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 8T9L | pdb_00008t9l

Pom34-Pom152 membrane attachment site yeast NPC


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Nuclear Pore Complex
Sample Components
Pom34-Pom152 Inner ring anchor complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles208392
Reported Resolution (Å)7
Resolution MethodFSC 0.143 CUT-OFF
Other Detailslocal resolution for the TMDs 10.5-12 Angstroms
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Targetcross correlation
Overall B Value
Fitting Procedure
DetailsRigid body docking and manual building with Chimera and coot
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification37651
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsPreliminary grid screening done manually with individual images of low magnification montages of candidate meshes.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONGautomatchGautomatch_v0.56_sm61_cu7.5
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONGctfGctf-v0.1.06_sm_20_cu7.5_x86_64
CTF CORRECTIONRELION3.0.7
MODEL FITTINGUCSF Chimera1.14
INITIAL EULER ASSIGNMENTRELION3.0.7
FINAL EULER ASSIGNMENTRELION3.0.7
CLASSIFICATIONRELION3.0.7
RECONSTRUCTIONRELION3.0.7
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF correction applied in RELION during the alignment and reconstruction26049