9YPE | pdb_00009ype

S. aureus YhaM D193A hexamer, 2 NTDs, hairpin RNA substrate


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherOther 
Sample
S. aureus YhaM D193A hexamer, 2 NTDs, hairpin RNA substrate
Sample Components
YhaM D193A hexamer
hairpin RNA substrate
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles224020
Reported Resolution (Å)3.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value129.7
Fitting Procedure
Details
Data Acquisition
Detector TypeTFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)52.97
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification165000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.7.0
IMAGE ACQUISITIONLeginon
CTF CORRECTIONcryoSPARC4.7.0
MODEL FITTINGUCSF ChimeraX
INITIAL EULER ASSIGNMENTcryoSPARC4.7.0
FINAL EULER ASSIGNMENTcryoSPARC4.7.0
CLASSIFICATIONcryoSPARC4.7.0
RECONSTRUCTIONcryoSPARC4.7.0
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2080911