8CA8

Crystal structure of SARS-CoV-2 Mpro-H172Y mutant, free enzyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	6y2e

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1M Bis Tris Propane pH 6.5, 0.2 MSodium acetate trihydrate, 20 % w/vPEG 3350, 10% v/vEthylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.398	α = 90
b = 54.273	β = 100.777
c = 45.021	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	1.003	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	44.23	98.7	0.999	12	4.9		18059			39.23

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	2.072			0.527	1.34

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	44.23	18059	933	98.489	0.211	0.2077	0.21	0.2712	0.28	43.513

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]
0.833		1.041	-0.565		-0.619

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.439
r_dihedral_angle_4_deg	17.417
r_dihedral_angle_3_deg	17.003
r_lrange_other	8.795
r_lrange_it	8.783
r_dihedral_angle_1_deg	8.43
r_scangle_it	6.734
r_scangle_other	6.734
r_mcangle_it	5.403
r_mcangle_other	5.378
r_scbond_it	4.689
r_scbond_other	4.687
r_mcbond_it	3.937
r_mcbond_other	3.913
r_angle_refined_deg	1.621
r_angle_other_deg	1.317
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_refined	0.21
r_nbd_other	0.192
r_symmetry_nbd_refined	0.191
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.17
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2335
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	1

Software

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