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13nn

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with T0407

Method: X-RAY DIFFRACTION D_max: 87.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13nn
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with T0407
keywords	PLpro, SARS-CoV-2, HYDROLASE; HYDROLASE
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	23.92 Å
rg_electron	23.29 Å
i0	21816800.00
molecular_weight	35757.0 kDa
excluded_volume	44747 Å³
envelope_volume	53699 Å³
shell_volume	20804 Å³
envelope_diameter	89.8 Å
shell_rg	28.60 Å
envelope_rg	23.64 Å
shape_rg	23.18 Å
total_rg	24.29 Å
total_atoms	2510
n_residues	313
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	87.1 Å
rg_real	24.11 Å
rg_real_error	0.75 Å
i0_real	2.1820e+07
i0_real_error	3.0500e+05
rg_reciprocal	24.07 Å
i0_reciprocal	21820000.0000
total_estimate	0.6373
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	24.5 Å
skewness	0.567
kurtosis	-0.040
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	3797000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 1.000; Sysdev: 0.203; Positv: 1.000; Valcen: 0.694; Smooth: 0.947

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Papain-like protease nsp3
formula_weight	39803.1 kDa
ec_number	3.4.19.12,3.4.22.-
mutation	C111S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2560

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKHV

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	5-methyl-2-phenyl-2,4-dihydro-3H-pyrazol-3-one
formula_weight	174.2 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	38

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6. Citations (1)

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length_a	82.840 Å
length_b	82.840 Å
length_c	133.670 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	2.590 Å
resolution_low	37.850 Å
r_factor	0.1852
r_work	0.1834
r_free	0.2228

fit	/app/data/saxs_computation/3n/13nn/13nn.fit
pddf	/app/data/pr_computation/3n/13nn/13nn.pr.out
profile	/app/data/saxs_computation/3n/13nn/13nn.dat

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with T0407

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