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9wv4

Crystal structure of human ZMYND8 MYND domain

Method: X-RAY DIFFRACTION D_max: 139.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wv4
deposition_date	2025-09-19
last_revision	2025-10-08
title	Crystal structure of human ZMYND8 MYND domain
keywords	ZMYND8, MYND domain, Metal binding protein, protein -protein interaction domain; METAL 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	39.99 Å
rg_electron	41.32 Å
i0	53873200.00
molecular_weight	55212.0 kDa
excluded_volume	67636 Å³
envelope_volume	99647 Å³
shell_volume	24004 Å³
envelope_diameter	139.0 Å
shell_rg	37.75 Å
envelope_rg	41.09 Å
shape_rg	41.30 Å
total_rg	41.14 Å
total_atoms	3817
n_residues	451
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	139.4 Å
rg_real	40.93 Å
rg_real_error	1.82 Å
i0_real	5.3870e+07
i0_real_error	1.0420e+06
rg_reciprocal	40.36 Å
i0_reciprocal	53840000.0000
total_estimate	0.7270
solution_quality	REASONABLE a REASONABLE solution
n_peaks	0
r_peak_primary	— Å
skewness	0.544
kurtosis	-0.596
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	1770000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.568; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.223; Smooth: 0.519

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	MYND-type zinc finger-containing chromatin reader ZMYND8
formula_weight	14938.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,C,A,D
atom_count	4107

NTTGSTIAEIRRLRIEIEKLQWLHQQELSEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKKKQWCANCKKEAIFYCCWNTSYCDYPCQQAHWPEHMKSCTQSATAPQQEADAE

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	8

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	290

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6. Citations (1)

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length_a	63.705 Å
length_b	71.188 Å
length_c	230.266 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.290 Å
resolution_low	38.670 Å
r_factor	0.2441
r_work	0.2425
r_free	0.2739

fit	/app/data/saxs_computation/wv/9wv4/9wv4.fit
pddf	/app/data/pr_computation/wv/9wv4/9wv4.pr.out
profile	/app/data/saxs_computation/wv/9wv4/9wv4.dat