9QPW | pdb_00009qpw

GluA4, resting state, structure of TMD/LBD

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UA8
experimental model	Other

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.112
f_angle_d	0.585
f_chiral_restr	0.041
f_plane_restr	0.008
f_bond_d	0.002

Sample
GluA4, resting state, structure of TMD/LBD

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	59714
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (3UA8)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	The TMD region of GluA4:G2restI and four GluA2 LBD monomers (PDB 3UA8) were rigid body fitted in Chimera. Manual model building, refinement and validation were performed using Refmac 5 Servalcat followed by model building in Coot and Real Space Refinement in Phenix.

Data Acquisition
Detector Type	GATAN K3 BIOCONTINUUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	4.1
CTF CORRECTION	RELION	4.1
MODEL FITTING	UCSF Chimera	1.18
MODEL REFINEMENT	PHENIX	1.19.2_4158
CLASSIFICATION	RELION	4.1
RECONSTRUCTION	RELION	4.1

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