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 7Y0D | pdb_00007y0d

Cryo-EM structure of the Mycobacterium smegmatis DNA integrity scanning protein (MsDisA).


ELECTRON MICROSCOPY
Sample
Cryo-EM structure of the Mycobacterium smegmatis DNA integrity scanning protein (MsDisA).
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsblotted for 3.5s
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles204932
Reported Resolution (Å)3.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value138.7
Fitting Procedure
DetailsModel from AlphaFold was used as the starting point (AF-A0R564-F1-model_v2.pdb).
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)27.75
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)2100
Maximum Defocus (nm)3300
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification130841
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.0
IMAGE ACQUISITIONEPU
MODEL FITTINGCoot0.9.5
MODEL FITTINGUCSF Chimera1.15
INITIAL EULER ASSIGNMENTcryoSPARC3.0
FINAL EULER ASSIGNMENTcryoSPARC3.0
RECONSTRUCTIONcryoSPARC3.0
MODEL REFINEMENTPHENIX1.19
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION973755Template Picker from cryoSparc 3.0 were used to pick total particles in the first extraction. Three rounds of reference-free 2d classification were carried to remove bad particles followed by NU-refinement.