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DOUBLE-STRANDED TARGET DNA
ENGAGED CSY COMPLEX FROM
PSEUDOMONAS AERUGINOSA (PA-14)
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
Freezing was carried out in a cold room at 4 degrees C and relative humidity of 98%. 5 ul sample was applied to plasma cleaned grid and manually blott ...
Freezing was carried out in a cold room at 4 degrees C and relative humidity of 98%. 5 ul sample was applied to plasma cleaned grid and manually blotted with Whatman 1 filter paper for 5-7 sec before plunge freezing.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
291227
Reported Resolution (Å)
3.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
The final map was reconstructed using several focused maps from different sub-regions of the complex. These were initially aligned to each other and t ...
The final map was reconstructed using several focused maps from different sub-regions of the complex. These were initially aligned to each other and then stitched using the vop maximum function in UCSF chimera. The resolution of the final composite map is 3.2 angstrom.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (5UZ9)
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
THE ATOMIC MODELS FOR CAS5F, CAS8F, CAS6F, AND
CAS7F FROM THE CSY ACR COMPLEX (PDB ID 5UZ9) WERE USED AS
INITIAL TEMPLATE MODELS FOR MODEL BUILDING. ...
THE ATOMIC MODELS FOR CAS5F, CAS8F, CAS6F, AND
CAS7F FROM THE CSY ACR COMPLEX (PDB ID 5UZ9) WERE USED AS
INITIAL TEMPLATE MODELS FOR MODEL BUILDING. THESE WERE
INDIVIDUALLY RIGID BODY-FITTED INTO THE RECONSTRUCTED MAPS USING
THE FIT MAP FUNCTION IN UCSF CHIMERA, AND RESIDUE REGISTERS AND
BACKBONE GEOMETRIES WERE FIXED IN COOT. MODELS FOR THE CRRNA AND
DNA STRANDS WERE ALSO MANUALLY BUILT INTO THE MAP USING COOT.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
0.58
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TALOS ARCTICA
Minimum Defocus (nm)
600
Maximum Defocus (nm)
1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
36000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
OBJECTIVE ASTIGMATISM WAS CORRECTED AT 36000X MAGNIFICATION USING THON RINGS VISUALIZED WITH A K2 CAMERA.
EM Software
Task
Software Package
Version
IMAGE ACQUISITION
Leginon
CTF CORRECTION
CTFFIND
4
INITIAL EULER ASSIGNMENT
RELION
2.1
FINAL EULER ASSIGNMENT
RELION
2.1
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
1543677
Particles were initially extracted binned by 2 with a box size of 144 pixels (2.3 Angstrom/pixel). The final processing was carried out with an unbinned particle stack with a box size of 288 pixels (1.15 Angstrom/pixel).