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9s06

Dark-state of CBD of TtCarH (TR-SFX, SACLA)

Method: X-RAY DIFFRACTION D_max: 94.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s06
deposition_date	2025-07-16
title	Dark-state of CBD of TtCarH (TR-SFX, SACLA)
keywords	;SFX, Room temperature, serial crystallography, CarH, photoreceptor, vitamin B12, cobalamin, coenzyme B12, time-resolved crystallography, DNA BINDING PROTEIN ;; DNA BINDING 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	29.54 Å
rg_electron	28.39 Å
i0	124965000.00
molecular_weight	90812.0 kDa
excluded_volume	114790 Å³
envelope_volume	136100 Å³
shell_volume	39404 Å³
envelope_diameter	97.7 Å
shell_rg	36.32 Å
envelope_rg	28.29 Å
shape_rg	28.40 Å
total_rg	29.13 Å
total_atoms	6413
n_residues	788
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	94.1 Å
rg_real	29.48 Å
rg_real_error	0.62 Å
i0_real	1.2500e+08
i0_real_error	1.6410e+06
rg_reciprocal	29.51 Å
i0_reciprocal	125000000.0000
total_estimate	0.8958
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.9 Å
skewness	0.294
kurtosis	-0.424
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	52580000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.923

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Probable transcriptional regulator
formula_weight	23259.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	6915

VRPEDLGTGLLEALLRGDLAGAEALFRRGLRFWGPEGVLEHLLLPVLREVGEAWHRGEIGVAEEHLASTFLRARLQELLDLAGFPPGPPVLVTTPPGERHEIGAMLAAYHLRRKGVPALYLGPDTPLPDLRALARRLGAGAVVLSAVLSEPLRALPDGALKDLAPRVFLGGQGAGPEEARRLGAEYMEDLKGLAEALWLPRGPEKEAIGHHHHHH

Source

organism	Thermus thermophilus
ncbi_taxonomy_id	274
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	5'-DEOXYADENOSINE
formula_weight	251.2 kDa
src_method	nat
entity_count	4

Entity 3 non-polymer

description	COBALAMIN
formula_weight	1330.4 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	357

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6. Citations (1)

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length_a	64.800 Å
length_b	71.090 Å
length_c	207.260 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.050 Å
resolution_low	50.000 Å
r_factor	0.1764
r_work	0.1742
r_free	0.2190

fit	/app/data/saxs_computation/s0/9s06/9s06.fit
pddf	/app/data/pr_computation/s0/9s06/9s06.pr.out
profile	/app/data/saxs_computation/s0/9s06/9s06.dat

Dark-state of CBD of TtCarH (TR-SFX, SACLA)

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

Diffraction