9EWO

Mpro from SARS-CoV-2 with R4A R298A double mutations

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG 3350, 0.12 mM benzamidine hydrochloride, 200 mM potassium formate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.326	α = 90
b = 53.464	β = 102.396
c = 46.081	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 PILATUS3 S 6M		2023-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9677	ESRF	ID23-1

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	3	53.88	91.5	0.992	6.3	5.4		16784

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	3	3.22			0.311

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	3.002	53.877	4097	198	76.337	0.198	0.1938	0.2754	74.837

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]
0.315		0.586	0.149		-0.657

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.464
r_dihedral_angle_6_deg	12.955
r_lrange_it	12.481
r_lrange_other	12.479
r_dihedral_angle_1_deg	8.891
r_scangle_it	7.997
r_scangle_other	7.953
r_mcangle_it	7.854
r_mcangle_other	7.851
r_dihedral_angle_2_deg	5.15
r_mcbond_it	4.845
r_mcbond_other	4.845
r_scbond_it	4.742
r_scbond_other	4.713
r_angle_refined_deg	1.158
r_angle_other_deg	0.394
r_nbd_refined	0.232
r_symmetry_nbd_other	0.208
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.183
r_nbd_other	0.178
r_symmetry_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.049
r_chiral_restr	0.048
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2311
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing