6Y2E

Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M MMT (DL-malic acid, MES and Tris base in the molar ratios 1:2:2), pH 7.0, 25% PEG 1,500

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.983	α = 90
b = 53.763	β = 101.242
c = 44.774	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 PILATUS3 2M		2020-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	1.75	48.53	100	0.082	0.089	0.034	0.999	15	6.8		27173

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.84	100		0.967	0.387	0.747	2.1	7.1

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	2BX4	1.75	48.53	27171	1309	99.971	0.174	0.1712	0.2224	25.186

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]
0.636		-0.445	0.706		-1.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.02
r_dihedral_angle_3_deg	16.155
r_dihedral_angle_4_deg	15.211
r_dihedral_angle_1_deg	7.865
r_lrange_it	6.467
r_lrange_other	6.188
r_scangle_it	4.371
r_scangle_other	4.37
r_scbond_it	2.868
r_scbond_other	2.866
r_mcangle_it	2.851
r_mcangle_other	2.85
r_mcbond_it	2.035
r_mcbond_other	2.028
r_angle_refined_deg	1.566
r_angle_other_deg	1.409
r_nbd_other	0.219
r_xyhbond_nbd_refined	0.211
r_nbd_refined	0.204
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_refined	0.186
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.17
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.077
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	2367
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms

Software

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