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9xfr

The crystal structure of SARS-CoV-2 Main protease in complex with inhibitor FD2-12

Method: X-RAY DIFFRACTION D_max: 73.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xfr
deposition_date	2025-10-29
last_revision	2026-05-27
title	The crystal structure of SARS-CoV-2 Main protease in complex with inhibitor FD2-12
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	22.15 Å
rg_electron	21.61 Å
i0	36959900.00
molecular_weight	31416.0 kDa
excluded_volume	30356 Å³
envelope_volume	49045 Å³
shell_volume	19821 Å³
envelope_diameter	75.8 Å
shell_rg	27.32 Å
envelope_rg	21.77 Å
shape_rg	21.61 Å
total_rg	22.16 Å
total_atoms	2364
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	73.6 Å
rg_real	22.26 Å
rg_real_error	0.52 Å
i0_real	3.6960e+07
i0_real_error	4.9030e+05
rg_reciprocal	22.24 Å
i0_reciprocal	36960000.0000
total_estimate	0.8613
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.0 Å
skewness	0.459
kurtosis	-0.397
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	11310000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.864; Smooth: 0.901

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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	2412

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTF

Source

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

Entity 2 non-polymer

description	2-(2-chlorophenyl)-7-(5-methylpyridin-3-yl)-5,7-diazaspiro[3.4]octane-6,8-dione
formula_weight	341.8 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	48

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6. Citations (1)

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length_a	113.206 Å
length_b	54.554 Å
length_c	45.263 Å
angle_alpha	90.00 °
angle_beta	100.67 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.154 Å
resolution_low	34.352 Å
r_factor	0.2101
r_work	0.2082
r_free	0.2510

fit	/app/data/saxs_computation/xf/9xfr/9xfr.fit
pddf	/app/data/pr_computation/xf/9xfr/9xfr.pr.out
profile	/app/data/saxs_computation/xf/9xfr/9xfr.dat

The crystal structure of SARS-CoV-2 Main protease in complex with inhibitor FD2-12

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