7WQ9

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M MES monohydrate pH 6.0, 20% w/v Polyethylene glycol monomethyl ether 2,000

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.387	α = 90
b = 55.248	β = 101.516
c = 46.901	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		2020-07-25	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	2.054	30	99.5	0.059	20.47	3.6		17239

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	2.054	2.13	98.7		0.494	2.3	3.3

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	2.054	21.594	16657	835	95.79	0.212	0.2097	0.2463	28.341

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]
-0.241		-0.314	0.442		-0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.602
r_dihedral_angle_other_3_deg	20.701
r_dihedral_angle_3_deg	15.877
r_dihedral_angle_4_deg	15.673
r_dihedral_angle_1_deg	8.253
r_lrange_it	6.54
r_lrange_other	6.484
r_scangle_it	4.569
r_scangle_other	4.468
r_mcangle_it	3.727
r_mcangle_other	3.727
r_scbond_it	2.939
r_scbond_other	2.861
r_mcbond_it	2.482
r_mcbond_other	2.478
r_angle_refined_deg	1.37
r_angle_other_deg	1.3
r_nbd_other	0.238
r_nbd_refined	0.226
r_symmetry_nbd_other	0.205
r_symmetry_nbd_refined	0.188
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.176
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_other	0.116
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2374
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms

Software

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