7B9K

Cryo-EM structure of the dihydrolipoyl transacetylase cubic core of the E. coli pyruvate dehydrogenase complex including lipoyl domains

ELECTRON MICROSCOPY

Sample
dihydrolipoyl transacetylase cubic core of the pyruvate dehydrogenase complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	2.5 microliters of sample, blot force 0, 15 second wait time, 3 second blot time

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	29434
Reported Resolution (Å)	3.16
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	O

Map-Model Fitting and Refinement
Id	1 (4N72, 1QJO)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)	GATAN K2 QUANTUM (4k x 4k)	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	30	28.11	28.11

Imaging Experiment	1	2	3
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS	FEI TITAN KRIOS	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7	2.7	2.7
Imaging Mode	BRIGHT FIELD	BRIGHT FIELD	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN	FIELD EMISSION GUN	FIELD EMISSION GUN
Acceleration Voltage (kV)	300	300	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	2.15
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	2.15
MODEL FITTING	PHENIX	1.16
INITIAL EULER ASSIGNMENT	cryoSPARC	2.15
FINAL EULER ASSIGNMENT	cryoSPARC	2.15
CLASSIFICATION	cryoSPARC	2.15
RECONSTRUCTION	cryoSPARC	2.15
MODEL REFINEMENT	PHENIX	1.16
MODEL REFINEMENT	REFMAC	5.8.0232

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		799790	automated template picking in CryoSPARC

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.