Experiment: 7KRI

FR6-bound SARS-CoV-2 Nsp9 RNA-replicase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6W9Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4	293	0.1M Sodium Citrate pH 4.0 2.2-2.4M Sodium Malonate

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.459	α = 90
b = 109.459	β = 90
c = 77.046	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2020-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95374	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.58	44.62	100	0.026	0.999	13.4	5.2		73088			23.15

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.61	99.9		0.619	0.602		10.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6W9Q	1.58	44.62	1.34	73051	3605	99.99	0.1786	0.1777	0.1796	0.1953	0.1964	random selection 5%	31.41

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	24.3467
f_angle_d	0.8608
f_chiral_restr	0.0526
f_bond_d	0.0059
f_plane_restr	0.0054

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2880
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	100

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing