9Z7Q | pdb_00009z7q

Cryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA

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	11.853
f_angle_d	0.625
f_chiral_restr	0.044
f_plane_restr	0.004
f_bond_d	0.003

Sample
Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA

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	194795
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details	cryoSPARC's non-uniform refinement with per particle CTF correction was used to generate the final reconstruction.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	Initial fitting was done in ChimeraX, followed by refinement in PHENIX. COOT was used to manually edit the structure to better fit the density before a final refinement in PHENIX

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
INITIAL EULER ASSIGNMENT	cryoSPARC	4.7.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.7.1
CLASSIFICATION	cryoSPARC	4.7.1
RECONSTRUCTION	cryoSPARC	4.7.1
MODEL REFINEMENT	PHENIX	1.21.2_5419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1621549	Particles identified using cryoSPARC's template picker. Templates generated from a de novo volume that contained 105809 particles.