← Back to search

9rj7

SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 84.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rj7
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	26.60 Å
rg_electron	25.56 Å
i0	74244600.00
molecular_weight	67224.0 kDa
excluded_volume	83990 Å³
envelope_volume	99802 Å³
shell_volume	32271 Å³
envelope_diameter	87.2 Å
shell_rg	33.10 Å
envelope_rg	25.68 Å
shape_rg	25.61 Å
total_rg	26.18 Å
total_atoms	9320
n_residues	604
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	84.5 Å
rg_real	26.47 Å
rg_real_error	0.41 Å
i0_real	7.4240e+07
i0_real_error	9.0150e+05
rg_reciprocal	26.51 Å
i0_reciprocal	74250000.0000
total_estimate	0.9042
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.2 Å
skewness	0.151
kurtosis	-0.548
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	39450000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

▶

4. Crystallography & Experiment

▶

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	9495

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	4-fluoranyl-~{N}-(pyridin-3-ylmethyl)-2,3-dihydroindole-1-carboxamide
formula_weight	271.3 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	161

▶

6. Citations (1)

▶

length_a	67.870 Å
length_b	100.430 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	1.897 Å
resolution_low	72.421 Å
r_factor	—
r_work	0.2052
r_free	0.2524

fit	/app/data/saxs_computation/rj/9rj7/9rj7.fit
pddf	/app/data/pr_computation/rj/9rj7/9rj7.pr.out
profile	/app/data/saxs_computation/rj/9rj7/9rj7.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