23ML | pdb_000023ml

Crystal structure of SARS-CoV-2 main protease Q189K mutant in complex with leritrelvir

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VH8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	1.0 M Ammonium sulfate, 0.1 M HEPES pH 7.0, 0.5% w/v Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.613	α = 90
b = 105.889	β = 103.243
c = 54.291	γ = 90

Symmetry
Space Group	P 1 21 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 6M		2024-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97923	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.16	52.945	93.8	0.156	0.994	12	6.2		26951

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.16	2.23			1.737	0.764	2.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.16	52.945	26710	1310	93.024	0.195	0.1918	0.1992	0.2533	0.2599	28.751

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]
-0.445		1.001	-0.338		0.281

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.424
r_dihedral_angle_6_deg	14.416
r_dihedral_angle_3_deg	14.313
r_lrange_it	7.862
r_lrange_other	7.854
r_dihedral_angle_1_deg	7.396
r_scangle_it	5.138
r_scangle_other	5.138
r_mcangle_it	4.169
r_mcangle_other	4.168
r_scbond_it	3.39
r_scbond_other	3.39
r_dihedral_angle_other_3_deg	3.203
r_mcbond_it	2.757
r_mcbond_other	2.754
r_angle_refined_deg	1.708
r_angle_other_deg	0.59
r_symmetry_nbd_refined	0.223
r_nbd_refined	0.213
r_symmetry_xyhbond_nbd_refined	0.206
r_nbd_other	0.203
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4713
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	90

Software

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