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 9BHU | pdb_00009bhu

Streptomyces griseus Family 2B encapsulin shell


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldQ54255 
Sample
Streptomyces griseus Family 2B encapsulin shell
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot force: 20 Blot time: 4 seconds
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles135027
Reported Resolution (Å)2.71
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsHomogeneous refinement with I symmetry imposed, per-particle defocus optimization, per-group CTF parameterization, spherical aberration fit enabled, t ...Homogeneous refinement with I symmetry imposed, per-particle defocus optimization, per-group CTF parameterization, spherical aberration fit enabled, tetrafoil fit enabled, Ewald sphere correction with negative curvature, and minimize over per-particle scale enabled.
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Targetcross-correlation coefficient
Overall B Value127.9
Fitting Procedure
DetailsAn AlphaFold-generated model was fit into the map using ChimeraX v1.5. The model was then refined iteratively by alternating rounds of manual refineme ...An AlphaFold-generated model was fit into the map using ChimeraX v1.5. The model was then refined iteratively by alternating rounds of manual refinement in Coot v8.9.1 and real-space refinements using PHENIX v1.20.1-4487.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)43.22
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS GLACIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification45000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.4.0+231114
IMAGE ACQUISITIONLeginon
CTF CORRECTIONcryoSPARC4.4.0+231114
MODEL FITTINGUCSF ChimeraX1.5
MODEL REFINEMENTCoot8.9.1
MODEL REFINEMENTPHENIX1.20.1-4487
INITIAL EULER ASSIGNMENTcryoSPARC4.4.0+231114
FINAL EULER ASSIGNMENTcryoSPARC4.4.0+231114
RECONSTRUCTIONcryoSPARC4.4.0+231114
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION159394