7QL8

SARS-COV2 Main Protease in complex with inhibitor MG78

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	MMT, PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.52	α = 90
b = 64.04	β = 90
c = 105.38	γ = 90

Symmetry
Space Group	P 21 21 2

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 EIGER X 16M		2021-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.807	40.69	86.101	0.9	3.57	6		29378

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	1.807	1.854			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	6y2e	1.807	40.688	24983	1248	86.101	0.238	0.2345	0.3002	49.403

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]
-1.553			-0.715		2.268

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.719
r_dihedral_angle_4_deg	20.624
r_dihedral_angle_3_deg	18.07
r_dihedral_angle_other_3_deg	16.223
r_lrange_it	8.145
r_lrange_other	8.118
r_dihedral_angle_1_deg	7.915
r_scangle_it	5.926
r_scangle_other	5.924
r_mcangle_it	5.419
r_mcangle_other	5.417
r_scbond_it	3.826
r_scbond_other	3.824
r_mcbond_other	3.688
r_mcbond_it	3.686
r_angle_refined_deg	1.52
r_angle_other_deg	1.23
r_symmetry_xyhbond_nbd_refined	0.306
r_nbd_other	0.212
r_nbd_refined	0.21
r_symmetry_nbd_other	0.18
r_symmetry_nbd_refined	0.174
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.152
r_metal_ion_refined	0.08
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.06
r_bond_other_d	0.008
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2329
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	42

Software

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