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9pqs

Crystal structure of the scFv-1E8b in complex with the synthetic glycoamino acid Pse-Ser

Method: X-RAY DIFFRACTION D_max: 58.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pqs
deposition_date	2025-07-23
title	Crystal structure of the scFv-1E8b in complex with the synthetic glycoamino acid Pse-Ser
keywords	antibody, complex, scfv, SUGAR BINDING PROTEIN; SUGAR 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	18.29 Å
rg_electron	17.38 Å
i0	22830000.00
molecular_weight	23995.0 kDa
excluded_volume	22968 Å³
envelope_volume	36193 Å³
shell_volume	17448 Å³
envelope_diameter	58.7 Å
shell_rg	23.47 Å
envelope_rg	17.64 Å
shape_rg	17.33 Å
total_rg	18.13 Å
total_atoms	1803
n_residues	231
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	58.1 Å
rg_real	18.20 Å
rg_real_error	0.23 Å
i0_real	2.2830e+07
i0_real_error	2.2600e+05
rg_reciprocal	18.21 Å
i0_reciprocal	22830000.0000
total_estimate	0.9000
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	22.8 Å
skewness	0.188
kurtosis	-0.453
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	6920000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	scFv-1E8b
formula_weight	28287.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1917

EVKLFQSGGGLVQPGGSLKLSCAASGIDFSRNWMTWVRRAPGKGLEWIGEIYPDSRTINYAPSLKDKFIISRDNAKKMLYLQMSKVRSEDTALYYCARRGVTTVVGTSWYFDVWGTGTTVTVSSAGGSSRSSSSGGGGSGGGGDIQMIQSPSSMFASLGDRVSLSCRASQGIRGNLDWYQQKPGGPIKLLIHSTSKLNSGVPSRFSGSGSGSDYSLTISSLESEDFADYYCLQRNAFPLTFGAGTKLELKRAGRLEHHHHHH

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 non-polymer

description	;(2S,4S,5S,6S)-5-acetamido-6-[(1S,2S)-1-acetamido-2-hydroxypropyl]-2-[(2S)-2-carboxy-2-({[(prop-2-en-1-yl)oxy]carbonyl}amino)ethoxy]-4-hydroxyoxane-2-carboxylic acid ;
formula_weight	505.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	6

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	102

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6. Citations (1)

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length_a	67.928 Å
length_b	67.928 Å
length_c	225.890 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	—

resolution	2.060 Å
resolution_low	46.360 Å
r_factor	0.1948
r_work	0.1929
r_free	0.2287

fit	/app/data/saxs_computation/pq/9pqs/9pqs.fit
pddf	/app/data/pr_computation/pq/9pqs/9pqs.pr.out
profile	/app/data/saxs_computation/pq/9pqs/9pqs.dat