← Back to search

9y5f

Crystal structure of rv-SNARE/sc-t-SNARE-5.s.8 complex

Method: X-RAY DIFFRACTION D_max: 127.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y5f
deposition_date	2025-09-04
title	Crystal structure of rv-SNARE/sc-t-SNARE-5.s.8 complex
keywords	membrane fusion proteins, synthetic fusogens, SNARE, protein design, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.09 Å
rg_electron	33.61 Å
i0	23550700.00
molecular_weight	36226.0 kDa
excluded_volume	44860 Å³
envelope_volume	58592 Å³
shell_volume	18276 Å³
envelope_diameter	135.4 Å
shell_rg	31.51 Å
envelope_rg	35.32 Å
shape_rg	33.63 Å
total_rg	33.37 Å
total_atoms	2534
n_residues	303
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	127.3 Å
rg_real	33.16 Å
rg_real_error	1.70 Å
i0_real	2.3550e+07
i0_real_error	4.6450e+05
rg_reciprocal	32.70 Å
i0_reciprocal	23540000.0000
total_estimate	0.6289
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	20.8 Å
skewness	0.770
kurtosis	-0.095
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	2697000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.072; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.011; Smooth: 0.946

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	rv-SNARE/sc-t
formula_weight	8671.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2534

MSSSSNEKLRETLREVEDVKNIMEDNRRLVERQGRQIDRLEEKADDLERSAERLSDNSEKLKRKYWWKNSK

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 polymer

description	sc-t-SNARE-5.s.8
formula_weight	28983.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SGGSSSEREKEIDEGLDRVSEIVKELKKMAEEMRRMIEEQGRRIERIEEKAEEAKEKIEEANERAEKLLKDPGGSGGSEELKKLEKEGEKLKELVEELDREIKELKEGMERLREMFEEAAKLSEEALEIMRRTRKLSEEELEEAKQKAKEQEKEKALKEKGGSGGSGGSEKVKRELAQIEERHQQILELEEKIKELLEMFKELSEKIEEQGQKIDRIEDKVSKAKEHVEKGVEDTKKAVKYQSKARRKK

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

▶

6. Citations (1)

▶

length_a	47.094 Å
length_b	47.094 Å
length_c	334.302 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	3.450 Å
resolution_low	33.300 Å
r_factor	0.2331
r_work	0.2267
r_free	0.2880

fit	/app/data/saxs_computation/y5/9y5f/9y5f.fit
pddf	/app/data/pr_computation/y5/9y5f/9y5f.pr.out
profile	/app/data/saxs_computation/y5/9y5f/9y5f.dat

Crystal structure of rv-SNARE/sc-t-SNARE-5.s.8 complex

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)