7QN9 | pdb_00007qn9

Cryo-EM structure of human full-length extrasynaptic alpha4beta3delta GABA(A)R in complex with GABA, histamine and nanobody Nb25 in a pre-open/closed state

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.321
f_angle_d	0.578
f_chiral_restr	0.042
f_plane_restr	0.005
f_bond_d	0.002

Sample
Human full-length extrasynaptic alpha4beta3delta GABA(A)R in complex with histamine and nanobody Nb25

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	92694
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

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

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	2100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.1.13
MODEL FITTING	Coot
MODEL REFINEMENT	REFMAC	5
MODEL REFINEMENT	PHENIX	1.19.2
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1

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