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9xg4

The crystal structure of SARS-CoV-1 Main protease in complex with inhibitor FD2-21

Method: X-RAY DIFFRACTION D_max: 81.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xg4
deposition_date	2025-10-29
last_revision	2026-05-27
title	The crystal structure of SARS-CoV-1 Main protease in complex with inhibitor FD2-21
keywords	SARS-CoV-1, Main protease, Inhibitor, VIRAL PROTEIN; VIRAL PROTEIN
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	22.78 Å
rg_electron	22.09 Å
i0	20529200.00
molecular_weight	34185.0 kDa
excluded_volume	42623 Å³
envelope_volume	50534 Å³
shell_volume	20015 Å³
envelope_diameter	80.0 Å
shell_rg	27.77 Å
envelope_rg	22.34 Å
shape_rg	22.15 Å
total_rg	22.63 Å
total_atoms	4731
n_residues	306
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	81.1 Å
rg_real	22.89 Å
rg_real_error	0.80 Å
i0_real	2.0530e+07
i0_real_error	3.4730e+05
rg_reciprocal	22.87 Å
i0_reciprocal	20530000.0000
total_estimate	0.8297
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.1 Å
skewness	0.488
kurtosis	-0.345
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	8883000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.656; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.824; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	33876.6 kDa
ec_number	3.4.22.69
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4937

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQ

Source

organism	Severe acute respiratory syndrome-related coronavirus
ncbi_taxonomy_id	694009
host_organism	Escherichia coli

Entity 2 non-polymer

description	7-(5-azanylpyridin-3-yl)-2-(2-chlorophenyl)-5,7-diazaspiro[3.4]octane-6,8-dione
formula_weight	342.8 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	197

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6. Citations (1)

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length_a	107.857 Å
length_b	82.127 Å
length_c	53.034 Å
angle_alpha	90.00 °
angle_beta	106.31 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.726 Å
resolution_low	32.067 Å
r_factor	0.1955
r_work	0.1943
r_free	0.2182

fit	/app/data/saxs_computation/xg/9xg4/9xg4.fit
pddf	/app/data/pr_computation/xg/9xg4/9xg4.pr.out
profile	/app/data/saxs_computation/xg/9xg4/9xg4.dat

The crystal structure of SARS-CoV-1 Main protease in complex with inhibitor FD2-21

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