7AJQ

cryo-EM structure of ExbBD from Serratia Marcescens


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YE4 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d23.0356
f_angle_d0.5234
f_chiral_restr0.0349
f_plane_restr0.0028
f_bond_d0.0021
Sample
5-ExbB + 2-ExbD complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK II
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles158000
Reported Resolution (Å)4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6YE4)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Targetcorrelation coefficient
Overall B Value169
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)4.58
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification139000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPUlatest
CTF CORRECTIONGctf1.06
MODEL FITTINGCoot0.8
INITIAL EULER ASSIGNMENTcryoSPARC2.0
FINAL EULER ASSIGNMENTcryoSPARC2.0
CLASSIFICATIONcryoSPARC2.0
RECONSTRUCTIONcryoSPARC2.0
MODEL REFINEMENTPHENIX1.17.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE1373000picking on 3028 images with best resolution