6WJT

2.0 Angstrom Resolution Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with S-Adenosyl-L-Homocysteine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6W75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 5.3 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: ComPAS (F10), 0.4M Potassium/Sodium tartrate; Soak and Cryo: 5mM SAH, 4M Sodium formate, 3 hrs.

Crystal Properties
Matthews coefficient	Solvent content
3.98	69.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.917	α = 90
b = 166.917	β = 90
c = 98.099	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	2020-04-03	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	30	100	0.101	0.101	0.11	0.044	16.7	6.5		105884		-3	34.2

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	2.03	100		0.795	0.795	0.866	0.34	0.933	3.2	6.6

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	6w75	2	29.79	100620	5233	99.8	0.1721	0.1711	0.1911	RANDOM	40.744

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]
1.35	0.67		1.35		-4.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.92
r_dihedral_angle_3_deg	8.207
r_dihedral_angle_4_deg	6.1
r_dihedral_angle_1_deg	2.423
r_angle_refined_deg	1.33
r_angle_other_deg	0.344
r_chiral_restr	0.059
r_gen_planes_refined	0.055
r_gen_planes_other	0.051
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.92
r_dihedral_angle_3_deg	8.207
r_dihedral_angle_4_deg	6.1
r_dihedral_angle_1_deg	2.423
r_angle_refined_deg	1.33
r_angle_other_deg	0.344
r_chiral_restr	0.059
r_gen_planes_refined	0.055
r_gen_planes_other	0.051
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6400
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	97

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.