Cryo-EM structure of NCLX with calcium (class 4a)

Method: ELECTRON MICROSCOPY D_max: 121.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ps2
deposition_date	2025-07-24
title	Cryo-EM structure of NCLX with calcium (class 4a)
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	40.10 Å
rg_electron	39.46 Å
i0	306526000.00
molecular_weight	160290.0 kDa
excluded_volume	208090 Å³
envelope_volume	282990 Å³
shell_volume	60303 Å³
envelope_diameter	130.8 Å
shell_rg	44.79 Å
envelope_rg	39.32 Å
shape_rg	39.47 Å
total_rg	39.79 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	121.3 Å
rg_real	40.02 Å
rg_real_error	0.82 Å
i0_real	3.0650e+08
i0_real_error	5.1690e+06
rg_reciprocal	40.10 Å
i0_reciprocal	306600000.0000
total_estimate	0.8691
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.6 Å
skewness	0.212
kurtosis	-0.536
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	26260000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.359

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	NCLX
formula_weight	64037.7 kDa
src_method	syn
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,A,B
atom_count	11395

MAGRWLDPLWAPGFLCVALILETASGAGDLSTKAHGHIQFSARGVNQTAMADCRAVCSLNTSDRCDFVKRNPDCHSEGGYLDYLKGIFCYFPPNLLPLAITLYVFWLLYLFLILGVTAAKFFCPNLSAISTSLKLSHNVAGVTFLAFGNGAPDIFSALVAFSDPRTAGLAIGALFGAGVLVTTVVAGGITILRPFMAASRPFLRDITFYMVAVFLTFTALYLGRITLVWALGYLGLYVFYVVTVIICTWVYQRQRSRSLVHSISETPELLTDSEEDQMSSNTNSYDYGEEYRPLLLGEETTGQILLQALNPLDYRKWRTQSISCKLLKVAKLPVEFLLLLTVPVVDPDKDDRNWKRPLNCLQLVISPLVLVLTLQSGVYGIYEIGGLLPVWAVVVIVGTALASVTFFATSNSEPPRLHWLFAFLGFLTSALWINAAATEVVNILRSLGVVFRLSNTVLGLTLLAWGNSIGDAFSDFTLARQGYPRMAFSACFGGIIFNILVGVGLGCLLQIVRSHASEVKLEPDGLLVWVLASALGLSLVFSLVSVPLQCFQLSKAYGLCLLLFYICFIVVVLLTEFGVIHLKAD

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	nat
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	70

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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	2.15 Å
resolution_method	—
num_particles	686084

fit	/app/data/saxs_computation/ps/9ps2/9ps2.fit
pddf	/app/data/pr_computation/ps/9ps2/9ps2.pr.out
profile	/app/data/saxs_computation/ps/9ps2/9ps2.dat