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9vol

Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)-2-methylphenoxy}butanoic acid derivative

Method: X-RAY DIFFRACTION D_max: 60.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vol
deposition_date	2025-07-01
last_revision	2025-12-03
title	Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)-2-methylphenoxy}butanoic acid derivative
keywords	Vitamin D receptor, 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	18.90 Å
rg_electron	17.87 Å
i0	26533800.00
molecular_weight	26891.0 kDa
excluded_volume	26229 Å³
envelope_volume	40443 Å³
shell_volume	18782 Å³
envelope_diameter	61.9 Å
shell_rg	24.24 Å
envelope_rg	18.15 Å
shape_rg	17.83 Å
total_rg	18.62 Å
total_atoms	2034
n_residues	248
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	60.9 Å
rg_real	18.79 Å
rg_real_error	0.36 Å
i0_real	2.6530e+07
i0_real_error	2.9920e+05
rg_reciprocal	18.81 Å
i0_reciprocal	26530000.0000
total_estimate	0.8115
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.7 Å
skewness	0.202
kurtosis	-0.345
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	4122000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Vitamin D3 receptor
formula_weight	30595.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2260

GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGSVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 2 polymer

description	Mediator of RNA polymerase II transcription subunit 1
formula_weight	1570.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

KNHPMLMNLLKDN

Entity 3 non-polymer

description	4-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}-2-methylphenoxy]butyric acid
formula_weight	578.6 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	180

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6. Citations (1)

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length_a	154.630 Å
length_b	41.600 Å
length_c	42.090 Å
angle_alpha	90.00 °
angle_beta	96.24 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.750 Å
resolution_low	41.840 Å
r_factor	0.1877
r_work	0.1865
r_free	0.2097

fit	/app/data/saxs_computation/vo/9vol/9vol.fit
pddf	/app/data/pr_computation/vo/9vol/9vol.pr.out
profile	/app/data/saxs_computation/vo/9vol/9vol.dat

Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)-2-methylphenoxy}butanoic acid derivative

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)