8AEB

SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide

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, 21% PEG 3350, 10% Glycerol, 8% DMSO

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.141	α = 90
b = 53.472	β = 101.304
c = 44.65	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 9M		2022-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980104	SOLEIL	PROXIMA 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	1.83	48.373	98.7	0.093	0.111	0.06	0.997	9.9	6.2		23313

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	1.83	1.88	89.8		1.22	1.464	0.8	0.476	1.2	6

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	1.83	48.373	22949	1170	97.11	0.186	0.1835	0.2341	31.676

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]
1.247		0.718	-0.583		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.954
r_dihedral_angle_6_deg	16.303
r_dihedral_angle_3_deg	15.408
r_lrange_it	8.806
r_lrange_other	8.765
r_dihedral_angle_1_deg	8.39
r_scangle_it	7.028
r_scangle_other	7.026
r_scbond_other	5.3
r_scbond_it	5.295
r_mcangle_other	4.736
r_mcangle_it	4.734
r_mcbond_it	3.963
r_mcbond_other	3.963
r_angle_refined_deg	2.067
r_angle_other_deg	0.714
r_metal_ion_refined	0.367
r_nbd_refined	0.253
r_symmetry_xyhbond_nbd_refined	0.249
r_symmetry_nbd_other	0.215
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.186
r_symmetry_nbd_refined	0.182
r_nbd_other	0.172
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2341
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	22

Software

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