SAXSdb — 1dzg

▼

1. Structure Basics

entry_id	1dzg
deposition_date	2000-02-28
title	N135Q-S380C-ANTITHROMBIN-III
keywords	BLOOD CLOTTING, SERPIN; BLOOD CLOTTING
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	37.79 Å
rg_electron	38.02 Å
i0	130916000.00
molecular_weight	93682.0 kDa
excluded_volume	117750 Å³
envelope_volume	149800 Å³
shell_volume	35800 Å³
envelope_diameter	134.3 Å
shell_rg	39.69 Å
envelope_rg	38.05 Å
shape_rg	38.00 Å
total_rg	38.16 Å
total_atoms	6589
n_residues	831
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

▼

3. P(r) Analysis (GNOM)

dmax	132.8 Å
rg_real	38.36 Å
rg_real_error	1.35 Å
i0_real	1.3090e+08
i0_real_error	2.2210e+06
rg_reciprocal	38.01 Å
i0_reciprocal	130900000.0000
total_estimate	0.6856
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	28.5 Å
skewness	0.557
kurtosis	-0.531
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	81720000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.455; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.543; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	ANTITHROMBIN-III
formula_weight	49131.1 kDa
mutation	YES
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I
atom_count	6593

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	3

Entity 4 non-polymer

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

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

▶

6. Citations (1)

▶

length_a	68.610 Å
length_b	99.540 Å
length_c	88.690 Å
angle_alpha	90.00 °
angle_beta	104.79 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.800 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2280
r_free	0.2970

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

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)