7BF5

Crystal structure of SARS-CoV-2 macrodomain in complex with ADP-ribose-phosphate (ADP-ribose-2'-phosphate, ADPRP)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293.15	30% broad-molecular-weight PEG smears, 0.1 M MgCl2, 0.1 M tris, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.617	α = 90
b = 111.339	β = 90
c = 195.184	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		2020-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00001	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	2.05	48.8	99.7	0.141	0.166	0.064	0.995	8.3	6.2		53878

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	2.05	2.12	99.8		0.839	0.998	0.387	0.695	1.9	6.3

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	6ywk	2.05	48.8	51148	2662	99.47	0.1792	0.1772	0.2168	RANDOM	26.716

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]
1.04			-0.39		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.092
r_dihedral_angle_4_deg	18.864
r_dihedral_angle_3_deg	12.823
r_dihedral_angle_1_deg	7.396
r_angle_refined_deg	1.426
r_angle_other_deg	1.363
r_chiral_restr	0.072
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.092
r_dihedral_angle_4_deg	18.864
r_dihedral_angle_3_deg	12.823
r_dihedral_angle_1_deg	7.396
r_angle_refined_deg	1.426
r_angle_other_deg	1.363
r_chiral_restr	0.072
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6488
Nucleic Acid Atoms
Solvent Atoms	514
Heterogen Atoms	175

Software

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