7NTQ | pdb_00007ntq

Crystal structure of the 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, 20% PEG 3350, 10% Glycerol, 10% DMSO

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.92	α = 90
b = 52.91	β = 102.88
c = 44.9	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	1.49	47.84	98.7	0.998	9.77	6.9		42066

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	1.49	1.59	91.9		0.51

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7K3T	1.495	43.809	42065	2104	98.712	0.173	0.1706	0.18	0.2132	0.22	23.691

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]
0.473		-0.229	0.034		-0.364

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.03
r_dihedral_angle_4_deg	12.973
r_dihedral_angle_3_deg	12.37
r_dihedral_angle_1_deg	7.279
r_angle_refined_deg	1.675
r_angle_other_deg	1.458
r_dihedral_angle_other_3_deg	0.764
r_symmetry_nbd_refined	0.302
r_symmetry_xyhbond_nbd_refined	0.278
r_nbd_refined	0.233
r_symmetry_nbd_other	0.188
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.17
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2368
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	44

Software

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