← Back to search

9ri4

SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 82.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ri4
deposition_date	2025-06-11
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	26.35 Å
rg_electron	25.50 Å
i0	141580000.00
molecular_weight	62458.0 kDa
excluded_volume	60159 Å³
envelope_volume	99335 Å³
shell_volume	32183 Å³
envelope_diameter	87.1 Å
shell_rg	33.09 Å
envelope_rg	25.63 Å
shape_rg	25.49 Å
total_rg	26.08 Å
total_atoms	4697
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	82.3 Å
rg_real	26.22 Å
rg_real_error	0.46 Å
i0_real	1.4160e+08
i0_real_error	1.8100e+06
rg_reciprocal	26.26 Å
i0_reciprocal	141600000.0000
total_estimate	0.9065
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.7 Å
skewness	0.145
kurtosis	-0.558
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	44050000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.982

▶

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	4986

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	2-azanyl-~{N}-[(1~{R},2~{S})-2-(4-chloranyl-3-fluoranyl-phenyl)cyclopropyl]-6-nitro-benzamide
formula_weight	349.7 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	268

▶

6. Citations (1)

▶

length_a	67.820 Å
length_b	100.150 Å
length_c	104.580 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	1.762 Å
resolution_low	72.332 Å
r_factor	—
r_work	0.2117
r_free	0.2565

fit	/app/data/saxs_computation/ri/9ri4/9ri4.fit
pddf	/app/data/pr_computation/ri/9ri4/9ri4.pr.out
profile	/app/data/saxs_computation/ri/9ri4/9ri4.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