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13mk

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr12961

Method: X-RAY DIFFRACTION D_max: 85.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13mk
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr12961
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	23.30 Å
i0	41019000.00
molecular_weight	33252.0 kDa
excluded_volume	32163 Å³
envelope_volume	53807 Å³
shell_volume	20829 Å³
envelope_diameter	90.2 Å
shell_rg	28.57 Å
envelope_rg	23.70 Å
shape_rg	23.22 Å
total_rg	23.93 Å
total_atoms	2504
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	85.7 Å
rg_real	24.01 Å
rg_real_error	0.83 Å
i0_real	4.1020e+07
i0_real_error	6.6100e+05
rg_reciprocal	23.96 Å
i0_reciprocal	41020000.0000
total_estimate	0.8261
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.1 Å
skewness	0.576
kurtosis	-0.050
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	5690000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.689; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.684; Smooth: 0.987

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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	2641

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKHV

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-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	N-(2,4-difluorophenyl)-N'-methylthiourea
formula_weight	202.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	137

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6. Citations (1)

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length_a	82.090 Å
length_b	82.090 Å
length_c	135.210 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	2.260 Å
resolution_low	35.550 Å
r_factor	0.1699
r_work	0.1686
r_free	0.1958

fit	/app/data/saxs_computation/3m/13mk/13mk.fit
pddf	/app/data/pr_computation/3m/13mk/13mk.pr.out
profile	/app/data/saxs_computation/3m/13mk/13mk.dat