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in situ S. pombe hibernating ribosome after 7 days of glucose depletion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.961 f_angle_d 0.397 f_chiral_restr 0.027 f_plane_restr 0.003 f_bond_d 0.002
Sample In situ cryo-ET Hibernating Ribosome from S. pombe under 7-day glucose depletion conditions
Specimen Preparation Sample Aggregation State CELL Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 88206 Reported Resolution (Å) 3.38 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 3.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 4000 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Objective Aperture 70 um
EM Software Task Software Package Version VOLUME SELECTION Warp 2.0.0dev36 MODEL REFINEMENT PHENIX 1.21.2_5419 CTF CORRECTION Warp 2.0.0dev36 RECONSTRUCTION Warp 2.0.0dev36
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3D CTF Estimation done in Warp