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Yeast 26S proteasome bound to ubiquitinated substrate (1D* motor state)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MPC
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.73 f_angle_d 0.98 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.005
Sample Substrate-engaged 26S proteasome in the 1D* state Sample Components proteasome substrate
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE Sample Vitrification Details specimens were manually blotted with Whatman #1 filter paper
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 34701 Reported Resolution (Å) 4.43 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5MPC) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) -1000 Maximum Defocus (nm) -2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 29000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details images were acquired in nanoprobe mode
EM Software Task Software Package Version IMAGE ACQUISITION Leginon 3.2 CTF CORRECTION MotionCorr2 2 CTF CORRECTION RELION 2.1 CTF CORRECTION CTFFIND 4 CTF CORRECTION Gctf MODEL FITTING UCSF Chimera 1.12 MODEL FITTING PHENIX 1.11-2580 INITIAL EULER ASSIGNMENT RELION 2.1 FINAL EULER ASSIGNMENT RELION 2.1 RECONSTRUCTION RELION 2.1 MODEL REFINEMENT PHENIX 1.11-2580
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction was performed by Relion during reconstruction 579361 Particles were selected using the Relion template-based particle picker