Cryo-EM structure of NCLX with calcium (class 3a)

Method: ELECTRON MICROSCOPY D_max: 122.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ps1
deposition_date	2025-07-24
title	Cryo-EM structure of NCLX with calcium (class 3a)
keywords	Membrane transporter, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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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	39.75 Å
rg_electron	39.02 Å
i0	307369000.00
molecular_weight	160290.0 kDa
excluded_volume	208090 Å³
envelope_volume	283120 Å³
shell_volume	60740 Å³
envelope_diameter	129.4 Å
shell_rg	44.63 Å
envelope_rg	38.77 Å
shape_rg	39.02 Å
total_rg	39.38 Å
total_atoms	11325
n_residues	1464
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	122.1 Å
rg_real	39.60 Å
rg_real_error	0.96 Å
i0_real	3.0740e+08
i0_real_error	5.3440e+06
rg_reciprocal	39.70 Å
i0_reciprocal	307400000.0000
total_estimate	0.8373
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.8 Å
skewness	0.198
kurtosis	-0.537
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	26560000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.60 Å
resolution_method	—
num_particles	150233

description	NCLX
formula_weight	64037.7 kDa
src_method	man
entity_count	3

Cryo-EM structure of NCLX with calcium (class 3a)

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Homo sapiens

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

fit	/app/data/saxs_computation/ps/9ps1/9ps1.fit
pddf	/app/data/pr_computation/ps/9ps1/9ps1.pr.out
profile	/app/data/saxs_computation/ps/9ps1/9ps1.dat

type	polypeptide(L)
strand_id	B,C,A
atom_count	11325