← Back to search

9s9r

Crystal structure of p53 cancer mutant Y220N

Method: X-RAY DIFFRACTION D_max: 76.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9s9r
deposition_date	2025-08-06
title	Crystal structure of p53 cancer mutant Y220N
keywords	p53, tumor suppressor, protein stability, protein unfolding disease, small-molecule stabilizer, cancer therapy, TRANSCRIPTION; TRANSCRIPTION
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	24.32 Å
rg_electron	23.35 Å
i0	36179900.00
molecular_weight	43632.0 kDa
excluded_volume	53400 Å³
envelope_volume	66316 Å³
shell_volume	23778 Å³
envelope_diameter	78.5 Å
shell_rg	30.17 Å
envelope_rg	23.19 Å
shape_rg	23.36 Å
total_rg	24.10 Å
total_atoms	3042
n_residues	392
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

▼

3. P(r) Analysis (GNOM)

dmax	76.0 Å
rg_real	24.24 Å
rg_real_error	0.44 Å
i0_real	3.6180e+07
i0_real_error	4.6660e+05
rg_reciprocal	24.26 Å
i0_reciprocal	36180000.0000
total_estimate	0.9128
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.9 Å
skewness	0.195
kurtosis	-0.586
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	3781000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.993

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Cellular tumor antigen p53
formula_weight	24541.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3431

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPNEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	nat
entity_count	5

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	343

▶

6. Citations (1)

▶

length_a	65.055 Å
length_b	71.019 Å
length_c	104.826 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	47.970 Å
r_factor	0.1875
r_work	0.1852
r_free	0.2286

fit	/app/data/saxs_computation/s9/9s9r/9s9r.fit
pddf	/app/data/pr_computation/s9/9s9r/9s9r.pr.out
profile	/app/data/saxs_computation/s9/9s9r/9s9r.dat

Crystal structure of p53 cancer mutant Y220N

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