7C8T

Complex Structure of SARS-CoV-2 3CL Protease with TG-0205221

X-RAY DIFFRACTION

---

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	3.5	293	14% PEG 1,000, 0.1 M citric acid, pH 3.5.

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.42	α = 90
b = 104.42	β = 90
c = 89.888	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	120	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	2.05	25	99.9	0.96	39.5	18.2		18754

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	2.05	2.12			0.99

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	2.05	24.17	18166	893	97.217	0.187	0.1843	0.2334	30.021

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]
-0.105	-0.052		-0.105		0.339

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.993
r_dihedral_angle_3_deg	15.346
r_dihedral_angle_4_deg	14.799
r_dihedral_angle_1_deg	7.873
r_lrange_it	6.048
r_lrange_other	5.837
r_scangle_it	2.96
r_scangle_other	2.959
r_dihedral_angle_other_3_deg	2.916
r_mcangle_other	2.553
r_mcangle_it	2.552
r_angle_refined_deg	1.904
r_scbond_it	1.826
r_scbond_other	1.826
r_mcbond_it	1.506
r_mcbond_other	1.485
r_angle_other_deg	1.445
r_nbd_other	0.31
r_symmetry_nbd_refined	0.267
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.172
r_chiral_restr	0.102
r_symmetry_xyhbond_nbd_other	0.09
r_symmetry_nbtor_other	0.083
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2369
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	data scaling
MOLREP	phasing