8RI4

Crystal structure of the SARS-CoV-2 Main Protease inhibited by (2-methylsulfanyl-6,7-dihydro-[1,4]dioxino[2,3-f]benzimidazol-3-yl)-(p-tolyl)methanone

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	20% PEG3350, 0.2 M Sodium Formate, 2.5 mM DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.02	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.247	α = 90
b = 54.004	β = 101.142
c = 44.68	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 EIGER X 9M		2021-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9801	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.7	43.84	99.8	0.095	0.12	0.072	0.993	8.4	5.1		29703

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	99.9		0.89	0.667	0.631	1.3	5.2

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	1.7	38.455	29702	1515	99.738	0.191	0.1892	0.2344	18.189

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]
0.386		-0.701	0.285		-0.367

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.631
r_dihedral_angle_6_deg	15.309
r_dihedral_angle_3_deg	12.873
r_lrange_it	7.146
r_lrange_other	7.091
r_dihedral_angle_1_deg	7.066
r_scangle_it	5.303
r_scangle_other	5.302
r_scbond_other	3.604
r_scbond_it	3.6
r_mcangle_it	3.069
r_mcangle_other	3.068
r_angle_refined_deg	2.418
r_mcbond_it	2.116
r_mcbond_other	2.115
r_angle_other_deg	0.836
r_dihedral_angle_other_3_deg	0.36
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_refined	0.23
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.167
r_nbd_other	0.161
r_symmetry_nbd_refined	0.143
r_chiral_restr	0.12
r_symmetry_nbtor_other	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_symmetry_xyhbond_nbd_other	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2302
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
MOLREP	phasing
Aimless	data scaling
XDS	data reduction
MxCuBE	data collection