8G1S | pdb_00008g1s

Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

ELECTRON MICROSCOPY

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Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.524
f_angle_d	0.625
f_chiral_restr	0.045
f_bond_d	0.004
f_plane_restr	0.004

Sample
Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand
Sample Components
DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega, DNA
RNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Vitrification was carried out in a chamber with the temperature set to 4 C.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	32246
Reported Resolution (Å)	3.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (6ALF)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	62

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	3500
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
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO	1.8.4
IMAGE ACQUISITION	Leginon	3.6
CTF CORRECTION	CTFFIND	4.1.14
MODEL FITTING	PHENIX	1.19.2
INITIAL EULER ASSIGNMENT	cryoSPARC	3.2.0
FINAL EULER ASSIGNMENT	cryoSPARC	3.2.0
MODEL REFINEMENT	PHENIX	1.19.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION			This is component 1 of 3DVA analysis of a particle stack of the Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand. Particles were already selected.