6VPC | pdb_00006vpc

Structure of the SpCas9 DNA adenine base editor - ABE8e

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UN3
experimental model	PDB	5F9R
experimental model	PDB	1Z3A

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.4935
f_angle_d	0.5431
f_chiral_restr	0.0358
f_plane_restr	0.0044
f_bond_d	0.002

Sample
CRISPR-Cas9 ABE8e in a substrate-bound state

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	The grids were rapidly plunged into liquid ethane using a FEI Vitrobot MarkIV maintained at 8C and 100% humidity, after being blotted for 4.5s with blot force 8.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	180927
Reported Resolution (Å)	3.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4UN3, 4UN3, 5F9R, 1Z3A)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	48

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
MODEL FITTING	Coot	0.8.9.1
INITIAL EULER ASSIGNMENT	cryoSPARC	2.11.0
FINAL EULER ASSIGNMENT	RELION	3.0
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.17.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION