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9wfa

Cryo-EM structure of psXR

Method: ELECTRON MICROSCOPY D_max: 71.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wfa
deposition_date	2025-08-21
title	Cryo-EM structure of psXR
keywords	rhodopsin, inward proton pump, 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	20.72 Å
rg_electron	19.32 Å
i0	10090900.00
molecular_weight	27753.0 kDa
excluded_volume	36520 Å³
envelope_volume	40269 Å³
shell_volume	18048 Å³
envelope_diameter	72.6 Å
shell_rg	25.13 Å
envelope_rg	19.65 Å
shape_rg	19.29 Å
total_rg	20.41 Å
total_atoms	1970
n_residues	245
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	71.0 Å
rg_real	20.78 Å
rg_real_error	0.60 Å
i0_real	1.0090e+07
i0_real_error	1.4950e+05
rg_reciprocal	20.77 Å
i0_reciprocal	10090000.0000
total_estimate	0.7942
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.6 Å
skewness	0.424
kurtosis	-0.253
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	1814000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	psXR
formula_weight	32057.4 kDa
mutation	N-terminal His6-tag
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1995

MSISLITDFALLAQSNLPETVSKVDFLSSGQYNLVYNAFSFAIATMLAAALFFFNVRGQVGQKYQLALIVSALVVSIAGYHYYRIFGSWEAAYSLQNGNYVLTGAPFNDAYRYVDWLLTVPLLLVETVAVLALPGMEARPLLIKLVVAAILMIATGYPGEISTDLNTRIVWGAVSTVPFIYILYILWIELSKSLLRQPEGVQTLVKNMRLLLLFSWGVYPIAYLLPMLGISGATADVGVQIGYTIADVLAKPIFGLLVFAIALEKTRVDAGEQPTKESPMTMISSHHHHHH

Source

organism	Gloeobacter violaceus
ncbi_taxonomy_id	33072
host_organism	Escherichia coli

Entity 2 non-polymer

description	RETINAL
formula_weight	284.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
formula_weight	568.9 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	25

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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	2.640 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.64 Å
resolution_method	—
num_particles	327293

fit	/app/data/saxs_computation/wf/9wfa/9wfa.fit
pddf	/app/data/pr_computation/wf/9wfa/9wfa.pr.out
profile	/app/data/saxs_computation/wf/9wfa/9wfa.dat

Cryo-EM structure of psXR

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