SAXSdb — 1dzh

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1. Structure Basics

entry_id	1dzh
deposition_date	2000-02-28
title	P14-FLUORESCEIN-N135Q-S380C-ANTITHROMBIN-III
keywords	BLOOD CLOTTING, SERPIN; BLOOD CLOTTING
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	37.72 Å
rg_electron	37.84 Å
i0	130653000.00
molecular_weight	93401.0 kDa
excluded_volume	117310 Å³
envelope_volume	149480 Å³
shell_volume	35781 Å³
envelope_diameter	131.7 Å
shell_rg	39.81 Å
envelope_rg	37.73 Å
shape_rg	37.82 Å
total_rg	38.01 Å
total_atoms	6572
n_residues	824
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	129.8 Å
rg_real	38.26 Å
rg_real_error	1.15 Å
i0_real	1.3070e+08
i0_real_error	2.1720e+06
rg_reciprocal	37.93 Å
i0_reciprocal	130600000.0000
total_estimate	0.7515
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	30.9 Å
skewness	0.547
kurtosis	-0.544
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	73570000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.512; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.603; Smooth: 0.628

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	ANTITHROMBIN-III
formula_weight	49519.5 kDa
mutation	YES
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I
atom_count	6609

HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKAQKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYVSDAFHKAFLEVNEEGCEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMGRVANPCVK

Source

organism	HOMO SAPIENS
common_name	HUMAN
ncbi_taxonomy_id	9606
host_organism	CRICETIDAE SP.

Entity 2 polymer

description	ANTITHROMBIN-III
formula_weight	49101.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMGRVANPCVK

Entity 3 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	2

Entity 4 branched

description	;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	3

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	37

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6. Citations (1)

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length_a	69.175 Å
length_b	99.865 Å
length_c	89.421 Å
angle_alpha	90.00 °
angle_beta	105.63 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.850 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2070
r_free	0.2580

fit	/app/data/saxs_computation/dz/1dzh/1dzh.fit
pddf	/app/data/pr_computation/dz/1dzh/1dzh.pr.out
profile	/app/data/saxs_computation/dz/1dzh/1dzh.dat

P14-FLUORESCEIN-N135Q-S380C-ANTITHROMBIN-III

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

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)