9Z7X | pdb_00009z7x

Cryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to target RNA with non-complementary PFS

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.612
f_angle_d	0.594
f_chiral_restr	0.044
f_plane_restr	0.005
f_bond_d	0.002

Sample
Type III-Bv CRISPR complex from Dissulfurispira thermophila bound to target RNA with a non-complementary PFS

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	358511
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Final reconstruction generated by non-uniform refinement with per particle CTF correction enabled.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	ChimeraX's fit in map command was used to fit Alphafold predicted structure of individual subunits followed by refinement in PHENIX and manual editing in COOT.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	65

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2000
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	45000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.7.1
IMAGE ACQUISITION	SerialEM	4.2.0
CTF CORRECTION	cryoSPARC	4.7.1
MODEL FITTING	UCSF ChimeraX	1.10.1
MODEL REFINEMENT	PHENIX	1.21.2_5419
INITIAL EULER ASSIGNMENT	cryoSPARC	4.7.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.7.1
CLASSIFICATION	cryoSPARC	4.7.1
RECONSTRUCTION	cryoSPARC	4.7.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3264182	Particles picked using a de novo template generated in CryoSPARC live that contained 329559 particles.