5S73

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
2.04	39.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.93	α = 90
b = 87.93	β = 90
c = 38.464	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		2020-07-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91258	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	1.06	88.23	99.6	0.077	1	6.3			108843

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	1.06	1.08	93.8		1.321	0.31			6203

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	1.06	88.09	108843	5788	85.81	0.2021	0.2009	0.2234	RANDOM	15.165

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]
-0.53			-0.53		1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.54
r_dihedral_angle_4_deg	18.464
r_dihedral_angle_3_deg	10.94
r_dihedral_angle_1_deg	6.87
r_mcangle_it	1.903
r_angle_refined_deg	1.734
r_angle_other_deg	1.596
r_mcbond_it	1.327
r_mcbond_other	1.326
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.54
r_dihedral_angle_4_deg	18.464
r_dihedral_angle_3_deg	10.94
r_dihedral_angle_1_deg	6.87
r_mcangle_it	1.903
r_angle_refined_deg	1.734
r_angle_other_deg	1.596
r_mcbond_it	1.327
r_mcbond_other	1.326
r_chiral_restr	0.087
r_bond_refined_d	0.013
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

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 R01GM133198.