6N2P

Helical assembly of the CARD9 CARD


ELECTRON MICROSCOPY
Sample
Helical assembly of the CARD9 CARD.
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsSample was incubated on the grid for 1 minute, subsequently washed/blotted 6 times in buffer, followed by addition of 3.5 ul buffer, which was blotted ...Sample was incubated on the grid for 1 minute, subsequently washed/blotted 6 times in buffer, followed by addition of 3.5 ul buffer, which was blotted by vitrobot for 5 seconds prior to plunging.
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles31908
Reported Resolution (Å)4
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsA 5.0 A high-resolution limit was used for particle alignment in frealign.
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise5.11
Angular Rotation-101.6
Map-Model Fitting and Refinement
Id1 (6E26)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details"Fit in map" in UCSF Chimera was used to fit the previously determined, lowest energy NMR solution structure (PDB ID 6E26) into the sharpened density ..."Fit in map" in UCSF Chimera was used to fit the previously determined, lowest energy NMR solution structure (PDB ID 6E26) into the sharpened density and to generate 9 symmetry-mates according to the determined helical parameters. The map was then iteratively refined in Phenix and Coot, maintaining strict non-crystallographic symmetry among the CARDs.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)50.9
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1250
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONEMAN2
PARTICLE SELECTIONRELION2.1
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
INITIAL EULER ASSIGNMENTRELION2.1
INITIAL EULER ASSIGNMENTFREALIGN
FINAL EULER ASSIGNMENTFREALIGN9.11
CLASSIFICATIONFREALIGN9.11
RECONSTRUCTIONFREALIGN9.11
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION141592Filaments were manually selected using e2helixboxer.py. Segments were extracted from filaments using RELION, using a 30 A shift between particles.