7NBR

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

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	6.5	293.15	0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate pH 6.5, 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.767	α = 90
b = 53.37	β = 101.833
c = 45.949	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		2020-06-09	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	2.4	48.13	99.9	0.093	0.101	0.039	0.999	15.6	6.7		10684

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	2.4	2.53	100		0.496	0.663		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	2.4	34.44	10684	512	99.85	0.184	0.1801	0.2694	52.68

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]
1.082		0.593	1.961		-3.026

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.343
r_dihedral_angle_3_deg	17.398
r_dihedral_angle_4_deg	15.229
r_lrange_it	8.787
r_lrange_other	8.787
r_dihedral_angle_1_deg	8.379
r_scangle_it	6.353
r_scangle_other	6.351
r_mcangle_it	6.169
r_mcangle_other	6.138
r_mcbond_it	4.334
r_mcbond_other	4.309
r_scbond_it	4.218
r_scbond_other	4.217
r_angle_refined_deg	1.927
r_angle_other_deg	1.496
r_symmetry_xyhbond_nbd_refined	0.226
r_nbd_refined	0.219
r_nbd_other	0.199
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.172
r_chiral_restr	0.171
r_symmetry_nbtor_other	0.082
r_xyhbond_nbd_other	0.038
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_dihedral_angle_other_3_deg	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2319
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
SCALA	data scaling