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 12AI | pdb_000012ai

Structure of mammalian Type 2 Inositol 1,4,5-trisphosphate receptor (IP3R2) in the presence of IP3/Ca2+/ATP


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Inositol 1,4,5-trisphosphate receptor type 2
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles151391
Reported Resolution (Å)3.64
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC4
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Targetfit to map
Overall B Value135.9
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)GATAN K2 SUMMIT (4k x 4k)GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)1.431.661.43
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification46100
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.7
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC4.7
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX
INITIAL EULER ASSIGNMENTcryoSPARC4.7
FINAL EULER ASSIGNMENTcryoSPARC4.7
CLASSIFICATIONcryoSPARC4.7
RECONSTRUCTIONcryoSPARC4.7
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION6026377