9G2K

Cryo-EM structure of IrtAB in outward-occluded state in nanodisc in complex with ADP-vanadate


ELECTRON MICROSCOPY

Starting Model(s)

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

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.4149
f_angle_d0.6391
f_chiral_restr0.0404
f_plane_restr0.0057
f_bond_d0.0036
Sample
IrtAB
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles150689
Reported Resolution (Å)3.14
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6TEJ)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)61.2
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv3.0
IMAGE ACQUISITIONEPU2.9
CTF CORRECTIONcryoSPARCv3.0
MODEL FITTINGCoot0.9.8.92
MODEL FITTINGISOLDE1.3
INITIAL EULER ASSIGNMENTcryoSPARCv3.0
FINAL EULER ASSIGNMENTcryoSPARCv3.0
RECONSTRUCTIONcryoSPARCv3.0
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION