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13pi

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr12314

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	13pi
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr12314
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	23.79 Å
rg_electron	23.16 Å
i0	22015700.00
molecular_weight	35790.0 kDa
excluded_volume	44720 Å³
envelope_volume	53646 Å³
shell_volume	20882 Å³
envelope_diameter	89.5 Å
shell_rg	28.52 Å
envelope_rg	23.56 Å
shape_rg	23.06 Å
total_rg	24.15 Å
total_atoms	2511
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	23.98 Å
rg_real_error	0.77 Å
i0_real	2.2020e+07
i0_real_error	3.2950e+05
rg_reciprocal	23.94 Å
i0_reciprocal	22020000.0000
total_estimate	0.8264
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.1 Å
skewness	0.569
kurtosis	-0.036
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	4368000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.692; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.720; Smooth: 0.942

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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	2662

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	2

Entity 4 non-polymer

description	3,4-dihydro-2~{H}-chromene-6-carboxamide
formula_weight	177.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	139

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6. Citations (1)

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length_a	81.820 Å
length_b	81.820 Å
length_c	133.750 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	2.150 Å
resolution_low	34.250 Å
r_factor	0.1896
r_work	0.1880
r_free	0.2234

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