8C1A

SARS-CoV-2 NSP3 macrodomain in complex with aztreonam

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7KQP

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
2.14	42.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.475	α = 90
b = 88.475	β = 90
c = 39.139	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		2020-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	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	1.9	62.639	95.2	1	62.9	10.8		249288

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	1.9	1.94			0.983

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	7KQP	1.9	62.639	22971	1228	94.839	0.173	0.1705	0.2141	19.547

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]
-1.106			-1.106		2.211

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.275
r_dihedral_angle_3_deg	12.631
r_dihedral_angle_1_deg	6.835
r_dihedral_angle_2_deg	5.034
r_lrange_it	5.022
r_lrange_other	5.003
r_scangle_it	3.934
r_scangle_other	3.933
r_mcangle_other	2.606
r_mcangle_it	2.604
r_scbond_it	2.497
r_scbond_other	2.496
r_mcbond_it	1.794
r_mcbond_other	1.794
r_angle_refined_deg	1.623
r_angle_other_deg	0.479
r_nbd_other	0.222
r_nbd_refined	0.219
r_symmetry_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.186
r_symmetry_nbd_refined	0.183
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.119
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.07
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	2520
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	32

Software

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