7KAQ

Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with Sec62, conformation 2 (C2)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.774
f_angle_d0.463
f_chiral_restr0.036
f_plane_restr0.003
f_bond_d0.002
Sample
Endoplasmic reticulum protein-transport machinery Sec complex from yeast with Sec61 pore ring mutated.
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles16679
Reported Resolution (Å)4
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsNon-uniform refinement from cryoSPARC
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)48.8
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification43478
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONWarp1.0.7
IMAGE ACQUISITIONSerialEM3.7
CTF CORRECTIONWarp1.0.7
CTF CORRECTIONcryoSPARC2.12
INITIAL EULER ASSIGNMENTcryoSPARC2.12
FINAL EULER ASSIGNMENTcryoSPARC2.12
RECONSTRUCTIONcryoSPARC2.12
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION195915autopicked particles