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9r9c

Crystal structure of TRIM24 PHD-bromodomain with XS839112

Method: X-RAY DIFFRACTION D_max: 78.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r9c
deposition_date	2025-05-19
last_revision	2026-06-03
title	Crystal structure of TRIM24 PHD-bromodomain with XS839112
keywords	TRIM-family protein, PHD finger, bromodomain, drug discovery, enantioselective protein affinity selection mass spectrometry, LIGASE; LIGASE
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	26.37 Å
rg_electron	25.84 Å
i0	56167500.00
molecular_weight	39413.0 kDa
excluded_volume	38259 Å³
envelope_volume	70427 Å³
shell_volume	23085 Å³
envelope_diameter	81.6 Å
shell_rg	32.84 Å
envelope_rg	25.54 Å
shape_rg	25.92 Å
total_rg	26.33 Å
total_atoms	2943
n_residues	355
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	78.5 Å
rg_real	26.39 Å
rg_real_error	0.59 Å
i0_real	5.6170e+07
i0_real_error	7.6010e+05
rg_reciprocal	26.38 Å
i0_reciprocal	56170000.0000
total_estimate	0.9060
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.9 Å
skewness	0.241
kurtosis	-0.756
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	6500000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.945

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Transcription intermediary factor 1-alpha
formula_weight	21318.4 kDa
ec_number	2.3.2.27
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3296

SPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	11

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	(4~{S})-6-[[1-(3-chloranyl-4-fluoranyl-phenyl)-1,2,3-triazol-4-yl]methylamino]-1,4-dimethyl-3,4-dihydroquinolin-2-one
formula_weight	399.8 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	311

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6. Citations (1)

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length_a	89.110 Å
length_b	36.823 Å
length_c	129.419 Å
angle_alpha	90.00 °
angle_beta	110.10 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.590 Å
resolution_low	60.800 Å
r_factor	0.1505
r_work	0.1481
r_free	0.1957

fit	/app/data/saxs_computation/r9/9r9c/9r9c.fit
pddf	/app/data/pr_computation/r9/9r9c/9r9c.pr.out
profile	/app/data/saxs_computation/r9/9r9c/9r9c.dat