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9qyd

PARP9 Macro domain 1, Free form

Method: X-RAY DIFFRACTION D_max: 53.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qyd
deposition_date	2025-04-17
last_revision	2025-05-28
title	PARP9 Macro domain 1, Free form
keywords	Macro domain, Free Form, PARP9, HYDROLASE; HYDROLASE
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	17.20 Å
rg_electron	15.94 Å
i0	8219270.00
molecular_weight	21664.0 kDa
excluded_volume	27435 Å³
envelope_volume	30329 Å³
shell_volume	15877 Å³
envelope_diameter	54.9 Å
shell_rg	22.08 Å
envelope_rg	16.21 Å
shape_rg	15.93 Å
total_rg	17.03 Å
total_atoms	1522
n_residues	195
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	53.6 Å
rg_real	17.06 Å
rg_real_error	0.25 Å
i0_real	8.2190e+06
i0_real_error	9.2310e+04
rg_reciprocal	17.08 Å
i0_reciprocal	8219000.0000
total_estimate	0.6461
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.3 Å
skewness	0.063
kurtosis	-0.453
angular_range	— – 0.4650 Å⁻¹
current_alpha	0.0000
highest_alpha	1865000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 0.257; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protein mono-ADP-ribosyltransferase PARP9
formula_weight	22002.6 kDa
ec_number	2.4.2.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1623

GAMGGNSKSLQVFRKMLTPRIELSVWKDDLTTHAVDAVVNAANEDLLHGGGLALALVKAGGFEIQEESKQFVARYGKVSAGEIAVTGAGRLPCKQIIHAVGPRWMEWDKQGCTGKLQRAIVSILNYVIYKNTHIKTVAIPALSSGIFQFPLNLCTKTIVETIRVSLQGKPMMSNLKEIHLVSNEDPTVAAFKAASEFILGKSE

Source

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

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	70

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6. Citations (1)

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length_a	39.701 Å
length_b	63.847 Å
length_c	69.530 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 2 2
int_tables_number	17
crystal_system	—

resolution	1.910 Å
resolution_low	47.030 Å
r_factor	0.1893
r_work	0.1868
r_free	0.2351

fit	/app/data/saxs_computation/qy/9qyd/9qyd.fit
pddf	/app/data/pr_computation/qy/9qyd/9qyd.pr.out
profile	/app/data/saxs_computation/qy/9qyd/9qyd.dat

PARP9 Macro domain 1, Free form

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