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9yp1

Rabbit Hemorrhagic Disease Virus Czech P domain

Method: X-RAY DIFFRACTION D_max: 77.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yp1
deposition_date	2025-10-13
title	Rabbit Hemorrhagic Disease Virus Czech P domain
keywords	lagovirus, 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	25.34 Å
rg_electron	24.31 Å
i0	81063700.00
molecular_weight	70298.0 kDa
excluded_volume	87773 Å³
envelope_volume	100350 Å³
shell_volume	33136 Å³
envelope_diameter	80.2 Å
shell_rg	32.62 Å
envelope_rg	24.42 Å
shape_rg	24.27 Å
total_rg	25.28 Å
total_atoms	4962
n_residues	669
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	77.5 Å
rg_real	25.18 Å
rg_real_error	0.49 Å
i0_real	8.1060e+07
i0_real_error	1.0740e+06
rg_reciprocal	25.23 Å
i0_reciprocal	81070000.0000
total_estimate	0.8109
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.0 Å
skewness	0.110
kurtosis	-0.535
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	17950000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 0.970; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Capsid protein
formula_weight	35097.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	5808

SKTVDSISPAGLLTTPDLTGVGNDNRWNGQIVGLQPVPGGFSTCNRHWNLNGSTYGWSSPRFADIDHRKGSASYTGSNATNVLQFWYANAGSAIDNPISQVAPDGFPDMSFVPFNGPGIPAAGWVGFGAIWNSNSGAPNVTTVQAYELGFATGAPGNLQPTTNTSGAQTVAKSIYAVVTGTAQNPAGLFVMASGIISTPNASAITYTPQPDRIVTTPGTPAAAPVGKNTPIMFASVVRRTGDVNATAGSVNGTQYGTGSQPLPVTIGLSLNNYSSALMPGQFFVWQLTFASGFMEIGLSVDGYFYAGTGASTTLIDLTELIDVRPVGPRPSKSTLVFNL

Source

organism	Rabbit hemorrhagic disease virus
common_name	RHDV
ncbi_taxonomy_id	11976
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	11

Entity 3 non-polymer

description	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
formula_weight	207.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	807

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6. Citations (1)

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length_a	62.968 Å
length_b	51.261 Å
length_c	94.270 Å
angle_alpha	90.00 °
angle_beta	101.05 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.370 Å
resolution_low	47.370 Å
r_factor	0.1512
r_work	0.1502
r_free	0.1715

fit	/app/data/saxs_computation/yp/9yp1/9yp1.fit
pddf	/app/data/pr_computation/yp/9yp1/9yp1.pr.out
profile	/app/data/saxs_computation/yp/9yp1/9yp1.dat