9TRC | pdb_00009trc

Bacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Bacterial antiviral defense protein PD-T7-3 (H122A) from Escherichia coli strain ECOR30 in complex with single-stranded DNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles452827
Reported Resolution (Å)2.92
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsNumber of particles after D2 symmetry expansion. Resolution calculated as the mean resolution value of the consensus map and two focus maps
Refinement Type
Symmetry TypePOINT
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 ACQUISITIONEPU3.11
CTF CORRECTIONcryoSPARC
INITIAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC4.7.1
MODEL REFINEMENTPHENIX1.21.2-5419
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION