7JZ0

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1) and S-Adenosyl-L-homocysteine (SAH).

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6W4H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	292	Protein: 4.7mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: Anions (E6), 0.1M Sodium acetate pH 4.6, 0.5M Sodium succinate; Soak: 17 hours, 0.2mM [M7Gppp]rArUrUrArArA, 5mM SAM, 5mM Manganese chloride, Cryo: 4M Sodium formate.

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.238	α = 90
b = 167.238	β = 90
c = 98.867	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	CCD	MARMOSAIC 300 mm CCD	BE	2020-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.15	50	100	0.09	0.09	0.097	0.036	26.6	7.1		86204		-3	42.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	100		1.239	1.239	1.335	0.493	0.735	1.8	7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6w4h	2.15	30	81799	4338	99.81	0.1745	0.1733	0.1981	RANDOM	55.875

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]
1.29	0.65		1.29		-4.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.651
r_dihedral_angle_3_deg	9
r_dihedral_angle_4_deg	8.747
r_dihedral_angle_1_deg	2.788
r_angle_refined_deg	1.344
r_angle_other_deg	0.381
r_chiral_restr	0.06
r_gen_planes_refined	0.053
r_gen_planes_other	0.047
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.651
r_dihedral_angle_3_deg	9
r_dihedral_angle_4_deg	8.747
r_dihedral_angle_1_deg	2.788
r_angle_refined_deg	1.344
r_angle_other_deg	0.381
r_chiral_restr	0.06
r_gen_planes_refined	0.053
r_gen_planes_other	0.047
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6496
Nucleic Acid Atoms	188
Solvent Atoms	398
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.