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13na

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr12973

Method: X-RAY DIFFRACTION D_max: 64.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13na
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr12973
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	23.80 Å
rg_electron	23.28 Å
i0	40957500.00
molecular_weight	33250.0 kDa
excluded_volume	32186 Å³
envelope_volume	54094 Å³
shell_volume	20896 Å³
envelope_diameter	90.2 Å
shell_rg	28.57 Å
envelope_rg	23.76 Å
shape_rg	23.20 Å
total_rg	23.91 Å
total_atoms	2505
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	64.9 Å
rg_real	22.54 Å
rg_real_error	0.12 Å
i0_real	3.9210e+07
i0_real_error	4.0770e+05
rg_reciprocal	23.96 Å
i0_reciprocal	40960000.0000
total_estimate	0.6860
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	24.3 Å
skewness	0.356
kurtosis	-0.480
angular_range	— – 0.3350 Å⁻¹
current_alpha	2.1320
highest_alpha	4809000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.987; Stabil: 0.990; Sysdev: 0.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	2536

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	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	3-(1H-pyrrol-1-yl)benzene-1-carbothioamide
formula_weight	202.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	31

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6. Citations (1)

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length_a	82.810 Å
length_b	82.810 Å
length_c	134.590 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	2.370 Å
resolution_low	30.430 Å
r_factor	0.1822
r_work	0.1809
r_free	0.2093

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