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1d2u

1.15 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS

Method: X-RAY DIFFRACTION D_max: 51.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d2u
deposition_date	1999-09-28
title	1.15 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS
keywords	NITRIC OXIDE TRANSPORT, FERRIC HEME, ANTIHISTAMINE, VASODILATOR, LIPOCALIN, BILAN BINDING PROTEIN, TRANSPORT PROTEIN; TRANSPORT 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	16.61 Å
rg_electron	15.18 Å
i0	8123000.00
molecular_weight	20899.0 kDa
excluded_volume	26141 Å³
envelope_volume	29243 Å³
shell_volume	15730 Å³
envelope_diameter	47.7 Å
shell_rg	21.55 Å
envelope_rg	15.50 Å
shape_rg	15.13 Å
total_rg	16.45 Å
total_atoms	1472
n_residues	184
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	51.5 Å
rg_real	16.44 Å
rg_real_error	0.30 Å
i0_real	8.1230e+06
i0_real_error	9.1040e+04
rg_reciprocal	16.46 Å
i0_reciprocal	8123000.0000
total_estimate	0.8083
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.1 Å
skewness	0.008
kurtosis	-0.458
angular_range	— – 0.4800 Å⁻¹
current_alpha	0.0000
highest_alpha	3423000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	NITROPHORIN 4
formula_weight	20292.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1737

ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQVESLGKYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEFSKFISTKENNCAYDNDSLKSLLTK

Source

organism	Rhodnius prolixus
ncbi_taxonomy_id	13249
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	AMMONIA
formula_weight	17.0 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	249

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6. Citations (1)

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length_a	69.920 Å
length_b	42.690 Å
length_c	52.750 Å
angle_alpha	90.00 °
angle_beta	93.82 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.150 Å
resolution_low	52.000 Å
r_factor	0.1300
r_work	0.1300
r_free	0.1900

fit	/app/data/saxs_computation/d2/1d2u/1d2u.fit
pddf	/app/data/pr_computation/d2/1d2u/1d2u.pr.out
profile	/app/data/saxs_computation/d2/1d2u/1d2u.dat

1.15 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS

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