6NSJ

CryoEM structure of Helicobacter pylori urea channel in closed state


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UX4 
Sample
urea channel of Helicobacter pylori
Specimen Preparation
Sample Aggregation State2D ARRAY
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles393930
Reported Resolution (Å)2.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC6
Map-Model Fitting and Refinement
Id1 (3UX4)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value71.9
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)72
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1400
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification46730
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONGautomatch0.56
IMAGE ACQUISITIONLeginon3.1
CTF CORRECTIONCTFFIND4.1.18
MODEL FITTINGUCSF Chimera1.9
INITIAL EULER ASSIGNMENTRELION2.0
FINAL EULER ASSIGNMENTRELION2.0
CLASSIFICATIONRELION2.0
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIX1.14
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE1221897