9TNS | pdb_00009tns

GABA-A receptor a3b3g2 + GABA-PRE + a3NB83

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.126
f_angle_d	0.557
f_chiral_restr	0.082
f_plane_restr	0.004
f_bond_d	0.003

Sample
alpha3-beta3-gamma2 GABA-A receptor in complex with GABA and nanobody a3NB83
Sample Components
GABA-A receptor
Nanobody a3NB83

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Number of Particles	81900
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1
Point Symmetry	C1
Point Symmetry	C1
Point Symmetry	C1
Point Symmetry	C1
Point Symmetry	C1
Point Symmetry	C1
Point Symmetry	C1
Point Symmetry	C1
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)	FEI FALCON IV (4k x 4k)	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	50.47	50.47	50.47

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	ARP/wARP	1.0.9
CTF CORRECTION	ARP/wARP	1.0.9
MODEL FITTING	UCSF Chimera	1.8
MODEL REFINEMENT	PHENIX	1.20.1_4487
INITIAL EULER ASSIGNMENT	cryoSPARC	4.4.1 to 4.7.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.1 to 4.7.1
RECONSTRUCTION	cryoSPARC	4.4.1 to 4.7.1
PARTICLE SELECTION	ARP/wARP	1.0.9
CTF CORRECTION	ARP/wARP	1.0.9
RECONSTRUCTION	cryoSPARC	4.4.1 to 4.7.1
PARTICLE SELECTION	cryoSPARC	4.4.1 to 4.7.1
PARTICLE SELECTION	cryoSPARC
RECONSTRUCTION	cryoSPARC
PARTICLE SELECTION	cryoSPARC
RECONSTRUCTION	cryoSPARC
PARTICLE SELECTION	ARP/wARP	1.0.9
CTF CORRECTION	ARP/wARP	1.0.9
INITIAL EULER ASSIGNMENT	cryoSPARC	4.4.1 to 4.7.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.1 to 4.7.1
RECONSTRUCTION	cryoSPARC	4.4.1 to 4.7.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		314781		314781	314781
PHASE FLIPPING AND AMPLITUDE CORRECTION		314781		314781	314781
PHASE FLIPPING AND AMPLITUDE CORRECTION
PHASE FLIPPING AND AMPLITUDE CORRECTION
PHASE FLIPPING AND AMPLITUDE CORRECTION		314781		314781	314781

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.