6PKV

Cryo-EM structure of the zebrafish TRPM2 channel in the apo conformation, processed with C4 symmetry


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6D73 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.926
f_angle_d0.833
f_chiral_restr0.05
f_plane_restr0.007
f_bond_d0.005
Sample
Transient receptor potential cation channel subfamily M member 2
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles58005
Reported Resolution (Å)4.3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsNo symmetry (C1) was imposed during reconstructions and classifications. C4 symmetry was imposed during the final 3D auto-refinement.
Refinement Type
Symmetry TypePOINT
Point SymmetryC4
Map-Model Fitting and Refinement
Id1 (6D73)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value150
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)750
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification22500
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.0
IMAGE ACQUISITIONLatitude
CTF CORRECTIONRELION3.0
CTF CORRECTIONGctf1.18
MODEL FITTINGCoot0.8.8
MODEL REFINEMENTPHENIX1.12-2829
INITIAL EULER ASSIGNMENTRELION3.0
FINAL EULER ASSIGNMENTRELION3.0
RECONSTRUCTIONRELION3.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION301199