SAXSdb — 9vxl

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1. Structure Basics

entry_id	9vxl
deposition_date	2025-07-19
title	CD38 in complex with 028 Fab
keywords	CAR, CD38, antibody, MEMBRANE PROTEIN; MEMBRANE 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	30.50 Å
rg_electron	29.81 Å
i0	88052600.00
molecular_weight	72926.0 kDa
excluded_volume	90846 Å³
envelope_volume	117860 Å³
shell_volume	34041 Å³
envelope_diameter	98.8 Å
shell_rg	35.90 Å
envelope_rg	29.48 Å
shape_rg	29.79 Å
total_rg	30.44 Å
total_atoms	5129
n_residues	664
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	97.2 Å
rg_real	30.48 Å
rg_real_error	0.67 Å
i0_real	8.8050e+07
i0_real_error	1.3890e+06
rg_reciprocal	30.49 Å
i0_reciprocal	88050000.0000
total_estimate	0.9040
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	35.5 Å
skewness	0.265
kurtosis	-0.566
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	13670000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.923

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	heavy chain of 028
formula_weight	23508.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	5280

QVQLVQSGAEVKKPGSSVKVSCKAFGGTFSSYAISWVRQAPGQGLEWMGRIIRFLGIANYAQKFQGRVTLIADKSTNTAYMELSSLRSEDTAVYYCAGEPGERDPDAVDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	light chain of 028
formula_weight	23194.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

DIQMTQSPSSLSASVGDRVTITCAASQGIRSWLAWYQQKPEKAPKSLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
formula_weight	27106.8 kDa
ec_number	3.2.2.-,3.2.2.6,2.4.99.20
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

QWSGPGTTKRFPETVLARCVKYTAIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFATSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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6. Citations (1)

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length_a	54.868 Å
length_b	235.879 Å
length_c	54.059 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	3.150 Å
resolution_low	40.170 Å
r_factor	0.2361
r_work	0.2328
r_free	0.2960

fit	/app/data/saxs_computation/vx/9vxl/9vxl.fit
pddf	/app/data/pr_computation/vx/9vxl/9vxl.pr.out
profile	/app/data/saxs_computation/vx/9vxl/9vxl.dat

CD38 in complex with 028 Fab

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)