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9rkf

Dark structure of beta-2 Adrenergic receptor with photoazolol in Dark state recorded at SwissFEL

Method: X-RAY DIFFRACTION D_max: 99.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rkf
deposition_date	2025-06-13
title	Dark structure of beta-2 Adrenergic receptor with photoazolol in Dark state recorded at SwissFEL
keywords	;GPCR, 7TM, Beta 2, ADRENERGIC, LIPIDIC CUBIC PHASE, LIPIDIC, MEMBRANE PROTEIN, PHOTO-SWITCHABLE COMPOUNDS, PHOTOAZOLOL-1, TIME RESOLVE CRYSTALLOGRAPHY ;; MEMBRANE PROTEIN
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	30.25 Å
rg_electron	29.44 Å
i0	43118400.00
molecular_weight	55042.0 kDa
excluded_volume	70199 Å³
envelope_volume	90054 Å³
shell_volume	27183 Å³
envelope_diameter	101.3 Å
shell_rg	34.65 Å
envelope_rg	29.39 Å
shape_rg	29.42 Å
total_rg	30.10 Å
total_atoms	7633
n_residues	442
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	99.0 Å
rg_real	30.49 Å
rg_real_error	0.75 Å
i0_real	4.3120e+07
i0_real_error	6.0720e+05
rg_reciprocal	30.39 Å
i0_reciprocal	43120000.0000
total_estimate	0.8558
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	26.7 Å
skewness	0.452
kurtosis	-0.556
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	10110000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.747; Smooth: 0.856

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	Beta-2 adrenergic receptor,Endolysin
formula_weight	50599.2 kDa
ec_number	3.2.1.17
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7669

ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	DODECAETHYLENE GLYCOL
formula_weight	546.6 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
formula_weight	356.5 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	~{N}-[4-[(~{E})-[2-[(2~{S})-2-oxidanyl-3-(propan-2-ylamino)propoxy]phenyl]diazenyl]phenyl]ethanamide
formula_weight	370.4 kDa
src_method	syn
entity_count	1

Entity 10 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	syn
entity_count	1

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	31

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6. Citations (1)

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length_a	111.940 Å
length_b	172.230 Å
length_c	41.230 Å
angle_alpha	90.00 °
angle_beta	106.20 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.450 Å
resolution_low	45.600 Å
r_factor	0.1842
r_work	0.1809
r_free	0.2186

fit	/app/data/saxs_computation/rk/9rkf/9rkf.fit
pddf	/app/data/pr_computation/rk/9rkf/9rkf.pr.out
profile	/app/data/saxs_computation/rk/9rkf/9rkf.dat