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1d8i

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.

Method: X-RAY DIFFRACTION D_max: 121.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d8i
deposition_date	1999-10-24
title	X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.
keywords	;RNA TRIPHOSPHATASE, BETA SUBUNIT, POLYNUCLEOTIDE 5'-TRIPHOSPHATASE, MRNA PROCESSING, MRNA CAPPING, NUCLEAR PROTEIN BETA BARREL, CATALYTIC DOMAIN, DIMER, SULFATE COMPLEX, 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	36.13 Å
rg_electron	36.12 Å
i0	148957000.00
molecular_weight	98130.0 kDa
excluded_volume	123020 Å³
envelope_volume	169090 Å³
shell_volume	40920 Å³
envelope_diameter	130.3 Å
shell_rg	40.09 Å
envelope_rg	36.22 Å
shape_rg	36.12 Å
total_rg	36.39 Å
total_atoms	6915
n_residues	864
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	121.9 Å
rg_real	36.43 Å
rg_real_error	0.99 Å
i0_real	1.4900e+08
i0_real_error	2.3440e+06
rg_reciprocal	36.25 Å
i0_reciprocal	148900000.0000
total_estimate	0.8266
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.3 Å
skewness	0.523
kurtosis	-0.371
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	30660000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.737; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.689

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	MRNA TRIPHOSPHATASE CET1
formula_weight	35691.5 kDa
ec_number	3.1.3.33
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	7329

HMYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSYEIFEGSKKVM

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	6

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	414

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6. Citations (1)

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length_a	121.358 Å
length_b	116.095 Å
length_c	82.310 Å
angle_alpha	90.00 °
angle_beta	110.25 °
angle_gamma	90.00 °
z_pdb	12

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.050 Å
resolution_low	25.000 Å
r_factor	—
r_work	0.2026
r_free	0.2696

fit	/app/data/saxs_computation/d8/1d8i/1d8i.fit
pddf	/app/data/pr_computation/d8/1d8i/1d8i.pr.out
profile	/app/data/saxs_computation/d8/1d8i/1d8i.dat

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.

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