ELECTRON MICROSCOPY

Sample

Mature conformer of a 6-helix bundle of RNA with clasp

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument LEICA EM GP
Cryogen Name ETHANE
Sample Vitrification Details 3 microlitre droplet, 4 second delay before blotting, 6 second blot, 0 second delay before plunging.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 337099
Reported Resolution (Å) 4.9
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 Correlation Coefficient
Overall B Value 303
Fitting Procedure ?
Details Helical templates and tetraloops were generated in RNAbuild. Kissing loops were modelling based on the PDB:2D1B structure. A combination of PHENIX RSR and ISOLDE were used to arrive at the final structure.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 60
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 750
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 130000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 3.2.0
IMAGE ACQUISITION EPU ?
CTF CORRECTION cryoSPARC 3.2.0
MODEL FITTING UCSF ChimeraX 1.2
MODEL FITTING ISOLDE 1.2
MODEL REFINEMENT PHENIX 1.19.2-4158-000
INITIAL EULER ASSIGNMENT cryoSPARC 3.2.0
FINAL EULER ASSIGNMENT cryoSPARC 3.2.0
CLASSIFICATION cryoSPARC 3.2.0
RECONSTRUCTION cryoSPARC 3.2.0
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF estimation (multi) from cryoSPARC.