9ASC | pdb_00009asc

Cryo-EM Structure of the Glycosyltransferase ArnC from Salmonella enterica in the UDP-bound State Determined on Talos Arctica microscope

ELECTRON MICROSCOPY

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	10.097
f_angle_d	0.442
f_chiral_restr	0.039
f_plane_restr	0.004
f_bond_d	0.003

Sample
Salmonella enterica ArnC in MSP1E3D1 nanodisc bound to UDP and Mn2+

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3 microliters of ArnC incorporated into nanodiscs was applied to a glow-discharged UltraAuFoil (1.2/1.3) 300 mesh grids (Quantifoil), blotted with fil ...	3 microliters of ArnC incorporated into nanodiscs was applied to a glow-discharged UltraAuFoil (1.2/1.3) 300 mesh grids (Quantifoil), blotted with filter paper for 3.5 s, and flash-frozen by plunging in liquid ethane cooled with liquid nitrogen. Grids were stored in liquid nitrogen.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	261104
Reported Resolution (Å)	2.96
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C4

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	39.88

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	500
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	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.32
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	3.32
MODEL FITTING	Coot	0.9.8.1
MODEL REFINEMENT	PHENIX	1.20.1-4487
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.2
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.2
CLASSIFICATION	cryoSPARC	3.3.2
RECONSTRUCTION	cryoSPARC	3.3.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2382682

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.