8C9L

Crystal structure of SARS-CoV-2 Mpro-S144A mutant, free enzyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other	6y2e

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1MBis Tris Propane pH 6.50.02 MSodium potassium phosphate pH 7.520 % w/vPEG 335010% v/vEthylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.074	α = 90
b = 53.694	β = 102.049
c = 44.707	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 PILATUS 6M-F		2022-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	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	1.7	48.38	98.59	0.999	16.97	5		28802			35.01

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	1.7	1.76	96.28		0.55

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6y2e	1.7	48.38	28798	1428	98.604	0.209	0.2069	0.21	0.244	0.24	37.975

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]
0.893		0.658	-1.056		-0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.513
r_dihedral_angle_4_deg	16.496
r_dihedral_angle_3_deg	15.6
r_dihedral_angle_1_deg	7.659
r_lrange_it	7.103
r_lrange_other	7.095
r_scangle_it	5.509
r_scangle_other	5.509
r_mcangle_it	4.117
r_mcangle_other	4.115
r_scbond_it	3.907
r_scbond_other	3.905
r_mcbond_it	3.13
r_mcbond_other	3.122
r_angle_refined_deg	1.612
r_angle_other_deg	1.397
r_symmetry_nbd_refined	0.237
r_nbd_refined	0.206
r_nbd_other	0.198
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.084
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2332
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms

Software

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