ELECTRON MICROSCOPY

Sample

Ligand-free Manduca sexta soluble guanylase cyclase variant

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Cryo-EM samples were prepared by applying 3 ul to a glow-discharged Quantifoil R1.2/1.3 holey-carbon cryo-EM grid. The grid was blotted for 4 s with Whatman #1 filter paper and then plunge-frozen in liquid ethane with a Mark IV Vitrobot (ThermoFisher) at 4 C and 100% humidity.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 264227
Reported Resolution (Å) 3.2
Resolution Method FSC 0.143 CUT-OFF
Other Details During refinement it became clear that there was minor interdomain flexibility within the 264,227 particles. In particular, the catalytic domain was at lower resolution and had considerable missing density. Separate masks were created for each domain, and local refinement as implemented in cryoSPARC was used to improve the resolution of the separate catalytic and H-NOX domains of the global map. The subsequent local refinement resulted in 3.0 A and 3.4 A maps for the H-NOX and catalytic domains respectively. Both have improved density for outer regions of the map and improved local resolution. A composite map was used for model building.
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 Refinement was performed using iterative rounds of Phenix real space refinement and manual modeling in Coot. Phenix refinement was performed for separate domains of the model using the higher-resolution local maps of those domains.
Data Acquisition
Detector Type FEI FALCON I (4k x 4k)
Electron Dose (electrons/Å2) 1.25
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 500
Maximum Defocus (nm) 1500
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 ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC ?
IMAGE ACQUISITION EPU ?
CTF CORRECTION cryoSPARC ?
MODEL FITTING UCSF ChimeraX ?
INITIAL EULER ASSIGNMENT cryoSPARC ?
FINAL EULER ASSIGNMENT cryoSPARC ?
CLASSIFICATION cryoSPARC ?
RECONSTRUCTION cryoSPARC ?
MODEL REFINEMENT PHENIX 1.21.1_5286
MODEL REFINEMENT Coot ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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