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Structure of GluN1a-GluN2D NMDA receptor in complex with agonists glycine and glutamate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WI1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.911 f_angle_d 0.586 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.004
Sample NMDA receptor with NMDA 1 incorperated with NMDA 2D
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot for 3 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 232194 Reported Resolution (Å) 3.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (6WI1) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Correlation coefficient Overall B Value 220 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 Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION Gctf MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION 3.1.1 INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.20.1-4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 505204