5UZ9 | pdb_00005uz9

Cryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type I-F crRNA-guided CRISPR surveillance complex

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.731
f_angle_d	0.942
f_chiral_restr	0.05
f_bond_d	0.006
f_plane_restr	0.006

Sample
Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRISPR surveillance(Csy)complex.

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Sample was applied to poly-L-lysine hydrobromide pre-treated amorphous carbon film coated over a holey grid. Excess sample was blotted with Whatman-1 ...	Sample was applied to poly-L-lysine hydrobromide pre-treated amorphous carbon film coated over a holey grid. Excess sample was blotted with Whatman-1 filter paper and plunge frozen. Manual plunge freezing was performed in a cold room.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	51212
Reported Resolution (Å)	3.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Per-frame dose weighting was performed using the RELION particle polishing method. A B-factor of -71 square angstrom was applied to sharpen the final ...	Per-frame dose weighting was performed using the RELION particle polishing method. A B-factor of -71 square angstrom was applied to sharpen the final map. Signal subtracted focused classification and refinement was performed for the "tail" region of the complex. This lead to a 4 angstrom (Gold standard FSC 0.143) map.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1	2	3
Refinement Space	REAL	REAL	REAL
Refinement Protocol	AB INITIO MODEL	RIGID BODY FIT	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Top scoring five models out of two hundred models generated using Rosetta were refined using Phenix and deposited as an ensemble atomic model for the ...	Top scoring five models out of two hundred models generated using Rosetta were refined using Phenix and deposited as an ensemble atomic model for the final EM map.	The docked Cas6F structure in the "head" region of the complex was reduced to C-alpha backbone.	Initially two copies were fitted using Chimera and then backbones and side chains were fixed using Coot, followed by real space refinement in Phenix.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	46

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	29000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Objective astigmatism was corrected at nominal magnification of 29000X, using Thon rings visualized with a K2 camera.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	FindEM
IMAGE ACQUISITION	Leginon
CTF CORRECTION	CTFFIND3	3
MODEL FITTING	Coot	0.8.7
INITIAL EULER ASSIGNMENT	RELION	1.4
FINAL EULER ASSIGNMENT	RELION	1.4
CLASSIFICATION	RELION	1.4
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	PHENIX	1.11.1
MODEL FITTING	UCSF Chimera	1.12
MODEL REFINEMENT	PHENIX	1.11.1
MODEL FITTING	UCSF Chimera	1.12
MODEL REFINEMENT	PHENIX	1.11.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE	Particles were ctf-corrected during 2D and 3D processing.	199348	Template based particle picking was done using FindEM program implemented in Appion processing package.

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.