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9v84

Crystal structure of complex Hit-1 with YTHDC1

Method: X-RAY DIFFRACTION D_max: 125.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v84
deposition_date	2025-05-29
title	Crystal structure of complex Hit-1 with YTHDC1
keywords	RNA-binding proteins, RNA, RNA BINDING PROTEIN; RNA BINDING 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	39.28 Å
rg_electron	38.89 Å
i0	320545000.00
molecular_weight	145370.0 kDa
excluded_volume	181500 Å³
envelope_volume	252450 Å³
shell_volume	54604 Å³
envelope_diameter	129.5 Å
shell_rg	44.48 Å
envelope_rg	37.77 Å
shape_rg	38.89 Å
total_rg	39.24 Å
total_atoms	10287
n_residues	1294
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	125.6 Å
rg_real	39.18 Å
rg_real_error	1.07 Å
i0_real	3.2050e+08
i0_real_error	5.1150e+06
rg_reciprocal	39.25 Å
i0_reciprocal	320600000.0000
total_estimate	0.8127
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	50.2 Å
skewness	0.255
kurtosis	-0.413
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	23260000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	YTH domain-containing protein 1
formula_weight	18471.4 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	B,A,C,D,E,F,G,H
atom_count	10507

TSKLKYVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESIDLYQVIHKM

Source

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

Entity 2 non-polymer

description	4-(2-bromanyl-6-fluoranyl-phenyl)carbonyl-~{N}-pyridin-3-yl-1~{H}-pyrrole-2-carboxamide
formula_weight	388.2 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	24

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	220

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6. Citations (1)

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length_a	54.160 Å
length_b	77.375 Å
length_c	105.238 Å
angle_alpha	112.72 °
angle_beta	93.18 °
angle_gamma	104.43 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.400 Å
resolution_low	29.468 Å
r_factor	0.2303
r_work	0.2283
r_free	0.2671

fit	/app/data/saxs_computation/v8/9v84/9v84.fit
pddf	/app/data/pr_computation/v8/9v84/9v84.pr.out
profile	/app/data/saxs_computation/v8/9v84/9v84.dat

Crystal structure of complex Hit-1 with YTHDC1

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