Structure of mutant SHP2

Method: X-RAY DIFFRACTION D_max: 129.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r16
deposition_date	2025-04-25
title	Structure of mutant SHP2
keywords	SHP2, PTPN11, HYDROLASE; HYDROLASE
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	38.23 Å
rg_electron	38.01 Å
i0	219553000.00
molecular_weight	117110.0 kDa
excluded_volume	145480 Å³
envelope_volume	195480 Å³
shell_volume	44293 Å³
envelope_diameter	133.5 Å
shell_rg	42.48 Å
envelope_rg	37.14 Å
shape_rg	38.02 Å
total_rg	38.26 Å
total_atoms	16343
n_residues	1019
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	129.6 Å
rg_real	38.45 Å
rg_real_error	1.22 Å
i0_real	2.1960e+08
i0_real_error	3.7340e+06
rg_reciprocal	38.32 Å
i0_reciprocal	219500000.0000
total_estimate	0.8677
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	37.9 Å
skewness	0.413
kurtosis	-0.519
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	36030000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.897; Smooth: 0.859

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (3)

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length_a	45.177 Å
length_b	212.158 Å
length_c	54.921 Å
angle_alpha	90.00 °
angle_beta	96.46 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.627 Å
resolution_low	27.780 Å
r_factor	0.2816
r_work	0.2804
r_free	0.3039

description	Tyrosine-protein phosphatase non-receptor type 11
formula_weight	61713.6 kDa
ec_number	3.1.3.48
mutation	Y62D
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	16635

Structure of mutant SHP2

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (3)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	252

fit	/app/data/saxs_computation/r1/9r16/9r16.fit
pddf	/app/data/pr_computation/r1/9r16/9r16.pr.out
profile	/app/data/saxs_computation/r1/9r16/9r16.dat