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9szz

p53-Y220C Core Domain Covalently Bound to a Vinyl-Sulfone Fragment

Method: X-RAY DIFFRACTION D_max: 75.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9szz
deposition_date	2025-10-16
last_revision	2026-05-27
title	p53-Y220C Core Domain Covalently Bound to a Vinyl-Sulfone Fragment
keywords	Tumor Suppressor, Cancer, Stabilization, Covalent, CELL CYCLE; CELL CYCLE
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	24.20 Å
rg_electron	23.49 Å
i0	67993000.00
molecular_weight	41555.0 kDa
excluded_volume	39307 Å³
envelope_volume	68576 Å³
shell_volume	24414 Å³
envelope_diameter	79.6 Å
shell_rg	30.30 Å
envelope_rg	23.29 Å
shape_rg	23.48 Å
total_rg	24.08 Å
total_atoms	3100
n_residues	397
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	75.4 Å
rg_real	24.13 Å
rg_real_error	0.51 Å
i0_real	6.7990e+07
i0_real_error	9.4860e+05
rg_reciprocal	24.15 Å
i0_reciprocal	67990000.0000
total_estimate	0.9133
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	73.0 Å
skewness	0.210
kurtosis	-0.579
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	6181000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Cellular tumor antigen p53
formula_weight	24530.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3598

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPCEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	3-bromanyl-1-benzothiophene 1,1-dioxide
formula_weight	245.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

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

Entity 7 non-polymer

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

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	429

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6. Citations (1)

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length_a	65.103 Å
length_b	71.050 Å
length_c	105.270 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.700 Å
resolution_low	48.000 Å
r_factor	0.1766
r_work	0.1756
r_free	0.2128

fit	/app/data/saxs_computation/sz/9szz/9szz.fit
pddf	/app/data/pr_computation/sz/9szz/9szz.pr.out
profile	/app/data/saxs_computation/sz/9szz/9szz.dat