7CX9

Crystal structure of the SARS-CoV-2 main protease in complex with INZ-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7C7P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1M MES pH5.0; 11% PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.236	α = 90
b = 82.9	β = 115.123
c = 51.489	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 PILATUS3 S 6M		2020-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.978531	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.73	19.44	97.2	0.057	0.019	0.999	21.6	10.1		37429

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.76	93.3		1.046	0.345	0.799	2.2

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	7C7P	1.73	19.44	37425	1767	96.943	0.172	0.1701	0.2092	30.052

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]
1.255		-0.68	0.859		-1.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.383
r_dihedral_angle_other_3_deg	27.819
r_dihedral_angle_3_deg	14.955
r_dihedral_angle_4_deg	12.151
r_lrange_it	8.292
r_lrange_other	8.185
r_dihedral_angle_1_deg	7.144
r_scangle_it	6.004
r_scangle_other	6.002
r_mcangle_it	4.328
r_mcangle_other	4.328
r_scbond_it	4
r_scbond_other	3.999
r_mcbond_it	3.206
r_mcbond_other	3.196
r_angle_refined_deg	1.867
r_angle_other_deg	1.509
r_symmetry_nbd_refined	0.223
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.215
r_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.176
r_nbd_other	0.166
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.045
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2283
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	19

Software

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