8CAJ

Crystal structure of SARS-CoV-2 Mpro-E166V mutant in complex with 13b-K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	0.2M Ammonium chloride, 0.1M Tris pH8.0, 20% w/vPEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.784	α = 90
b = 53.524	β = 99.906
c = 45.468	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 16M		2022-10-19	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	2.2	44.83	98.8	0.997	5.4	3.5		13861

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	2.27			0.527

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6y2e	2.2	44.83	13860	676	98.592	0.266	0.2612	0.3645	51.706

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]
1.995		0.439	-0.686		-1.378

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.762
r_dihedral_angle_3_deg	18.563
r_dihedral_angle_4_deg	10.835
r_lrange_it	9.056
r_lrange_other	9.055
r_dihedral_angle_1_deg	8.494
r_mcangle_it	5.302
r_mcangle_other	5.302
r_scangle_it	4.645
r_scangle_other	4.643
r_mcbond_other	3.322
r_mcbond_it	3.321
r_scbond_it	2.8
r_scbond_other	2.799
r_dihedral_angle_other_3_deg	1.63
r_angle_refined_deg	1.448
r_angle_other_deg	1.157
r_nbd_refined	0.227
r_symmetry_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.174
r_nbd_other	0.164
r_symmetry_nbd_refined	0.11
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr	0.056
r_bond_refined_d	0.005
r_gen_planes_refined	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	2331
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	43

Software

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