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9xym

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13698

Method: X-RAY DIFFRACTION D_max: 74.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xym
deposition_date	2025-08-26
title	Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13698
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	22.29 Å
rg_electron	21.67 Å
i0	37997400.00
molecular_weight	31759.0 kDa
excluded_volume	30616 Å³
envelope_volume	49395 Å³
shell_volume	19878 Å³
envelope_diameter	76.3 Å
shell_rg	27.49 Å
envelope_rg	21.93 Å
shape_rg	21.68 Å
total_rg	22.22 Å
total_atoms	2389
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	74.9 Å
rg_real	22.38 Å
rg_real_error	0.46 Å
i0_real	3.8000e+07
i0_real_error	5.2700e+05
rg_reciprocal	22.36 Å
i0_reciprocal	38000000.0000
total_estimate	0.8672
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.7 Å
skewness	0.472
kurtosis	-0.365
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	11200000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	33825.5 kDa
ec_number	3.4.22.69
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2407

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	;(1R,2S,5S)-6,6-dimethyl-N-[(2S)-4-(methylsulfanyl)-1-oxobutan-2-yl]-3-[N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide ;
formula_weight	465.5 kDa
src_method	nat
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	11

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6. Citations (1)

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length_a	45.388 Å
length_b	53.489 Å
length_c	113.716 Å
angle_alpha	90.00 °
angle_beta	101.22 °
angle_gamma	90.00 °
z_pdb	4

space_group	I 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.870 Å
resolution_low	48.280 Å
r_factor	0.2026
r_work	0.1998
r_free	0.2534

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

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13698

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