6TKO | pdb_00006tko

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

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IBL
experimental model	PDB	4JQI

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.3097
f_angle_d	0.4114
f_chiral_restr	0.0392
f_plane_restr	0.0017
f_bond_d	0.0015

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 State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blotted for 2-3 seconds before plunging. Liquid ethane maintained at 92.15 K.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	403991
Reported Resolution (Å)	3.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Half 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 Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6IBL, 4JQI, 4JQI, 4JQI, 4JQI)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	Correlation coefficient
Overall B Value	80.6
Fitting Procedure
Details	Initial 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 Type	GATAN K2 QUANTUM (4k x 4k)	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	50	45

Imaging Experiment	1	2
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS	FEI TITAN KRIOS
Minimum Defocus (nm)	1200	1200
Maximum Defocus (nm)	3000	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7	2.7
Imaging Mode	BRIGHT FIELD	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	105000	130000
Calibrated Magnification
Source	FIELD EMISSION GUN	FIELD EMISSION GUN
Acceleration Voltage (kV)	300	300
Imaging Details	Data 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
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM	3.8.0 beta
CTF CORRECTION	Warp	1.0.6
CTF CORRECTION	RELION	3.1
MODEL FITTING	Coot	0.8.9.2
IMAGE ACQUISITION	EPU	2.3.0.79
INITIAL EULER ASSIGNMENT	RELION	3.0.7
FINAL EULER ASSIGNMENT	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.17.1-3660
MODEL REFINEMENT	REFMAC	5

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		10161197

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.