23MK | pdb_000023mk

Crystal structure of SARS-CoV-2 main protease P168 deletion and A173V 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	0.1M Sodium acetate trihydrate pH 8.0, 16% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.751	α = 90
b = 53.166	β = 102.715
c = 46.271	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 PILATUS3 6M		2024-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97907	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	2.2	48.07	99.1	0.1439	0.9918	15.45	6.48		14491

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	2.2	2.27			0.4743	0.8382	4.54

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	2.2	48.07	13816	663	99.054	0.173	0.1701	0.1781	0.2383	0.2459	31.479

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]
0.75		-1.097	-0.929		0.612

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.443
r_dihedral_angle_6_deg	14.701
r_dihedral_angle_3_deg	13.676
r_dihedral_angle_1_deg	8.518
r_lrange_it	8.126
r_lrange_other	8.124
r_scangle_it	5.537
r_scangle_other	5.535
r_mcangle_it	4.312
r_mcangle_other	4.312
r_scbond_it	3.611
r_scbond_other	3.61
r_mcbond_it	2.939
r_mcbond_other	2.932
r_dihedral_angle_other_3_deg	2.147
r_angle_refined_deg	1.78
r_angle_other_deg	0.603
r_nbd_refined	0.231
r_nbd_other	0.22
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.099
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.088
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	2295
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	51

Software

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