← Back to search

13ms

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr13952

Method: X-RAY DIFFRACTION D_max: 64.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	13ms
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr13952
keywords	PLpro, SARS-CoV-2, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	23.69 Å
rg_electron	23.18 Å
i0	40852900.00
molecular_weight	33198.0 kDa
excluded_volume	32125 Å³
envelope_volume	53405 Å³
shell_volume	20756 Å³
envelope_diameter	90.0 Å
shell_rg	28.50 Å
envelope_rg	23.64 Å
shape_rg	23.09 Å
total_rg	23.80 Å
total_atoms	2502
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

▼

3. P(r) Analysis (GNOM)

dmax	64.6 Å
rg_real	22.41 Å
rg_real_error	0.13 Å
i0_real	3.9110e+07
i0_real_error	4.1660e+05
rg_reciprocal	23.85 Å
i0_reciprocal	40850000.0000
total_estimate	0.6857
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	25.2 Å
skewness	0.361
kurtosis	-0.471
angular_range	— – 0.3350 Å⁻¹
current_alpha	2.0270
highest_alpha	4502000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.986; Stabil: 0.991; Sysdev: 0.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

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	2643

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	3-oxo-3-(piperidin-1-yl)propanenitrile
formula_weight	152.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	141

▶

6. Citations (1)

▶

length_a	81.540 Å
length_b	81.540 Å
length_c	135.390 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	2.180 Å
resolution_low	38.030 Å
r_factor	0.1734
r_work	0.1722
r_free	0.1976

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