Crystal structure of SARS-CoV-2 main protease with a deletion of Asn51

Method: X-RAY DIFFRACTION D_max: 78.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9vuw
deposition_date	2025-07-14
title	Crystal structure of SARS-CoV-2 main protease with a deletion of Asn51
keywords	Severe acute respiratory syndrome coronavirus 2, main protease, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	22.56 Å
rg_electron	21.86 Å
i0	19374500.00
molecular_weight	33006.0 kDa
excluded_volume	41120 Å³
envelope_volume	48373 Å³
shell_volume	19522 Å³
envelope_diameter	79.3 Å
shell_rg	27.50 Å
envelope_rg	21.99 Å
shape_rg	21.85 Å
total_rg	22.65 Å
total_atoms	2312
n_residues	300
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	78.7 Å
rg_real	22.68 Å
rg_real_error	0.56 Å
i0_real	1.9370e+07
i0_real_error	2.3880e+05
rg_reciprocal	22.65 Å
i0_reciprocal	19370000.0000
total_estimate	0.6641
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.6 Å
skewness	0.498
kurtosis	-0.330
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	7526000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.859; Smooth: 0.973

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (1)

▶

length_a	97.353 Å
length_b	80.607 Å
length_c	51.514 Å
angle_alpha	90.00 °
angle_beta	114.75 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.600 Å
resolution_low	59.570 Å
r_factor	0.1939
r_work	0.1930
r_free	0.2113

description	3C-like proteinase nsp5
formula_weight	33681.4 kDa
ec_number	3.4.22.69
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2670

Crystal structure of SARS-CoV-2 main protease with a deletion of Asn51

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

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

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	288

fit	/app/data/saxs_computation/vu/9vuw/9vuw.fit
pddf	/app/data/pr_computation/vu/9vuw/9vuw.pr.out
profile	/app/data/saxs_computation/vu/9vuw/9vuw.dat