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Inner spoke ring of the yeast NPC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other
Sample Nuclear Pore Complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 208392 Reported Resolution (Å) 6.6 Resolution Method FSC 0.143 CUT-OFF Other Details Multibody extracted spoke image stack processed in CryoSPARC Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details Rigid body docking of 3D map of Nucleoporins in the spoke complex with Chimera followed by flexible fitting and rebuilding in Coot.
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3500 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 Calibrated Magnification 37651 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Preliminary grid screening done manually with individual images of low magnification montages of candidate meshes.
EM Software Task Software Package Version PARTICLE SELECTION Gautomatch Gautomatch_v0.56_sm61_cu7.5 IMAGE ACQUISITION SerialEM CTF CORRECTION Gctf Gctf-v0.1.06_sm_20_cu7.5_x86_64 CTF CORRECTION RELION 3.0.7 MODEL FITTING UCSF Chimera 1.14 MODEL REFINEMENT MDFF MODEL REFINEMENT Coot 0.8.9.2 INITIAL EULER ASSIGNMENT RELION 3.0.7 FINAL EULER ASSIGNMENT cryoSPARC 3.3.2 CLASSIFICATION RELION 3.0.7 RECONSTRUCTION cryoSPARC 3.3.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction applied in RELION during
the alignment and reconstruction 26049