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9x6q

Crystal structure of the Songling virus nucleoprotein

Method: X-RAY DIFFRACTION D_max: 136.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x6q
deposition_date	2025-10-15
last_revision	2025-11-19
title	Crystal structure of the Songling virus nucleoprotein
keywords	Orthonairovirus songlingense, viral nucleoprotein monomer, VIRAL PROTEIN; VIRAL 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	39.83 Å
rg_electron	40.33 Å
i0	171881000.00
molecular_weight	107390.0 kDa
excluded_volume	134680 Å³
envelope_volume	177920 Å³
shell_volume	39085 Å³
envelope_diameter	146.8 Å
shell_rg	42.65 Å
envelope_rg	39.97 Å
shape_rg	40.32 Å
total_rg	40.49 Å
total_atoms	7557
n_residues	955
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	136.6 Å
rg_real	40.44 Å
rg_real_error	1.37 Å
i0_real	1.7190e+08
i0_real_error	3.2640e+06
rg_reciprocal	40.07 Å
i0_reciprocal	171800000.0000
total_estimate	0.7435
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	30.7 Å
skewness	0.534
kurtosis	-0.437
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	30270000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.585; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.551; Smooth: 0.356

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Nucleoprotein
formula_weight	54208.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7586

SSQLTFSDKGGLDTWYKGFKSSLGFDLLSTLTYSESLCKEVLGPHSLDIKSASREKDAEIARLMHERLKDMAPVYECAWTSCDGIVRRSFDWFEKNKDHKNMKWSKEYESLKKAVPSSDQVLQYQEAALEWRNAIKYEINSFTTASKDSVVKIYRVGADIVTDIQDLLKDMQRRRNTALKIEPGQEKAPALHIEAFKEWLDSKDYTAPCPWGSWTKKNKGGTSLAVTACAGLVNKKYRTRDQLKAELETIGTEVEAMGELAEFDKNFCKEQGTFFKSLWSTVDGFLSGTQAGSKNSGFVQQGSAIDTAFSSHYWAWKAGVRPELFPTLSSMLFNLGKAPLGKAKVIKKLKESPFVWAQTMSEMFSQVESDAIHMHPGILTPGRICSDMVCAFGAFPVAEPAKIRDGSSSPRFLLNLRSDGENPAGQSICALFREYKQEYSGWQDQEIVPVEHMLHQSFLSKHGPFVNVYQVQGLALAVKIQGI

Source

organism	Orthonairovirus songlingense
ncbi_taxonomy_id	3060504
host_organism	Escherichia coli KRX

Entity 2 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	29

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6. Citations (2)

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length_a	54.490 Å
length_b	113.352 Å
length_c	215.687 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 21 21
int_tables_number	18
crystal_system	orthorhombic

resolution	2.520 Å
resolution_low	34.270 Å
r_factor	0.2141
r_work	0.2117
r_free	0.2572

fit	/app/data/saxs_computation/x6/9x6q/9x6q.fit
pddf	/app/data/pr_computation/x6/9x6q/9x6q.pr.out
profile	/app/data/saxs_computation/x6/9x6q/9x6q.dat