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9vnx

Crystal Structure of the mutant ROR gamma LBD With Compound 28

Method: X-RAY DIFFRACTION D_max: 64.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vnx
deposition_date	2025-07-01
title	Crystal Structure of the mutant ROR gamma LBD With Compound 28
keywords	nuclear receptor, agonist, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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	19.58 Å
rg_electron	18.63 Å
i0	29674300.00
molecular_weight	27857.0 kDa
excluded_volume	26854 Å³
envelope_volume	42970 Å³
shell_volume	19286 Å³
envelope_diameter	65.5 Å
shell_rg	24.83 Å
envelope_rg	18.93 Å
shape_rg	18.61 Å
total_rg	19.31 Å
total_atoms	2106
n_residues	251
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	64.8 Å
rg_real	19.50 Å
rg_real_error	0.34 Å
i0_real	2.9670e+07
i0_real_error	3.4710e+05
rg_reciprocal	19.51 Å
i0_reciprocal	29670000.0000
total_estimate	0.8067
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.6 Å
skewness	0.269
kurtosis	-0.299
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	6151000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Nuclear receptor ROR-gamma
formula_weight	29754.3 kDa
mutation	K469A/R473A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2299

EAPYASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFSTETESPVGLSK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Nuclear receptor coactivator 1
formula_weight	1776.1 kDa
ec_number	2.3.1.48
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

RHKILHRLLQEGSPS

Entity 3 non-polymer

description	;(2~{R})-~{N}-[5-(5-cyano-6-propan-2-yloxy-pyridin-3-yl)-1-(trifluoromethyl)pyrazol-3-yl]-1-ethanoyl-4-propan-2-ylsulfonyl-piperazine-2-carboxamide ;
formula_weight	571.6 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	149

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6. Citations (1)

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length_a	61.664 Å
length_b	61.664 Å
length_c	155.779 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	1.930 Å
resolution_low	57.340 Å
r_factor	0.1891
r_work	0.1875
r_free	0.2182

fit	/app/data/saxs_computation/vn/9vnx/9vnx.fit
pddf	/app/data/pr_computation/vn/9vnx/9vnx.pr.out
profile	/app/data/saxs_computation/vn/9vnx/9vnx.dat

Crystal Structure of the mutant ROR gamma LBD With Compound 28

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)