6WQ3 | pdb_00006wq3

Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with 7-methyl-GpppA and S-adenosyl-L-homocysteine.

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	6.5	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: Anions (A10), 0.1M MES pH 6.5, 0.6M tri-Sodium citrate; Soak and Cryo: 1mM SAH, 0.5mM GpppA, 2M Lithium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
4.34	71.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.648	α = 90
b = 169.648	β = 90
c = 52.055	γ = 120

Symmetry
Space Group	P 31 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	2020-04-23	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)	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	2.1	30	98.8	0.075	0.075	0.081	0.028	0.995	21.1	7.7		50035		-3	45.4

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	2.1	2.14	98.9		0.811	0.811	0.868	0.3	0.755	2.3	7.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6w4h	2.1	28.31	47173	2511	98.81	0.1671	0.1661	0.17	0.1859	0.19	RANDOM	53.778

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]
0.43	0.21		0.43		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.879
r_dihedral_angle_4_deg	11.27
r_dihedral_angle_3_deg	9.172
r_dihedral_angle_1_deg	3.036
r_angle_refined_deg	1.266
r_angle_other_deg	0.533
r_chiral_restr	0.054
r_gen_planes_refined	0.048
r_gen_planes_other	0.045
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.879
r_dihedral_angle_4_deg	11.27
r_dihedral_angle_3_deg	9.172
r_dihedral_angle_1_deg	3.036
r_angle_refined_deg	1.266
r_angle_other_deg	0.533
r_chiral_restr	0.054
r_gen_planes_refined	0.048
r_gen_planes_other	0.045
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3223
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	153

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.