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 9B9Q | pdb_00009b9q

Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7S4Q 
Sample
Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry
Sample Components
Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry
SNAP-tag-targeting peptide cargo protein
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot force: 20 Blot time: 4 seconds Wait time: 0 seconds
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles12967
Reported Resolution (Å)3.14
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsHomogeneous refinement was performed against the intial ab-initio map using I symmetry, per-particle defocus optimization, per-group CTF paramterizati ...Homogeneous refinement was performed against the intial ab-initio map using I symmetry, per-particle defocus optimization, per-group CTF paramterization, and Ewald sphere correction.
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (7S4Q)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Targetcross-correlation coefficient
Overall B Value93.1
Fitting Procedure
DetailsChimeraX v1.2.5 was first used to place the starting model (PDB: 7S4Q) in the cryo-EM map by using the fit in map command. The model was then manually ...ChimeraX v1.2.5 was first used to place the starting model (PDB: 7S4Q) in the cryo-EM map by using the fit in map command. The model was then manually refined using Coot v 0.9.8.1, followed by iterative real-space refinements in Phenix v1.20.1-4487-000. BioMT operators were identified from the cryo-EM map using map_symmetry command in Phenix then applied to the model using the apply_ncs command to assemble the complete shell. Real-space refinement was repeated in Phenix with NCS constraints applied. The BioMT operators were then identified using find_ncs command in Phenix and applied to the header of a protomer of the NCS-refined model.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)39.18
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI ARCTICA
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 SELECTIONcryoSPARC3.10.0
IMAGE ACQUISITIONLeginon
CTF CORRECTIONcryoSPARC3.10.0
MODEL FITTINGUCSF ChimeraX1.2.5
INITIAL EULER ASSIGNMENTcryoSPARC3.10.0
FINAL EULER ASSIGNMENTcryoSPARC3.10.0
RECONSTRUCTIONcryoSPARC3.10.0
MODEL REFINEMENTPHENIXv1.20.1-4487-000
MODEL REFINEMENTCootv0.9.8.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION37600