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9rj0

SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 85.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rj0
deposition_date	2025-06-12
last_revision	2025-07-09
title	SARS-CoV-2 with a bound inhibitor
keywords	protease, inhibitor, 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	26.63 Å
rg_electron	25.59 Å
i0	75844800.00
molecular_weight	67816.0 kDa
excluded_volume	84656 Å³
envelope_volume	101290 Å³
shell_volume	32651 Å³
envelope_diameter	87.8 Å
shell_rg	33.22 Å
envelope_rg	25.70 Å
shape_rg	25.64 Å
total_rg	26.21 Å
total_atoms	9389
n_residues	608
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	85.9 Å
rg_real	26.50 Å
rg_real_error	0.57 Å
i0_real	7.5840e+07
i0_real_error	1.1060e+06
rg_reciprocal	26.54 Å
i0_reciprocal	75850000.0000
total_estimate	0.8945
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.4 Å
skewness	0.151
kurtosis	-0.543
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	41010000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.932

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	33825.5 kDa
ec_number	3.4.22.69
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9669

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	1-(benzimidazol-1-yl)-3-[(4~{S})-6-fluoranyl-3,4-dihydro-2~{H}-thiochromen-4-yl]urea
formula_weight	342.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	280

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6. Citations (1)

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length_a	68.050 Å
length_b	100.750 Å
length_c	104.530 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.709 Å
resolution_low	72.541 Å
r_factor	—
r_work	0.2024
r_free	0.2419

fit	/app/data/saxs_computation/rj/9rj0/9rj0.fit
pddf	/app/data/pr_computation/rj/9rj0/9rj0.pr.out
profile	/app/data/saxs_computation/rj/9rj0/9rj0.dat

SARS-CoV-2 with a bound inhibitor

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