8UH5 | pdb_00008uh5

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-272

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8DOX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1 M MES, pH 5.8, 15% PEG6000, 3% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2	38.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.003	α = 90
b = 53.078	β = 102.17
c = 45.783	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 EIGER X 16M		2022-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1	SPring-8	BL41XU

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	1.74	55.72	99.85	0.9989	11.9	8.6		27421

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	1.74	1.77			0.3184

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.74	55.72	26028	1393	99.82	0.19602	0.1939	0.2	0.23299	0.24	RANDOM	46.261

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]
1.46		-0.17	0.24		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.856
r_dihedral_angle_2_deg	12.048
r_long_range_B_refined	10.809
r_long_range_B_other	10.807
r_scangle_other	8.989
r_dihedral_angle_1_deg	7.773
r_scbond_it	6.456
r_scbond_other	6.454
r_mcangle_it	6.214
r_mcangle_other	6.212
r_mcbond_it	4.936
r_mcbond_other	4.934
r_angle_refined_deg	2.144
r_angle_other_deg	0.792
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2367
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
CrystalClear	data scaling
MOLREP	phasing