9ZW3 | pdb_00009zw3

Quasibacillus thermotolerans T=4 encapsulin pore mutant variant Letter11


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Quasibacillus thermotolerans T=4 encapsulin pore mutant variant Letter11
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles44759
Reported Resolution (Å)2.4
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsThe final map was generated using homogeneous refinement against the ab-initio map with I symmetry imposed, per-particle defocus optimization, per-gro ...The final map was generated using homogeneous refinement against the ab-initio map with I symmetry imposed, per-particle defocus optimization, per-group CTF parameterization, spherical aberration fitting enabled, tetrafoil fitting enabled, anisotropic magnification fitting enabled, and Ewald sphere correcting enabled with a negative 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 Value79.3
Fitting Procedure
DetailsA starting model of a single protomer was generated using AlphaFold 3, and individual protomers were fit into the volume of an asymmetric unit using U ...A starting model of a single protomer was generated using AlphaFold 3, and individual protomers were fit into the volume of an asymmetric unit using UCSF ChimeraX v 1.8. The model containing a single asymmetric unit consisting of four protomers was then manually refined using Coot v 0.9.8.1, followed by real-space refinement in PHENIX v 1.20.1-4487-000. Non-crystallographic symmetry (NCS) operators were then applied to generate a complete NCS-expanded shell, which was refined against the map using PHENIX real-space refinement.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)51.5
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.7.1
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC4.7.1
MODEL FITTINGUCSF ChimeraX1.8
MODEL REFINEMENTCoot0.9.8.1
MODEL REFINEMENTPHENIX1.20.1-4487-000
INITIAL EULER ASSIGNMENTcryoSPARC4.7.1
FINAL EULER ASSIGNMENTcryoSPARC4.7.1
RECONSTRUCTIONcryoSPARC4.7.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION68033