6EF0

Yeast 26S proteasome bound to ubiquitinated substrate (1D* motor state)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MPC 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.73
f_angle_d0.98
f_chiral_restr0.056
f_bond_d0.008
f_plane_restr0.005
Sample
Substrate-engaged 26S proteasome in the 1D* state
Sample Components
proteasome
substrate
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification Detailsspecimens were manually blotted with Whatman #1 filter paper
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles34701
Reported Resolution (Å)4.43
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (5MPC)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)50
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 ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification29000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Detailsimages were acquired in nanoprobe mode
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONLeginon3.2
CTF CORRECTIONMotionCorr22
CTF CORRECTIONRELION2.1
CTF CORRECTIONCTFFIND4
CTF CORRECTIONGctf
MODEL FITTINGUCSF Chimera1.12
MODEL FITTINGPHENIX1.11-2580
INITIAL EULER ASSIGNMENTRELION2.1
FINAL EULER ASSIGNMENTRELION2.1
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.11-2580
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF correction was performed by Relion during reconstruction579361Particles were selected using the Relion template-based particle picker