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 7S66 | pdb_00007s66

Extended conformation of nighttime state KaiC


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K0C 
Sample
Extended state hexamer of nighttime state phosphomutant KaiC (KaiC-EA)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsGrids with applied sample were manually blotted with filter paper (Whatman No.1) for 3 seconds in a 4 C cold room before plunge freezing in liquid eth ...Grids with applied sample were manually blotted with filter paper (Whatman No.1) for 3 seconds in a 4 C cold room before plunge freezing in liquid ethane cooled by liquid nitrogen.
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsGrids with applied sample were manually blotted with filter paper (Whatman No.1) for 3 seconds in a 4 C cold room before plunge freezing in liquid eth ...Grids with applied sample were manually blotted with filter paper (Whatman No.1) for 3 seconds in a 4 C cold room before plunge freezing in liquid ethane cooled by liquid nitrogen.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles91869
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC6
Map-Model Fitting and Refinement
Id1 (3K0C)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)4851
Imaging Experiment12
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICAFEI TALOS ARCTICA
Minimum Defocus (nm)-800-500
Maximum Defocus (nm)-17001500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.72.7
Imaging ModeBRIGHT FIELDBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDERFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification3600036000
Calibrated Magnification4347843478
SourceFIELD EMISSION GUNFIELD EMISSION GUN
Acceleration Voltage (kV)200200
Imaging DetailsSample was imaged at a 40 degree tilt.Sample was imaged at 0 degree tilt.
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONLeginon
CTF CORRECTIONRELION3.0
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTCoot
IMAGE ACQUISITIONLeginon
INITIAL EULER ASSIGNMENTRELION3.0
FINAL EULER ASSIGNMENTRELION3.0
CLASSIFICATIONRELION3.0
RECONSTRUCTIONRELION3.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF Refinement performed in Relion2016826