9GIJ

Crystal structure of SARS-CoV-2 Mpro with compound 5

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	PCB: 0.100000 M pH:6.00 ; PEG 1500: 25.000000 %w/v

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.15	α = 90
b = 81.226	β = 114.78
c = 51.732	γ = 90

Symmetry
Space Group	C 1 2 1

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		2022-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9995	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.47	47.01	96.1	0.056	10.1	4.5		261893

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	1.47	1.5			0.824

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.476	47.01	54783	4593	96.09	0.1386	0.1354	0.1769	RANDOM	33.05

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]
1.8		-0.12	0.97		-1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.883
r_dihedral_angle_3_deg	12.314
r_dihedral_angle_4_deg	11.05
r_dihedral_angle_1_deg	6.873
r_mcangle_it	3.447
r_mcbond_other	2.695
r_mcbond_it	2.694
r_rigid_bond_restr	1.498
r_angle_refined_deg	1.388
r_angle_other_deg	1.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.883
r_dihedral_angle_3_deg	12.314
r_dihedral_angle_4_deg	11.05
r_dihedral_angle_1_deg	6.873
r_mcangle_it	3.447
r_mcbond_other	2.695
r_mcbond_it	2.694
r_rigid_bond_restr	1.498
r_angle_refined_deg	1.388
r_angle_other_deg	1.304
r_chiral_restr	0.073
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2340
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	35

Software

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