Experiment: 6M71

SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors

ELECTRON MICROSCOPY

Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	2.485
f_angle_d	0.482
f_chiral_restr	0.041
f_plane_restr	0.004
f_bond_d	0.003

Sample
SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details	blot for 3 seconds before plunging.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	110176
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The particle set was used to perform homogeneous refinement, yielding a resolution of 3.1-angstrom. After local refinement, the final resolution reach ...	The particle set was used to perform homogeneous refinement, yielding a resolution of 3.1-angstrom. After local refinement, the final resolution reached 2.9-angstrom.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6NUR, 6NUR, 6NUR, 6NUR)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	correlation coefficient
Overall B Value	65
Fitting Procedure
Details	After the corresponding amino acids were replaced with those from 2019-nCoV, the model was manually built in Coot with the guidance of the cryo-EM map ...	After the corresponding amino acids were replaced with those from 2019-nCoV, the model was manually built in Coot with the guidance of the cryo-EM map, and in combination with real space refinement with Phenix.

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2000
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)	300
Imaging Details	Preliminary grid screening was performed manually.

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM	3-7-3
CTF CORRECTION	cryoSPARC	2.9.1
MODEL FITTING	UCSF Chimera	1.14
MODEL REFINEMENT	PHENIX	1.16
INITIAL EULER ASSIGNMENT	cryoSPARC	2.9.1
FINAL EULER ASSIGNMENT	cryoSPARC	2.9.1
CLASSIFICATION	cryoSPARC	2.9.1
RECONSTRUCTION	cryoSPARC	2.9.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	The CTF correction was done by patch CTF correction.	2334248	The particles were automatically selected using blob pickier (diameter range from 100 angstroms to 150 angstroms)