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Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9P2R
pdb_00009p2r
10.2210/pdb9p2r/pdb
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FASTA
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Binary MMCIF
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Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
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Binary MMCIF Zipped(.gz)
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Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
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
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 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 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
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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