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1dq3

CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI

Method: X-RAY DIFFRACTION D_max: 89.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dq3
deposition_date	1999-12-30
title	CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI
keywords	Endonuclease, PI-PfuI, Intein-encoded, 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	25.98 Å
rg_electron	24.84 Å
i0	44883400.00
molecular_weight	53139.0 kDa
excluded_volume	67072 Å³
envelope_volume	81026 Å³
shell_volume	27802 Å³
envelope_diameter	93.2 Å
shell_rg	31.45 Å
envelope_rg	25.25 Å
shape_rg	24.84 Å
total_rg	25.60 Å
total_atoms	3756
n_residues	454
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	89.1 Å
rg_real	25.98 Å
rg_real_error	0.71 Å
i0_real	4.4880e+07
i0_real_error	6.4340e+05
rg_reciprocal	25.98 Å
i0_reciprocal	44880000.0000
total_estimate	0.8730
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.2 Å
skewness	0.362
kurtosis	-0.293
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	11500000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	ENDONUCLEASE
formula_weight	53160.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4088

CIDGKAKIIFENEGEEHLTTMEEMYERYKHLGEFYDEEYNRWGIDVSNVPIYVKSFDPESKRVVKGKVNVIWKYELGKDVTKYEIITNKGTKILTSPWHPFFVLTPDFKIVEKRADELKEGDILIGGMPDGEDYKFIFDYWLAGFIAGDGCFDKYHSHVKGHEYIYDRLRIYDYRIETFEIINDYLEKTFGRKYSIQKDRNIYYIDIKARNITSHYLKLLEGIDNGIPPQILKEGKNAVLSFIAGLFDAEGHVSNKPGIELGMVNKRLIEDVTHYLNALGIKARIREKLRKDGIDYVLHVEEYSSLLRFYELIGKNLQNEEKREKLEKVLSNHKGGNFGLPLNFNAFKEWASEYGVEFKTNGSQTIAIINDERISLGQWHTRNRVSKAVLVKMLRKLYEATKDEEVKRMLHLIEGLEVVRHITTTNEPRTFYDLTVENYQNYLAGENGMIFVHN

Source

organism	Pyrococcus furiosus
ncbi_taxonomy_id	2261
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	332

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6. Citations (1)

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length_a	56.550 Å
length_b	85.280 Å
length_c	65.410 Å
angle_alpha	90.00 °
angle_beta	112.94 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	30.000 Å
r_factor	0.1920
r_work	0.1920
r_free	0.2320

fit	/app/data/saxs_computation/dq/1dq3/1dq3.fit
pddf	/app/data/pr_computation/dq/1dq3/1dq3.pr.out
profile	/app/data/saxs_computation/dq/1dq3/1dq3.dat

CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI

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