ELECTRON MICROSCOPY

Sample

Monomeric photosystem I

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Delay time 30 s Blot time 2 s Blot force 0 Drain time 0 s
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 712866
Reported Resolution (Å) 1.74
Resolution Method FSC 0.143 CUT-OFF
Other Details Resolution as reported by CryoSPARC, using its mask auto-tightening procedure.
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 Alphafold2 predictions fetched from AlphaFold-DB were placed into the map by rigid body fitting. Termini not supported by the map were trimmed. Every residue was visually inspected at least once, and its fit to density adjusted if necessary, using ISOLDE.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 40
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 400
Maximum Defocus (nm) 1400
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 Topaz 0.2.5
IMAGE ACQUISITION EPU ?
CTF CORRECTION cryoSPARC 4.5
MODEL FITTING UCSF ChimeraX 1.8
INITIAL EULER ASSIGNMENT cryoSPARC 4.5
FINAL EULER ASSIGNMENT cryoSPARC 4.5
CLASSIFICATION cryoSPARC 4.5
RECONSTRUCTION cryoSPARC 4.5
MODEL REFINEMENT ISOLDE 1.8
MODEL REFINEMENT Servalcat 0.4.88
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF estimation job in CryoSPARC, run with default settings.
Feedback Form
Name
Email
Institute
Feedback