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 8U4Z | pdb_00008u4z

Klebsiella pneumoniae encapsulin-associated DyP peroxidase


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BOJ 
Sample
Klebsiella pneumoniae family 1 encapsulin-associated DyP peroxidase
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot force: 5 Blot time: 2 seconds
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles431317
Reported Resolution (Å)2.39
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsUnmasked local refinement was performed with D3 symmetry imposed.
Refinement Type
Symmetry TypePOINT
Point SymmetryD3
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation coefficient
Overall B Value107.7
Fitting Procedure
DetailsInitial fitting was performed using ChimeraX v1.2.5. The model was then manually refined and mutated using Coot v9.8.1 followed by real-space refineme ...Initial fitting was performed using ChimeraX v1.2.5. The model was then manually refined and mutated using Coot v9.8.1 followed by real-space refinement using Phenix v1.20.1-4487-000.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50.02
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1800
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 SELECTIONcryoSPARC4.4.0+231114
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC4.4.0+231114
MODEL FITTINGUCSF ChimeraX1.2.5
MODEL FITTINGCoot0.9.8
MODEL REFINEMENTPHENIX1.20.1-4487-000
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 CORRECTION2603020