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9w13

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with ZEN-P

Method: X-RAY DIFFRACTION D_max: 69.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w13
deposition_date	2025-07-25
last_revision	2026-03-18
title	Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with ZEN-P
keywords	ZEN-P, ER-alpha, TRANSCRIPTION; TRANSCRIPTION
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	23.24 Å
rg_electron	22.34 Å
i0	99523300.00
molecular_weight	52720.0 kDa
excluded_volume	51064 Å³
envelope_volume	82840 Å³
shell_volume	29678 Å³
envelope_diameter	72.0 Å
shell_rg	30.32 Å
envelope_rg	22.49 Å
shape_rg	22.34 Å
total_rg	22.97 Å
total_atoms	3974
n_residues	492
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	69.0 Å
rg_real	23.07 Å
rg_real_error	0.36 Å
i0_real	9.9520e+07
i0_real_error	1.2480e+06
rg_reciprocal	23.11 Å
i0_reciprocal	99530000.0000
total_estimate	0.9081
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.7 Å
skewness	0.100
kurtosis	-0.531
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	19310000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Estrogen receptor
formula_weight	29701.0 kDa
mutation	Y537S
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4084

GAGAGSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDAHRLHAPTSAILHRLLQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	(4S,6R,12E)-4-methyl-6,16,18-tris(oxidanyl)-3-oxabicyclo[12.4.0]octadeca-1(14),12,15,17-tetraene-2,8-dione
formula_weight	334.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	96

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6. Citations (1)

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length_a	53.062 Å
length_b	101.765 Å
length_c	195.648 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.050 Å
resolution_low	24.690 Å
r_factor	0.1825
r_work	0.1803
r_free	0.2240

fit	/app/data/saxs_computation/w1/9w13/9w13.fit
pddf	/app/data/pr_computation/w1/9w13/9w13.pr.out
profile	/app/data/saxs_computation/w1/9w13/9w13.dat