SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 82.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rjf
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

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	26.61 Å
rg_electron	25.59 Å
i0	75207800.00
molecular_weight	67280.0 kDa
excluded_volume	83878 Å³
envelope_volume	100220 Å³
shell_volume	32383 Å³
envelope_diameter	87.2 Å
shell_rg	33.15 Å
envelope_rg	25.69 Å
shape_rg	25.66 Å
total_rg	26.16 Å
total_atoms	9307
n_residues	603
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

▼

3. P(r) Analysis (GNOM)

dmax	82.5 Å
rg_real	26.47 Å
rg_real_error	0.52 Å
i0_real	7.5210e+07
i0_real_error	1.1560e+06
rg_reciprocal	26.52 Å
i0_reciprocal	75210000.0000
total_estimate	0.9063
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.8 Å
skewness	0.151
kurtosis	-0.550
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	40470000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.970

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (1)

▶

length_a	67.910 Å
length_b	100.790 Å
length_c	104.490 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	1.893 Å
resolution_low	72.542 Å
r_factor	—
r_work	0.2341
r_free	0.2713

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

type	polypeptide(L)
strand_id	A,B
atom_count	9307

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

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	3-(5-bromanylpyridin-3-yl)-1-[(1~{R})-1-phenylethyl]imidazolidine-2,4-dione
formula_weight	360.2 kDa
src_method	syn
entity_count	2

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