HD6 defensin filament with IP6

Method: ELECTRON MICROSCOPY D_max: 122.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r7m
deposition_date	2025-05-14
title	HD6 defensin filament with IP6
keywords	filament, intestinal, IP5, phytic acid, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
method	ELECTRON MICROSCOPY

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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	39.44 Å
rg_electron	39.04 Å
i0	635379000.00
molecular_weight	181280.0 kDa
excluded_volume	215910 Å³
envelope_volume	299200 Å³
shell_volume	62528 Å³
envelope_diameter	130.5 Å
shell_rg	46.19 Å
envelope_rg	38.44 Å
shape_rg	39.06 Å
total_rg	39.33 Å
total_atoms	12400
n_residues	1536
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	122.3 Å
rg_real	39.18 Å
rg_real_error	0.94 Å
i0_real	6.3540e+08
i0_real_error	1.0070e+07
rg_reciprocal	39.35 Å
i0_reciprocal	635500000.0000
total_estimate	0.8936
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.0 Å
skewness	0.089
kurtosis	-0.508
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	71110000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.870

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.90 Å
resolution_method	—
num_particles	87585

description	Defensin-6
formula_weight	3719.3 kDa
src_method	man
entity_count	48

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v
atom_count	12410

HD6 defensin filament with IP6

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

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

description	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	5

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	10

fit	/app/data/saxs_computation/r7/9r7m/9r7m.fit
pddf	/app/data/pr_computation/r7/9r7m/9r7m.pr.out
profile	/app/data/saxs_computation/r7/9r7m/9r7m.dat