8C19

SARS-CoV-2 NSP3 macrodomain in complex with 1-methyl-4-[5-(morpholin-4-ylcarbonyl)-2-furyl]-1H-pyrrolo[2,3-b]pyridine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100 mM CHES pH 9.5, 30% PEG3000

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.604	α = 90
b = 88.604	β = 90
c = 39.826	γ = 90

Symmetry
Space Group	P 43

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 XE 16M		2020-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.896844	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.95	39.83	100	0.994	5.5	13.4		22915

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2			0.603

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.95	39.656	22807	1034	99.598	0.182	0.1794	0.2262	27.636

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]
-1.966			-1.966		3.932

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.015
r_dihedral_angle_3_deg	13.808
r_dihedral_angle_1_deg	6.977
r_lrange_it	6.246
r_lrange_other	6.22
r_dihedral_angle_2_deg	5.779
r_scangle_it	5.34
r_scangle_other	5.339
r_scbond_it	3.471
r_scbond_other	3.47
r_mcangle_other	3.211
r_mcangle_it	3.21
r_mcbond_it	2.293
r_mcbond_other	2.271
r_angle_refined_deg	1.528
r_angle_other_deg	0.504
r_nbd_refined	0.216
r_symmetry_nbd_other	0.19
r_nbd_other	0.184
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.14
r_xyhbond_nbd_refined	0.125
r_symmetry_nbd_refined	0.09
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2526
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing