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9pxp

Fem-1 homolog B (FEM1B) in complex with VU0416476

Method: X-RAY DIFFRACTION D_max: 116.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pxp
deposition_date	2025-08-06
last_revision	2025-11-26
title	Fem-1 homolog B (FEM1B) in complex with VU0416476
keywords	FEM1B, ligand, E3 ligase, 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	32.72 Å
rg_electron	32.80 Å
i0	141904000.00
molecular_weight	63176.0 kDa
excluded_volume	60866 Å³
envelope_volume	113770 Å³
shell_volume	30769 Å³
envelope_diameter	121.5 Å
shell_rg	37.01 Å
envelope_rg	32.45 Å
shape_rg	32.82 Å
total_rg	33.02 Å
total_atoms	4785
n_residues	660
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	116.3 Å
rg_real	33.00 Å
rg_real_error	1.11 Å
i0_real	1.4190e+08
i0_real_error	2.1630e+06
rg_reciprocal	32.88 Å
i0_reciprocal	141900000.0000
total_estimate	0.8431
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.9 Å
skewness	0.469
kurtosis	-0.301
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	11310000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.692; Smooth: 0.942

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Protein fem-1 homolog B
formula_weight	39295.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4798

GHMEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNGHAKVVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHTTVTNSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQRADPNAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVELLLSHADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLPPIHAYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGGGGSGGGSKKRLLLGLDR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-tert-butyl-4,5-dichloropyridazin-3(2H)-one
formula_weight	221.1 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2

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6. Citations (1)

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length_a	129.542 Å
length_b	129.542 Å
length_c	140.193 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 4 21 2
int_tables_number	90
crystal_system	tetragonal

resolution	3.000 Å
resolution_low	47.570 Å
r_factor	0.2925
r_work	0.2906
r_free	0.3273

fit	/app/data/saxs_computation/px/9pxp/9pxp.fit
pddf	/app/data/pr_computation/px/9pxp/9pxp.pr.out
profile	/app/data/saxs_computation/px/9pxp/9pxp.dat

Fem-1 homolog B (FEM1B) in complex with VU0416476

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