Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T169S Mutant

Method: X-RAY DIFFRACTION D_max: 75.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xyx
deposition_date	2025-08-26
title	Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T169S Mutant
keywords	Protease, SARS-CoV-2, Mpro, COVID-19, VIRAL PROTEIN, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	22.40 Å
rg_electron	21.67 Å
i0	20115000.00
molecular_weight	33634.0 kDa
excluded_volume	41915 Å³
envelope_volume	49340 Å³
shell_volume	19873 Å³
envelope_diameter	76.0 Å
shell_rg	27.34 Å
envelope_rg	21.86 Å
shape_rg	21.66 Å
total_rg	22.47 Å
total_atoms	2357
n_residues	305
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	75.4 Å
rg_real	22.50 Å
rg_real_error	0.61 Å
i0_real	2.0120e+07
i0_real_error	2.9520e+05
rg_reciprocal	22.48 Å
i0_reciprocal	20110000.0000
total_estimate	0.8610
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.9 Å
skewness	0.466
kurtosis	-0.363
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	8070000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.932

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	114.490 Å
length_b	53.258 Å
length_c	44.704 Å
angle_alpha	90.00 °
angle_beta	101.15 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.670 Å
resolution_low	43.900 Å
r_factor	0.2143
r_work	0.2120
r_free	0.2601

description	3C-like proteinase nsp5
formula_weight	33811.5 kDa
ec_number	3.4.22.69
mutation	T169S
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2418

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T169S Mutant

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	9

fit	/app/data/saxs_computation/xy/9xyx/9xyx.fit
pddf	/app/data/pr_computation/xy/9xyx/9xyx.pr.out
profile	/app/data/saxs_computation/xy/9xyx/9xyx.dat