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9xg2

The crystal structure of SARS-CoV-2 Main protease in complex with inhibitor FD2-21

Method: X-RAY DIFFRACTION D_max: 74.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xg2
deposition_date	2025-10-29
last_revision	2026-05-27
title	The crystal structure of SARS-CoV-2 Main protease in complex with inhibitor FD2-21
keywords	SARS-CoV-2, 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	22.13 Å
rg_electron	21.62 Å
i0	36536400.00
molecular_weight	31189.0 kDa
excluded_volume	30126 Å³
envelope_volume	49152 Å³
shell_volume	19839 Å³
envelope_diameter	75.5 Å
shell_rg	27.30 Å
envelope_rg	21.83 Å
shape_rg	21.62 Å
total_rg	22.17 Å
total_atoms	2347
n_residues	305
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	74.5 Å
rg_real	22.25 Å
rg_real_error	0.49 Å
i0_real	3.6540e+07
i0_real_error	4.9550e+05
rg_reciprocal	22.23 Å
i0_reciprocal	36540000.0000
total_estimate	0.8604
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.2 Å
skewness	0.466
kurtosis	-0.385
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	11440000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.987

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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	33697.4 kDa
ec_number	3.4.22.69
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2427

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTF

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
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	80

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6. Citations (1)

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length_a	113.584 Å
length_b	54.757 Å
length_c	45.151 Å
angle_alpha	90.00 °
angle_beta	100.62 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.039 Å
resolution_low	44.377 Å
r_factor	0.1947
r_work	0.1922
r_free	0.2374

fit	/app/data/saxs_computation/xg/9xg2/9xg2.fit
pddf	/app/data/pr_computation/xg/9xg2/9xg2.pr.out
profile	/app/data/saxs_computation/xg/9xg2/9xg2.dat

The crystal structure of SARS-CoV-2 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