7C8U

The crystal structure of COVID-19 main protease in complex with GC376

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2M Lithium chloride, 0.1M Hepes pH 7, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.303	α = 90
b = 53.874	β = 101.576
c = 45.233	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		2020-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	2.35	48.57	99.2	0.065	0.065	0.036	0.998	9.7	3		11269

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	2.35	2.43			0.347	0.418	0.23	0.889

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	NONE	1q2w	2.35	44.352	11226	563	98.742	0.215	0.2115	0.2728	40.478

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]
		-0.013	-0.013		0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.104
r_dihedral_angle_4_deg	15.332
r_dihedral_angle_3_deg	13.32
r_dihedral_angle_1_deg	6.949
r_dihedral_angle_other_3_deg	5.499
r_lrange_it	4.984
r_lrange_other	4.984
r_mcangle_it	2.895
r_mcangle_other	2.892
r_scangle_other	2.844
r_scangle_it	2.624
r_angle_other_deg	2.391
r_mcbond_it	1.715
r_mcbond_other	1.709
r_scbond_it	1.568
r_scbond_other	1.567
r_angle_refined_deg	1.247
r_symmetry_nbd_refined	0.217
r_symmetry_nbd_other	0.209
r_nbd_refined	0.191
r_nbd_other	0.191
r_nbtor_refined	0.157
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_other	0.071
r_symmetry_nbtor_other	0.062
r_chiral_restr	0.046
r_bond_other_d	0.036
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2323
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	29

Software

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