ELECTRON MICROSCOPY

Sample

CalC6_3 with DHR extensions, hepatmer

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 45077
Reported Resolution (Å) 4.62
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details For the heptamer, CalC6_3 with DHR extension hexamer design model was used as a starting model. A single chain for the heptamer was isolated in PyMOL, and 7 copies of this chain were fitted to the map in UCSF Chimera to reform the channel. The heptamer was refined using several rounds of relaxation and minimization, performed on the complete structures, which were manually inspected for errors each time using ISOLDE in UCSF ChimeraX, Coot, and PHENIX real-space refinement. The final model quality was analyzed using MolProbity.
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 47.32
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 800
Maximum Defocus (nm) 1800
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC ?
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION cryoSPARC ?
MODEL FITTING UCSF Chimera ?
INITIAL EULER ASSIGNMENT cryoSPARC ?
FINAL EULER ASSIGNMENT cryoSPARC ?
CLASSIFICATION cryoSPARC ?
RECONSTRUCTION cryoSPARC ?
MODEL REFINEMENT UCSF ChimeraX ?
MODEL REFINEMENT ISOLDE ?
MODEL REFINEMENT Coot ?
MODEL REFINEMENT PHENIX ?
MODEL REFINEMENT PyMOL ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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