6Z2E

Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone

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, HANGING DROP	7.5	293.15	0.12 M Ethylene glycols (0.3 M Diethylene glycol, 0.3 M Triethylene glycol, 0.3 M Tetraethylene glycol, 0.3 M Pentaethylene glycol), 0.1 M buffer system 2 (1.0 M Sodium HEPES, MOPS (acid), pH 7.5), pH 7.5, 30% Precipitant mix 3 (20% glycerol, 10% PEG 4000)

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.083	α = 90
b = 104.083	β = 90
c = 91.246	γ = 120

Symmetry
Space Group	P 61 2 2

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		2020-04-22	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)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	45.62	100	0.074	0.075	0.012	1	32.4	38.5		32640

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	100		1.574	1.595	0.257	0.861		38

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	1.7	45.247	32594	1625	99.982	0.195	0.192	0.2434	32.48

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]
-0.334	-0.167		-0.334		1.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.738
r_dihedral_angle_4_deg	15.901
r_dihedral_angle_3_deg	13.75
r_dihedral_angle_1_deg	7.513
r_lrange_it	6.893
r_lrange_other	6.828
r_scangle_it	5.148
r_scangle_other	5.147
r_mcangle_it	3.919
r_mcangle_other	3.918
r_scbond_it	3.548
r_scbond_other	3.416
r_mcbond_it	2.881
r_mcbond_other	2.881
r_angle_refined_deg	1.814
r_angle_other_deg	1.442
r_dihedral_angle_other_3_deg	1.398
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.204
r_xyhbond_nbd_refined	0.202
r_nbd_other	0.202
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.172
r_metal_ion_refined	0.13
r_symmetry_xyhbond_nbd_refined	0.129
r_chiral_restr	0.088
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2368
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	70

Software

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