7C8R

Complex Structure of SARS-CoV-2 3CL Protease with TG-0203770

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZU4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	10% PEG 4000, 0.1 M sodium acetate trihydrate, pH 4.0.

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.39	α = 90
b = 104.39	β = 90
c = 90.233	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	RAYONIX MX300-HS		2020-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1.0	NSRRC	TPS 05A

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	2.3	25	99.8	0.92	22.9	11.6		13388

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	2.3	2.38			0.92

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	2ZU4	2.3	24.17	13343	681	99.537	0.203	0.2002	0.2483	31.468

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]
0.056	0.028		0.056		-0.183

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.213
r_dihedral_angle_4_deg	20.87
r_dihedral_angle_3_deg	15.168
r_dihedral_angle_1_deg	8.495
r_lrange_it	7.261
r_lrange_other	7.26
r_scangle_it	4.256
r_scangle_other	4.255
r_dihedral_angle_other_3_deg	4.106
r_mcangle_it	3.653
r_mcangle_other	3.652
r_scbond_it	2.77
r_scbond_other	2.769
r_mcbond_other	2.391
r_mcbond_it	2.39
r_angle_refined_deg	1.625
r_angle_other_deg	1.297
r_symmetry_nbd_refined	0.238
r_nbd_other	0.226
r_nbd_refined	0.199
r_symmetry_nbd_other	0.198
r_xyhbond_nbd_refined	0.192
r_symmetry_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_other	0.155
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2329
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing