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 9E5E | pdb_00009e5e

Escherichia coli DyP peroxidase-loaded encapsulin shell


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldA0A3L1NQK1 
in silico modelAlphaFoldA0A747AN60 
Sample
Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsGrids were frozen with a blot force of 20, blot time of 4 seconds, 100% humidity, and chamber temperature of 22 degrees C.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles286236
Reported Resolution (Å)2.17
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsHomogeneous refinement was used against an ab-initio map with I symmetry, per-particle defocus optimization enabled, per-group CTF parameter optimizat ...Homogeneous refinement was used against an ab-initio map with I symmetry, per-particle defocus optimization enabled, per-group CTF parameter optimization enabled, and Ewald sphere correction enabled using a positive curvature sign.
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Targetcross-correlation coefficient
Overall B Value85.5
Fitting Procedure
DetailsThe AlphaFold model was placed using ChimeraX, followed by iterative manual refinement in Coot followed by Phenix real space refinements.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)39.91
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv.4.1.2
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARCV.4.1.2
MODEL FITTINGUCSF ChimeraX1.8
INITIAL EULER ASSIGNMENTcryoSPARCv.4.1.2
FINAL EULER ASSIGNMENTcryoSPARCv.4.1.2
RECONSTRUCTIONcryoSPARCv.4.1.2
MODEL REFINEMENTCoot0.9.8
MODEL REFINEMENTPHENIX1.2.1-4487
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION292965