6WKS

Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R24

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	10% (v/v) MPD, 0.1M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
4.44	72.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.067	α = 90
b = 168.067	β = 90
c = 52.304	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	PIXEL	DECTRIS PILATUS 6M-F		2020-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9792	APS	24-ID-C

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	1.8	30.002	99.9	0.13	0.13	0.13	0.042	0.997	13.6	20.02		78401			34.91

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	1.8	1.867	100		1.656	1.658	1.698	0.3742	0.707	1.35	18.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3r24	1.8	30.002	78401	3909	99.972	0.154	0.152	0.188	43.686

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]
-0.342	-0.171		-0.342		1.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.896
r_dihedral_angle_4_deg	17.672
r_dihedral_angle_3_deg	14.392
r_scangle_it	9.964
r_scbond_it	8.785
r_lrange_it	8.725
r_mcangle_it	7.228
r_rigid_bond_restr	6.541
r_dihedral_angle_1_deg	6.316
r_mcbond_it	6.118
r_angle_refined_deg	1.851
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.233
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.126
r_chiral_restr	0.124
r_bond_refined_d	0.015
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3163
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	103

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing