9EUS

Mpro from SARS-CoV-2 with R298A mutation

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG 3350, 0.18 mM benzamidine hydrochloride, 200 mM potassium formate

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.825	α = 90
b = 53.392	β = 101.046
c = 114.514	γ = 90

Symmetry
Space Group	P 1 21 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		2022-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03323	PETRA III, DESY	P11

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	2	48.23	97.7	0.994	6	7		245946

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	2	2.05			0.579

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	2	48.227	35275	1739	97.404	0.23	0.2279	0.2773	39.615

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]
-1.888		-0.71	-0.925		2.872

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.067
r_dihedral_angle_3_deg	14.004
r_dihedral_angle_2_deg	9.56
r_dihedral_angle_1_deg	8.058
r_lrange_other	7.622
r_lrange_it	7.62
r_scangle_it	5.764
r_scangle_other	5.763
r_mcangle_it	4.703
r_mcangle_other	4.703
r_scbond_it	3.785
r_scbond_other	3.784
r_mcbond_it	3.199
r_mcbond_other	3.195
r_angle_refined_deg	1.625
r_angle_other_deg	0.69
r_symmetry_xyhbond_nbd_other	0.306
r_nbd_refined	0.188
r_nbtor_refined	0.165
r_symmetry_nbd_other	0.156
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.137
r_nbd_other	0.123
r_symmetry_nbd_refined	0.098
r_ncsr_local_group_1	0.083
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4658
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	18

Software

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