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9qod

;APH(2'')-IVa with a fragment ;

Method: X-RAY DIFFRACTION D_max: 111.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qod
deposition_date	2025-03-26
last_revision	2026-02-11
title	;APH(2'')-IVa with a fragment ;
keywords	inhibitor, complex, enzyme, ANTIBIOTIC; ANTIBIOTIC
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	33.96 Å
rg_electron	33.81 Å
i0	141420000.00
molecular_weight	64762.0 kDa
excluded_volume	63283 Å³
envelope_volume	116530 Å³
shell_volume	30156 Å³
envelope_diameter	119.9 Å
shell_rg	38.29 Å
envelope_rg	33.61 Å
shape_rg	33.78 Å
total_rg	34.13 Å
total_atoms	4916
n_residues	594
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	111.2 Å
rg_real	34.20 Å
rg_real_error	1.07 Å
i0_real	1.4140e+08
i0_real_error	2.3280e+06
rg_reciprocal	34.05 Å
i0_reciprocal	141400000.0000
total_estimate	0.8102
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.8 Å
skewness	0.466
kurtosis	-0.515
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	8901000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.708; Smooth: 0.346

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	APH(2'')-Id
formula_weight	37596.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5109

MGSSHHHHHHSSGLVPRGSHMRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSIKIK

Source

organism	Enterococcus casseliflavus
ncbi_taxonomy_id	37734
host_organism	Escherichia coli

Entity 2 non-polymer

description	5-chloranyl-4-(1~{H}-pyrazol-5-yl)-1~{H}-pyrrolo[2,3-b]pyridine
formula_weight	218.6 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	165

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6. Citations (1)

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length_a	75.820 Å
length_b	65.269 Å
length_c	77.617 Å
angle_alpha	90.00 °
angle_beta	91.53 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.290 Å
resolution_low	49.950 Å
r_factor	0.1896
r_work	0.1870
r_free	0.2403

fit	/app/data/saxs_computation/qo/9qod/9qod.fit
pddf	/app/data/pr_computation/qo/9qod/9qod.pr.out
profile	/app/data/saxs_computation/qo/9qod/9qod.dat

;APH(2'')-IVa with a fragment ;

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