6Y7M

Crystal structure of the complex resulting from the reaction between the SARS-CoV main protease and tert-butyl (1-((S)-3-cyclohexyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.1 MES, 6% PEG 6,000, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.905	α = 90
b = 82.247	β = 104.465
c = 53.131	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 S 6M		2019-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0000	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	1.9	43.67	99.4	0.048	0.056	0.028	0.998	12.8	3.9		35225

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	99.1		0.639	0.742	0.372	0.88	2.2	3.8

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	1.9	42.356	35112	1700	98.993	0.209	0.2062	0.2576	48.235

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]
-2.775		1.733	1.732		0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.941
r_dihedral_angle_4_deg	18.135
r_dihedral_angle_3_deg	15.721
r_lrange_it	9.061
r_lrange_other	9.027
r_dihedral_angle_1_deg	7.877
r_scangle_it	6.9
r_scangle_other	6.898
r_mcangle_it	5.865
r_mcangle_other	5.865
r_scbond_it	4.857
r_scbond_other	4.857
r_mcbond_it	4.333
r_mcbond_other	4.33
r_angle_refined_deg	1.822
r_angle_other_deg	1.45
r_dihedral_angle_other_3_deg	0.321
r_nbd_refined	0.214
r_nbd_other	0.197
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.184
r_chiral_restr	0.179
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.157
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2371
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	46

Software

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