8GC4

Domoate-bound GluK2 kainate receptor in partially-open conformation 3


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.7785
f_angle_d0.8562
f_chiral_restr0.0639
f_plane_restr0.0063
f_bond_d0.0062
Sample
Homotetrameric GluK2 bound with DOQ state 4
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles73190
Reported Resolution (Å)3.93
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target0.85
Overall B Value70
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeOTHER
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf1.06
MODEL FITTINGUCSF ChimeraX1.4
MODEL REFINEMENTPHENIX1.20.1.4487
INITIAL EULER ASSIGNMENTRELION4.0
FINAL EULER ASSIGNMENTRELION4.0
CLASSIFICATIONRELION4.0
RECONSTRUCTIONRELION4.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2481151Initially picked particles that are later classified in several rounds of 2D and 3D classifications. The number of final classes for this dataset is 4 of which this state represents "class 2" and contains 100389 as the final number of particles.