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1dfv

CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN MONOMER

Method: X-RAY DIFFRACTION D_max: 78.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dfv
deposition_date	1999-11-22
title	CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN MONOMER
keywords	NEUTROPHIL, NGAL, LIPOCALIN, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	25.64 Å
rg_electron	24.75 Å
i0	26905600.00
molecular_weight	40810.0 kDa
excluded_volume	51567 Å³
envelope_volume	64772 Å³
shell_volume	22611 Å³
envelope_diameter	79.1 Å
shell_rg	30.96 Å
envelope_rg	24.56 Å
shape_rg	24.73 Å
total_rg	25.63 Å
total_atoms	2878
n_residues	347
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	78.6 Å
rg_real	25.70 Å
rg_real_error	0.52 Å
i0_real	2.6910e+07
i0_real_error	4.0600e+05
rg_reciprocal	25.69 Å
i0_reciprocal	26910000.0000
total_estimate	0.8918
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.4 Å
skewness	0.348
kurtosis	-0.656
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	5356000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.900

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	HUMAN NEUTROPHIL GELATINASE
formula_weight	20515.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3011

QDSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	unidentified baculovirus

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	133

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6. Citations (1)

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length_a	115.021 Å
length_b	115.021 Å
length_c	117.638 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	2.600 Å
resolution_low	20.000 Å
r_factor	0.2810
r_work	0.2810
r_free	0.2930

fit	/app/data/saxs_computation/df/1dfv/1dfv.fit
pddf	/app/data/pr_computation/df/1dfv/1dfv.pr.out
profile	/app/data/saxs_computation/df/1dfv/1dfv.dat