6Y2G

Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M sodium citrate tribasic dihydrate, 0.2 M potassium sodium tartrate tetrahydrate, 0.2 M sodium oxamate), 0.1 M buffer system 3 (1.0 M tris (base), bicine, pH 8.5), pH 8.5, 30% precipitant mix 1 (20% v/v PEG 500 methyl ether, 10% PEG 20,000))

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.566	α = 90
b = 101.602	β = 90
c = 103.696	γ = 90

Symmetry
Space Group	P 21 21 21

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	2.2	49.84	100	0.17	0.177	0.048	0.998	13.1	13.1		37519			35.58

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	2.2	2.32	100		0.414	0.662	2.1	12.1

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2BX4	2.2	41.355	37448	1761	99.947	0.191	0.189	0.2343	5.07	41.09

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]
-0.015			-0.076		0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.326
r_dihedral_angle_6_deg	15.862
r_lrange_other	9.93
r_lrange_it	9.928
r_dihedral_angle_1_deg	7.738
r_dihedral_angle_2_deg	7.719
r_scangle_it	7.495
r_scangle_other	7.494
r_mcangle_it	6.492
r_mcangle_other	6.492
r_scbond_it	4.985
r_scbond_other	4.984
r_mcbond_it	4.432
r_mcbond_other	4.431
r_angle_refined_deg	1.62
r_angle_other_deg	0.759
r_dihedral_angle_other_3_deg	0.64
r_nbd_refined	0.22
r_symmetry_nbd_other	0.202
r_symmetry_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.183
r_nbd_other	0.17
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4669
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	86

Software

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