32GD | pdb_000032gd

Bacterial antiviral defense protein PD-T7-3 obtained from a sample containing single-stranded DNA and tRNA


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles128877
Reported Resolution (Å)2.95
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD2
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)29
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS GLACIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification92000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
IMAGE ACQUISITIONEPU3.13
CTF CORRECTIONcryoSPARC
INITIAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX2.0_5936
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION