7JMI

Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots - Frame 29 - State 3 (S3)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TB4 
Sample
Ryanodine receptor 1 bound to FKBP1B
Specimen Preparation
Sample Aggregation State3D ARRAY
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles791956
Reported Resolution (Å)4.5
Resolution MethodOTHER
Other DetailsRESMAP and visual inspection. FSC not possible as no half-sets are available with the manifold embedding method
Refinement Type
Symmetry TypePOINT
Point SymmetryC4
Map-Model Fitting and Refinement
Id1 (5TB4)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
Detailsfitted to a model domain by domain with the rigid-body fit function in COOT 71, using multiple starting models to avoid model bias (PDB ID: 5TB4, 5T9R ...fitted to a model domain by domain with the rigid-body fit function in COOT 71, using multiple starting models to avoid model bias (PDB ID: 5TB4, 5T9R, 5TAP, 5T9V, 5TAL, 5TAQ) 22. The models were then refined in real-space using phenix.real_space_refine
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONLeginon
MODEL FITTINGPHENIX
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION