement in PHENIX. Chemical restraints for formoterol were calculated in eLBOW using AM1 optimisation.
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)5045
Imaging Experiment12
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOSFEI TITAN KRIOS
Minimum Defocus (nm)12001200
Maximum Defocus (nm)30003000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.72.7
Imaging ModeBRIGHT FIELDBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDERFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000130000
Calibrated Magnification
SourceFIELD EMISSION GUNFIELD EMISSION GUN
Acceleration Voltage (kV)300300
Imaging DetailsData collected with a stage-tilt of 30deg; two non-overlapping exposures per hole and multi-hole image-shift data acquisition strategies (3x3 holes per stage shift).Data collected with a stage-tilt of 30deg; two non-overlapping exposures per hole using image-shift.
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM3.8.0 beta
CTF CORRECTIONWarp1.0.6
CTF CORRECTIONRELION3.1
MODEL FITTINGCoot0.8.9.2
IMAGE ACQUISITIONEPU2.3.0.79
INITIAL EULER ASSIGNMENTRELION3.0.7
FINAL EULER ASSIGNMENTRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.17.1-3660
MODEL REFINEMENTREFMAC5
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION10161197