6YWK

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with HEPES

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293.15	33% BMW PgSmear, 0.1M MgCl2 and 0.1M HEPES 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.227	α = 90
b = 111.765	β = 90
c = 196.369	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 16M		2020-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00003	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	49.09	100	0.138	0.155	0.052	0.998	10.7	8.5		45087

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	99.9		0.925	1.064	0.374	0.762	2	7.9

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	6wen	2.2	49.09	42785	2228	99.94	0.1781	0.1763	0.2139	RANDOM	39.63

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]
0.6			-0.2		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.69
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_3_deg	13.414
r_dihedral_angle_1_deg	7.691
r_angle_refined_deg	1.383
r_angle_other_deg	1.292
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.69
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_3_deg	13.414
r_dihedral_angle_1_deg	7.691
r_angle_refined_deg	1.383
r_angle_other_deg	1.292
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6496
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	135

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	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.