7WQ8

Crystal structure of SARS-CoV-2 main protease in complex with Z-DEVD-FMK

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.15 M DL-Malic acid pH 7.0, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.178	α = 90
b = 54.636	β = 101.134
c = 45.279	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	CCD	RAYONIX MX300HE		2020-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.00000	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	30	98.83	0.067	19.69	3.8		13674

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	95.43		0.35	3.73	3.8

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	6Y2E, 6LU7	2.2	27.532	13639	664	98.805	0.18	0.1782	0.2221	31.689

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]
-0.197		-0.403	0.114		0.225

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.466
r_dihedral_angle_4_deg	18.568
r_dihedral_angle_3_deg	16.387
r_dihedral_angle_1_deg	8.21
r_lrange_it	7.791
r_lrange_other	7.563
r_scangle_it	5.268
r_scangle_other	5.147
r_dihedral_angle_other_3_deg	4.314
r_mcangle_it	4.131
r_mcangle_other	4.131
r_scbond_it	3.511
r_scbond_other	3.399
r_mcbond_it	2.646
r_mcbond_other	2.643
r_angle_refined_deg	1.429
r_angle_other_deg	1.329
r_symmetry_xyhbond_nbd_refined	0.26
r_nbd_refined	0.205
r_symmetry_nbd_other	0.196
r_nbd_other	0.193
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.169
r_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
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	65
Heterogen Atoms

Software

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