7MLG

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C63

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.1 M BTP, pH 6.5, 20% PEG3350, 0.2 M potassium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.45	α = 90
b = 53.318	β = 101.88
c = 45.474	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 EIGER2 X 16M		2021-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

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	2.5	48.11	97.9	0.998	12.52	2.8		9329

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	2.5	2.59	99.1		0.786	1.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 6Y2E	2.5	48.11	8670	434	97.6	0.22899	0.224	0.268	RANDOM	59.42

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]
-0.98		-1.6	0.82		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.914
r_dihedral_angle_4_deg	18.516
r_dihedral_angle_3_deg	13.995
r_dihedral_angle_1_deg	7.02
r_scangle_other	5.406
r_mcangle_it	5.396
r_mcangle_other	5.395
r_mcbond_it	3.173
r_mcbond_other	3.173
r_scbond_it	3.154
r_scbond_other	3.153
r_angle_other_deg	1.239
r_angle_refined_deg	1.237
r_chiral_restr	0.05
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2347
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing