11KC | pdb_000011kc

Cryo-EM determined structure of designed nanoparticle O43-TM


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOther 
Sample
two component de novo designed nanoparticle with trans-membrane domain O43-TM
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsWait time: 7.5 seconds Blot time: 0.5 seconds Blot force: 0 seconds
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles42340
Reported Resolution (Å)4.07
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryO
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetCross-correlation coefficient
Overall B Value163.2
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)4747.32
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS 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 Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.4.1
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC4.4.1
MODEL FITTINGUCSF ChimeraX
INITIAL EULER ASSIGNMENTcryoSPARC4.4.1
FINAL EULER ASSIGNMENTcryoSPARC4.4.1
CLASSIFICATIONcryoSPARC4.4.1
RECONSTRUCTIONcryoSPARC4.4.1
RECONSTRUCTIONcryoSPARC4.6.0
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION