7NTS

Crystal structure of the SARS-CoV-2 Main Protease with oxidized C145

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7K3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M NaFormate, 20% PEG 3350, 10% DMSO, 10% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.69	α = 90
b = 52.96	β = 102.95
c = 44.85	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 EIGER X 16M		2020-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.978564	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.477	47.828	97.1	0.998	11.7	7.1		42473

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.57	93.6		0.7

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	7K3T	1.477	47.828	42468	2124	97.207	0.168	0.1657	0.2072	21.072

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]
0.82		-0.64	0.061		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.277
r_dihedral_angle_4_deg	12.733
r_dihedral_angle_3_deg	12.083
r_dihedral_angle_1_deg	7.483
r_angle_refined_deg	1.7
r_angle_other_deg	1.516
r_nbd_refined	0.217
r_nbd_other	0.201
r_xyhbond_nbd_refined	0.2
r_symmetry_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.156
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2359
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing
XDS	data processing
Coot	model building