7NBS

Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with the HCV NS3/4A inhibitor telaprevir

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	7.5	293.15	0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH 7.5, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.69	α = 90
b = 54.625	β = 101.404
c = 48.277	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 6M		2020-09-07	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	48.748	100	0.073	0.079	0.03	0.999	15.6	6.7		30908

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	100		0.462	0.688	1.8	6.5

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	48.7	30908	1536	99.987	0.208	0.2061	0.256	27.156

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]
-0.368		-1.338	1.247		-0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.437
r_dihedral_angle_4_deg	22.489
r_dihedral_angle_3_deg	13.982
r_dihedral_angle_1_deg	7.895
r_lrange_it	5.818
r_lrange_other	5.782
r_scangle_it	4.274
r_scangle_other	4.273
r_dihedral_angle_other_3_deg	4.176
r_mcangle_it	3.333
r_mcangle_other	3.333
r_scbond_it	2.827
r_scbond_other	2.826
r_mcbond_it	2.284
r_mcbond_other	2.284
r_angle_refined_deg	1.665
r_angle_other_deg	1.464
r_xyhbond_nbd_refined	0.21
r_nbd_refined	0.204
r_nbd_other	0.197
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.17
r_symmetry_nbd_refined	0.168
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2351
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
SCALA	data scaling