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9voh

Vitamin D receptor complex with a 4-(m-carboran-1-yl)phenoxyacetic acid derivative

Method: X-RAY DIFFRACTION D_max: 62.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9voh
deposition_date	2025-07-01
last_revision	2025-12-03
title	Vitamin D receptor complex with a 4-(m-carboran-1-yl)phenoxyacetic 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	19.02 Å
rg_electron	18.01 Å
i0	26524800.00
molecular_weight	26855.0 kDa
excluded_volume	26180 Å³
envelope_volume	41075 Å³
shell_volume	18950 Å³
envelope_diameter	64.2 Å
shell_rg	24.31 Å
envelope_rg	18.28 Å
shape_rg	17.97 Å
total_rg	18.75 Å
total_atoms	2031
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	62.8 Å
rg_real	18.92 Å
rg_real_error	0.36 Å
i0_real	2.6520e+07
i0_real_error	3.2910e+05
rg_reciprocal	18.94 Å
i0_reciprocal	26530000.0000
total_estimate	0.8786
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.209
kurtosis	-0.339
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	4423000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.968

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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	2166

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-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba- closo-dodecaboran-1-yl}phenoxy]acetic acid
formula_weight	536.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	123

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6. Citations (1)

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length_a	156.250 Å
length_b	41.420 Å
length_c	42.240 Å
angle_alpha	90.00 °
angle_beta	96.49 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.980 Å
resolution_low	41.970 Å
r_factor	0.1938
r_work	0.1922
r_free	0.2253

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

Vitamin D receptor complex with a 4-(m-carboran-1-yl)phenoxyacetic 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)