7BGJ | pdb_00007bgj

C. thermophilum Pyruvate Dehydrogenase Complex Core

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CT0

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	22.7131
f_angle_d	1.1134
f_chiral_restr	0.0595
f_bond_d	0.0075
f_plane_restr	0.0061

Sample
Native 60-mer core of Pyruvate Dehydrogenase Complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	For plunging, blot force 2 and blotting time of 6 sec were applied.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	29516
Reported Resolution (Å)	6.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (6CT0)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value	103.25
Fitting Procedure
Details	The initial model was used to generate our model using MODELLER. This inital model was fitted into the density using ChimeraX and refined in real space using PHENIX.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	30

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	45000
Calibrated Magnification	44067
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Xmipp	3.0
IMAGE ACQUISITION	EPU	2.6
IMAGE ACQUISITION	Scipion	2.0
IMAGE ACQUISITION	RELION	3.0
IMAGE ACQUISITION	Xmipp	3
IMAGE ACQUISITION	MotionCorr2	2.03
IMAGE ACQUISITION	Gctf	1.06
CTF CORRECTION	Gctf	1.06
MODEL FITTING	UCSF Chimera	0.94
INITIAL EULER ASSIGNMENT	RELION	3.0
FINAL EULER ASSIGNMENT	RELION	3.0
CLASSIFICATION	RELION	3.0
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	MODELLER	9.22
MODEL REFINEMENT	PHENIX	1.18-3845

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		205251	Automated selection with template derived from manual selection