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9rfx

Crystal structure of Endothiapepsin in complex with follow-up compound EOS71605 from ECBL

Method: X-RAY DIFFRACTION D_max: 65.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rfx
deposition_date	2025-06-05
title	Crystal structure of Endothiapepsin in complex with follow-up compound EOS71605 from ECBL
keywords	crystallographic fragment screening, Endothiapepsin, ECBL-96 fragment library, 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	20.26 Å
rg_electron	19.38 Å
i0	36429000.00
molecular_weight	31683.0 kDa
excluded_volume	30842 Å³
envelope_volume	47600 Å³
shell_volume	20562 Å³
envelope_diameter	66.1 Å
shell_rg	25.69 Å
envelope_rg	19.54 Å
shape_rg	19.33 Å
total_rg	20.08 Å
total_atoms	2401
n_residues	330
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	65.3 Å
rg_real	20.19 Å
rg_real_error	0.37 Å
i0_real	3.6430e+07
i0_real_error	4.3260e+05
rg_reciprocal	20.20 Å
i0_reciprocal	36430000.0000
total_estimate	0.8954
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.2 Å
skewness	0.263
kurtosis	-0.392
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	6365000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Endothiapepsin
formula_weight	33813.9 kDa
ec_number	3.4.23.22
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2753

STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGATTPTLGFASK

Entity 2 non-polymer

description	2-[3,5-bis(fluoranyl)phenoxy]-2-methyl-propan-1-amine
formula_weight	201.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	280

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6. Citations (1)

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length_a	45.220 Å
length_b	73.360 Å
length_c	52.420 Å
angle_alpha	90.00 °
angle_beta	109.16 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.180 Å
resolution_low	42.720 Å
r_factor	0.1552
r_work	0.1550
r_free	0.1685

fit	/app/data/saxs_computation/rf/9rfx/9rfx.fit
pddf	/app/data/pr_computation/rf/9rfx/9rfx.pr.out
profile	/app/data/saxs_computation/rf/9rfx/9rfx.dat