23LY | pdb_000023ly

Crystal structure of SARS-CoV-2 main protease E166V 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, HANGING DROP		289	0.1 M Ammonium citrate tribasic pH 6.0, 14% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.837	α = 90
b = 106.317	β = 103.218
c = 54.145	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	1.56	53.16	99.7	0.076	0.997	12.2	5.2		76106

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	1.56	1.59			0.859	0.615	2.4

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	1.56	53.159	75840	3863	99.355	0.15	0.1475	0.1552	0.1974	0.2082	21.353

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]
2.516		-0.094	1.641		-3.704

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.799
r_lrange_it	16.758
r_lrange_other	15.702
r_dihedral_angle_6_deg	15.512
r_dihedral_angle_3_deg	13.928
r_scangle_it	10.414
r_scangle_other	10.412
r_mcangle_it	8.871
r_mcangle_other	8.87
r_scbond_it	7.151
r_scbond_other	7.149
r_dihedral_angle_1_deg	6.913
r_mcbond_it	5.956
r_mcbond_other	5.938
r_rigid_bond_restr	3.609
r_dihedral_angle_other_3_deg	3.319
r_angle_refined_deg	1.8
r_angle_other_deg	0.617
r_symmetry_nbd_refined	0.343
r_nbd_refined	0.219
r_nbd_other	0.214
r_symmetry_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.179
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.085
r_symmetry_xyhbond_nbd_other	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4702
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	96

Software

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