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9qpd

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

Method: X-RAY DIFFRACTION D_max: 112.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qpd
deposition_date	2025-03-27
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	32.91 Å
rg_electron	33.07 Å
i0	69033400.00
molecular_weight	67813.0 kDa
excluded_volume	85539 Å³
envelope_volume	112880 Å³
shell_volume	30502 Å³
envelope_diameter	116.6 Å
shell_rg	36.97 Å
envelope_rg	32.67 Å
shape_rg	33.07 Å
total_rg	33.44 Å
total_atoms	4806
n_residues	592
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	112.7 Å
rg_real	33.26 Å
rg_real_error	1.13 Å
i0_real	6.9030e+07
i0_real_error	1.2490e+06
rg_reciprocal	33.12 Å
i0_reciprocal	69020000.0000
total_estimate	0.6036
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	30.5 Å
skewness	0.505
kurtosis	-0.444
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	12060000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.708; Smooth: 0.774

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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	B,A
atom_count	4874

MGSSHHHHHHSSGLVPRGSHMRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSIKIK

Source

organism	Enterococcus casseliflavus
ncbi_taxonomy_id	37734
host_organism	Escherichia coli

Entity 2 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1H-PYRROLO[2,3-B]PYRIDINE
formula_weight	118.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	50

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6. Citations (1)

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length_a	79.107 Å
length_b	64.553 Å
length_c	72.327 Å
angle_alpha	90.00 °
angle_beta	91.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.300 Å
resolution_low	53.840 Å
r_factor	0.2003
r_work	0.1978
r_free	0.2465

fit	/app/data/saxs_computation/qp/9qpd/9qpd.fit
pddf	/app/data/pr_computation/qp/9qpd/9qpd.pr.out
profile	/app/data/saxs_computation/qp/9qpd/9qpd.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