SAXSdb — 9zxm

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1. Structure Basics

entry_id	9zxm
deposition_date	2026-01-05
title	DDB1 delta with compound 6
keywords	E3 Ligase, DNA-encoded library, 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	29.80 Å
rg_electron	28.59 Å
i0	125002000.00
molecular_weight	89551.0 kDa
excluded_volume	112690 Å³
envelope_volume	142280 Å³
shell_volume	40325 Å³
envelope_diameter	103.7 Å
shell_rg	36.91 Å
envelope_rg	28.45 Å
shape_rg	28.52 Å
total_rg	29.62 Å
total_atoms	12563
n_residues	803
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	93.8 Å
rg_real	29.65 Å
rg_real_error	0.55 Å
i0_real	1.2500e+08
i0_real_error	1.8590e+06
rg_reciprocal	29.72 Å
i0_reciprocal	125000000.0000
total_estimate	0.9020
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.2 Å
skewness	0.175
kurtosis	-0.483
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	22420000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA damage-binding protein 1
formula_weight	95773.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	12813

MHHHHHHVDEENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	;(3S,5S)-1-{(4P)-4-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-3-[(propan-2-yl)oxy]benzene-1-carbonyl}-N-methyl-5-phenylpiperidine-3-carboxamide ;
formula_weight	536.6 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	182

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6. Citations (1)

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length_a	67.755 Å
length_b	115.924 Å
length_c	120.374 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.195 Å
resolution_low	33.110 Å
r_factor	—
r_work	0.1911
r_free	0.2461

fit	/app/data/saxs_computation/zx/9zxm/9zxm.fit
pddf	/app/data/pr_computation/zx/9zxm/9zxm.pr.out
profile	/app/data/saxs_computation/zx/9zxm/9zxm.dat

DDB1 delta with compound 6

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