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1dbi

CRYSTAL STRUCTURE OF A THERMOSTABLE SERINE PROTEASE

Method: X-RAY DIFFRACTION D_max: 52.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dbi
deposition_date	1999-11-02
title	CRYSTAL STRUCTURE OF A THERMOSTABLE SERINE PROTEASE
keywords	HYDROLASE; HYDROLASE
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	17.79 Å
rg_electron	16.65 Å
i0	15507400.00
molecular_weight	28788.0 kDa
excluded_volume	35483 Å³
envelope_volume	38073 Å³
shell_volume	18540 Å³
envelope_diameter	51.2 Å
shell_rg	23.41 Å
envelope_rg	16.85 Å
shape_rg	16.66 Å
total_rg	17.55 Å
total_atoms	2025
n_residues	271
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	52.4 Å
rg_real	17.62 Å
rg_real_error	0.21 Å
i0_real	1.5510e+07
i0_real_error	1.6010e+05
rg_reciprocal	17.64 Å
i0_reciprocal	15510000.0000
total_estimate	0.9061
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.016
kurtosis	-0.530
angular_range	— – 0.4450 Å⁻¹
current_alpha	0.0000
highest_alpha	4253000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	AK.1 SERINE PROTEASE
formula_weight	29789.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2281

WTPNDTYYQGYQYGPQNTYTDYAWDVTKGSSGQEIAVIDTGVDYTHPDLDGKVIKGYDFVDNDYDPMDLNNHGTHVAGIAAAETNNATGIAGMAPNTRILAVRALDRNGSGTLSDIADAIIYAADSGAEVINLSLGCDCHTTTLENAVNYAWNKGSVVVAAAGNNGSSTTFEPASYENVIAVGAVDQYDRLASFSNYGTWVDVVAPGVDIVSTITGNRYAYMSGTSMASPHVAGLAALLASQGRNNIEIRQAIEQTADKISGTGTYFKYGRINSYNAVTY

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	246

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6. Citations (1)

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length_a	44.050 Å
length_b	51.680 Å
length_c	52.780 Å
angle_alpha	90.00 °
angle_beta	96.10 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.1820
r_free	0.2470

fit	/app/data/saxs_computation/db/1dbi/1dbi.fit
pddf	/app/data/pr_computation/db/1dbi/1dbi.pr.out
profile	/app/data/saxs_computation/db/1dbi/1dbi.dat

CRYSTAL STRUCTURE OF A THERMOSTABLE SERINE PROTEASE

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