23MI | pdb_000023mi

Crystal structure of SARS-CoV-2 main protease M49T 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	0.1 M Tris pH 8.0, 30% w/v Polyethylene glycol monomethyl ether 2,000

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.784	α = 90
b = 106.314	β = 103.002
c = 54.055	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	1.7	52.725	94	0.113	0.991	8.6	4.2		55394

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	1.7	1.73			0.557	0.635	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	1.7	52.725	55340	2751	93.92	0.173	0.1705	0.1785	0.2165	0.2208	20.87

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]
-0.076		0.918	-0.088		-0.234

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.255
r_dihedral_angle_6_deg	13.239
r_dihedral_angle_3_deg	12.716
r_dihedral_angle_1_deg	6.954
r_lrange_it	6.371
r_lrange_other	6.114
r_scangle_it	4.078
r_scangle_other	4.078
r_mcangle_it	3.126
r_mcangle_other	3.126
r_scbond_it	2.605
r_scbond_other	2.605
r_mcbond_it	2.042
r_mcbond_other	2.04
r_angle_refined_deg	1.594
r_dihedral_angle_other_3_deg	1.269
r_angle_other_deg	0.535
r_symmetry_nbd_refined	0.221
r_nbd_refined	0.213
r_nbd_other	0.199
r_symmetry_nbd_other	0.194
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.166
r_ncsr_local_group_1	0.092
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.053
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	4783
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	102

Software

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