6NE0 | pdb_00006ne0

Structure of double-stranded target DNA engaged Csy complex from Pseudomonas aeruginosa (PA-14)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UZ9

Sample
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).

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.