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13ra

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with 5X-0942

Method: X-RAY DIFFRACTION D_max: 84.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13ra
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with 5X-0942
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	23.66 Å
rg_electron	23.14 Å
i0	40967200.00
molecular_weight	33226.0 kDa
excluded_volume	32153 Å³
envelope_volume	53621 Å³
shell_volume	20854 Å³
envelope_diameter	89.4 Å
shell_rg	28.42 Å
envelope_rg	23.57 Å
shape_rg	23.06 Å
total_rg	23.77 Å
total_atoms	2503
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	84.5 Å
rg_real	23.86 Å
rg_real_error	0.76 Å
i0_real	4.0970e+07
i0_real_error	6.2160e+05
rg_reciprocal	23.82 Å
i0_reciprocal	40970000.0000
total_estimate	0.8259
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.8 Å
skewness	0.580
kurtosis	-0.033
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	6121000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.692; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.712; Smooth: 0.951

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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	2766

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	(2E)-3,6-dimethyl-1,3-benzothiazol-2(3H)-imine
formula_weight	178.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	263

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6. Citations (1)

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length_a	81.740 Å
length_b	81.740 Å
length_c	134.820 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	2.000 Å
resolution_low	25.200 Å
r_factor	0.1697
r_work	0.1685
r_free	0.1961

fit	/app/data/saxs_computation/3r/13ra/13ra.fit
pddf	/app/data/pr_computation/3r/13ra/13ra.pr.out
profile	/app/data/saxs_computation/3r/13ra/13ra.dat