8Y1V | pdb_00008y1v

Structure of GluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7YFF

Sample
N-methyl-D-aspartate receptors

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details
Embedding Material	nanodisc
Embedding Details	The protein sample of N-methyl-D-aspartate receptors was reconstructed into artificial nanodiscs composed by soya bean lecithin and MSP1E3D1 protein.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	82019
Reported Resolution (Å)	4.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (7YFF)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	DIRECT ELECTRON DE-10 (5k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	2500
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	3.1.1
IMAGE ACQUISITION	SerialEM	3.7.11
CTF CORRECTION	RELION	3.1.1
INITIAL EULER ASSIGNMENT	RELION	3.1.1
FINAL EULER ASSIGNMENT	RELION	3.1.1
CLASSIFICATION	RELION	3.1.1
RECONSTRUCTION	RELION	3.1.1
MODEL REFINEMENT	PHENIX	1.20.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		605501