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13pd

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr16677

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13pd
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr16677
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	23.31 Å
i0	21561600.00
molecular_weight	35567.0 kDa
excluded_volume	44507 Å³
envelope_volume	53430 Å³
shell_volume	20747 Å³
envelope_diameter	91.2 Å
shell_rg	28.56 Å
envelope_rg	23.66 Å
shape_rg	23.21 Å
total_rg	24.29 Å
total_atoms	2496
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	24.12 Å
rg_real_error	0.77 Å
i0_real	2.1560e+07
i0_real_error	3.0380e+05
rg_reciprocal	24.07 Å
i0_reciprocal	21560000.0000
total_estimate	0.8212
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.5 Å
skewness	0.567
kurtosis	-0.048
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	3745000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.678; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.687; Smooth: 0.951

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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	2529

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	4-(1H-pyrrol-1-yl)aniline
formula_weight	158.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	21

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6. Citations (1)

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length_a	82.950 Å
length_b	82.950 Å
length_c	133.280 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	2.620 Å
resolution_low	35.210 Å
r_factor	0.2232
r_work	0.2218
r_free	0.2530

fit	/app/data/saxs_computation/3p/13pd/13pd.fit
pddf	/app/data/pr_computation/3p/13pd/13pd.pr.out
profile	/app/data/saxs_computation/3p/13pd/13pd.dat

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr16677

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