6MM9

Diheteromeric NMDA receptor GluN1/GluN2A in the '1-Knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1

ELECTRON MICROSCOPY

Sample
Diheteromeric NMDA receptor GluN1/GluN2A in the '1-Knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Sample was blotted for 3 seconds at blot force 1.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	94934
Reported Resolution (Å)	5.97
Resolution Method	FSC 0.143 CUT-OFF
Other Details	After additional rounds of refinement/further classification, the final particle set for each class was exported to cisTEM (Grant et al., 2018). Furth ...	After additional rounds of refinement/further classification, the final particle set for each class was exported to cisTEM (Grant et al., 2018). Further refinement in cisTEM was carried out by masking out the micelle, while keeping the TMD of the receptors for alignment. The area outside of the mask was filtered to 20 A and down-weighted for alignment. For a more accurate and conservative resolution estimate, the cisTEM-generated half-maps were used in RELION to generate the Fourier Shell Coefficient (FSC) curve, and the resolution was calculated at FSC = 0.143 (Scheres and Chen, 2012).
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4PE5, 5TQ0, 5I57, 5UOW)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 BASE (4k x 4k)
Electron Dose (electrons/Å**2)	52

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

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf
MODEL FITTING	UCSF Chimera
MODEL FITTING	PyMOL
INITIAL EULER ASSIGNMENT	RELION
FINAL EULER ASSIGNMENT	RELION
CLASSIFICATION	RELION
RECONSTRUCTION	cisTEM
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

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

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 R01GM133198.