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9rjr

SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 83.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rjr
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	26.65 Å
rg_electron	25.62 Å
i0	77018500.00
molecular_weight	67739.0 kDa
excluded_volume	84283 Å³
envelope_volume	101030 Å³
shell_volume	32576 Å³
envelope_diameter	87.7 Å
shell_rg	33.22 Å
envelope_rg	25.74 Å
shape_rg	25.68 Å
total_rg	26.23 Å
total_atoms	9342
n_residues	605
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	83.9 Å
rg_real	26.52 Å
rg_real_error	0.44 Å
i0_real	7.7020e+07
i0_real_error	1.1210e+06
rg_reciprocal	26.56 Å
i0_reciprocal	77020000.0000
total_estimate	0.7417
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	82.5 Å
skewness	0.161
kurtosis	-0.541
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	41490000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 0.291; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	9644

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	1-[[3,4-bis(fluoranyl)phenyl]methyl]-3-(5-bromanylpyridin-3-yl)imidazolidine-2,4-dione
formula_weight	382.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	291

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6. Citations (1)

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length_a	68.120 Å
length_b	100.110 Å
length_c	104.310 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	1.705 Å
resolution_low	72.228 Å
r_factor	—
r_work	0.1973
r_free	0.2293

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