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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 W ...
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
598571
Reported Resolution (Å)
3.6
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Non-Uniform (NU) refinement was performed on the higher resolution 3D class. The resulting 3.6 A consensus density resembled previous sGC structures i ...
Non-Uniform (NU) refinement was performed on the higher resolution 3D class. The resulting 3.6 A consensus density resembled previous sGC structures in the extended, NO-bound state. Other refinement strategies were attempted, but did not lead to higher resolution global map densities.
To improve local resolution of the domains of CYR715-bound sGC, local refinement was also performed. Separate masks were created for each domain, and local refinement as implemented in cryoSPARC was used to improve the resolution of the catalytic and H-NOX domains of the global map. The subsequent local refinement resulted in 3.5 A and 3.4 A maps for the H-NOX and catalytic domains respectively. These maps were then combined with the consensus map to create the composite map herein.
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 separ ...
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
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
1.25
Imaging Experiment
1
Date of Experiment
Temperature (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
EM Software
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
1226641
Autopicking was used to produce a stack of 2,299,895 particles. Particles showing poor alignment or broken complexes were removed using a series of 2D classification steps, leaving a particle stack of 902,997 particles that resembled sGC dimers.