5S74

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	0.1	293.15	30% PEG 3K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.877	α = 90
b = 87.877	β = 90
c = 38.634	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 PILATUS 6M		2020-05-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91188	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	0.95	62.27	80.8	0.074	1	9.1			138299

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.95	0.97	7.4		1.226	0.33			685

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	FOURIER SYNTHESIS	THROUGHOUT	6WOJ	0.96	62.22	138299	7019	81.8	0.1769	0.1765	0.1852	RANDOM	12.467

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]
-0.33			-0.33		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.177
r_dihedral_angle_4_deg	22.812
r_dihedral_angle_3_deg	11.353
r_dihedral_angle_1_deg	6.857
r_angle_refined_deg	1.838
r_mcangle_it	1.778
r_angle_other_deg	1.666
r_mcbond_it	1.224
r_mcbond_other	1.223
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.177
r_dihedral_angle_4_deg	22.812
r_dihedral_angle_3_deg	11.353
r_dihedral_angle_1_deg	6.857
r_angle_refined_deg	1.838
r_mcangle_it	1.778
r_angle_other_deg	1.666
r_mcbond_it	1.224
r_mcbond_other	1.223
r_chiral_restr	0.095
r_bond_refined_d	0.017
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	2526
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	24

Software

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