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 9OH4 | pdb_00009oh4

Cryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7UUX 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d25.386
f_angle_d0.528
f_chiral_restr0.035
f_plane_restr0.005
f_bond_d0.003
Sample
The structure of mouse cGAS in complex with a bubble DNA
Sample Components
mouse cGAS
The forward strand of bubble DNA
The reverse strand of bubble DNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsFilter paper blotted with blot force 2 and blot time 2s, and plunge-frozen in liquid ethane using a Vitrobot Mark IV at 4 degree Celsius and 100% humi ...Filter paper blotted with blot force 2 and blot time 2s, and plunge-frozen in liquid ethane using a Vitrobot Mark IV at 4 degree Celsius and 100% humidity.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles62441
Reported Resolution (Å)3.48
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsParticles are randomly split into two halves.
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (5N6I, 5N6I, 5N6I, 5N6I, 5N6I, 5N6I, 5N6I, 5N6I)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement TargetCross-correlation coefficient
Overall B Value87.5
Fitting Procedure
DetailsInitial local fitting was done using UCSF ChimeraX, and then COOT was used for manual building.
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1200
Maximum Defocus (nm)1800
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 SELECTIONcryoSPARCv4.3.1
IMAGE ACQUISITIONEPU1.12 - 3.7
CTF CORRECTIONcryoSPARCv4.3.1
MODEL FITTINGUCSF ChimeraXversion 1.9
INITIAL EULER ASSIGNMENTcryoSPARCv4.3.1
FINAL EULER ASSIGNMENTcryoSPARCv4.3.1
CLASSIFICATIONcryoSPARCv4.3.1
RECONSTRUCTIONcryoSPARCv4.3.1
MODEL REFINEMENTPHENIX1.18.2_3874:
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2969717A total of 2,969,717 particles were auto-picked using Blob Picker in CryoSPARC.