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9psa

Crystal structure of C. elegans PUF-3 in complex with RNA III-9

Method: X-RAY DIFFRACTION D_max: 90.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9psa
deposition_date	2025-07-25
title	Crystal structure of C. elegans PUF-3 in complex with RNA III-9
keywords	RNA binding, Caenorhabditis elegans, PUF-3, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	27.27 Å
rg_electron	27.20 Å
i0	35403100.00
molecular_weight	43400.0 kDa
excluded_volume	53096 Å³
envelope_volume	67649 Å³
shell_volume	22227 Å³
envelope_diameter	92.3 Å
shell_rg	32.54 Å
envelope_rg	27.52 Å
shape_rg	27.23 Å
total_rg	27.66 Å
total_atoms	3026
n_residues	369
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	90.6 Å
rg_real	27.55 Å
rg_real_error	0.83 Å
i0_real	3.5400e+07
i0_real_error	5.3010e+05
rg_reciprocal	27.47 Å
i0_reciprocal	35400000.0000
total_estimate	0.6231
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.527
kurtosis	-0.383
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	6787000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 0.999; Sysdev: 0.127; Positv: 1.000; Valcen: 0.783; Smooth: 0.578

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PUM-HD domain-containing protein
formula_weight	43478.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3054

SGDGEGNVSDSVTLQDVLANDALVEFATDKNGCRFLQEHYPTENDNDVHQKLFRKLVEDRAIFLSLCSNMFGNFFVQRVLECSNTEEQEILTEHLATDLYNLCLDKSACRVIQLAIQKLDVHLATRLSLELRDTHLVRLSIDQNGNHVIQKIVKTLPVSSWTFLVDFFADDDNLIHVCQDKYGCRVIQSTVETLSTDQYAQCYQHRVILLRSLMAGVTRNCTQLASNEFANYVVQHVIKCGDALAVYRDIIIEQCLLQNLLSMSQEKYASHVVEVAFECAPYRLVAEMMNEIFEGYIPHPDTNRDALDILLFHQYGNYVVQQMIQTCVLGQNARDQKQSEMYGMWLEKIHGRVMRNAHRLERFSSGKKIIEALQSMSLY

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 2 polymer

description	RNA III-9
formula_weight	3491.1 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

CUGUCAAAAUG

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	27

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6. Citations (1)

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length_a	143.377 Å
length_b	143.377 Å
length_c	120.042 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 62 2 2
int_tables_number	180
crystal_system	—

resolution	2.860 Å
resolution_low	34.350 Å
r_factor	0.2271
r_work	0.2247
r_free	0.2496

fit	/app/data/saxs_computation/ps/9psa/9psa.fit
pddf	/app/data/pr_computation/ps/9psa/9psa.pr.out
profile	/app/data/saxs_computation/ps/9psa/9psa.dat

Crystal structure of C. elegans PUF-3 in complex with RNA III-9

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)