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9rkh

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

Method: X-RAY DIFFRACTION D_max: 99.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rkh
deposition_date	2025-06-13
title	Dark structure of beta-2 Adrenergic receptor with photoazolol in Dark state recorded at LCLS
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	29.45 Å
i0	42680000.00
molecular_weight	54714.0 kDa
excluded_volume	69793 Å³
envelope_volume	89636 Å³
shell_volume	27195 Å³
envelope_diameter	100.2 Å
shell_rg	34.57 Å
envelope_rg	29.36 Å
shape_rg	29.44 Å
total_rg	30.04 Å
total_atoms	7596
n_residues	441
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	99.9 Å
rg_real	30.48 Å
rg_real_error	0.93 Å
i0_real	4.2680e+07
i0_real_error	7.4740e+05
rg_reciprocal	30.38 Å
i0_reciprocal	42680000.0000
total_estimate	0.8553
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	26.9 Å
skewness	0.451
kurtosis	-0.558
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	9834000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.731; Smooth: 0.907

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Beta-2 adrenergic receptor,Endolysin
formula_weight	50528.1 kDa
ec_number	3.2.1.17
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7649

DEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL

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	2

Entity 4 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	DODECAETHYLENE GLYCOL
formula_weight	546.6 kDa
src_method	syn
entity_count	3

Entity 6 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 7 non-polymer

description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
formula_weight	356.5 kDa
src_method	syn
entity_count	7

Entity 8 non-polymer

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

Entity 9 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	26

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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	2.500 Å
resolution_low	28.330 Å
r_factor	0.1950
r_work	0.1931
r_free	0.2183

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