6X0O

Single-Particle Cryo-EM Structure of Arabinosyltransferase EmbB from Mycobacterium smegmatis


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PTY 
Sample
Integral membrane indolylacetylinositol arabinosyltransferase EmbB
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles57970
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsCombined with K2 dataset
Refinement Type
Symmetry TypePOINT
Number of Particles57970
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsCombined with Falcon III dataset
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3PTY)
Refinement Space
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)78.0277.53
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONGautomatch0.53
IMAGE ACQUISITIONLeginon3.4
CTF CORRECTIONcryoSPARC2
CTF CORRECTIONRELION2.1
CTF CORRECTIONcisTEM1
MODEL FITTINGUCSF Chimera1.13
MODEL FITTINGCoot0.8
INITIAL EULER ASSIGNMENTcryoSPARC2
FINAL EULER ASSIGNMENTcryoSPARC2
RECONSTRUCTIONcryoSPARC2
PARTICLE SELECTIONGautomatch0.53
CTF CORRECTIONcryoSPARC2
CTF CORRECTIONRELION2.1
CTF CORRECTIONcisTEM1
INITIAL EULER ASSIGNMENTcryoSPARC2
FINAL EULER ASSIGNMENTcryoSPARC2
RECONSTRUCTIONcryoSPARC2
MODEL REFINEMENTPHENIX1.14
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION162271
PHASE FLIPPING AND AMPLITUDE CORRECTION700201