Cyclic nucleotide binding transcription factor Bd2879 - apo form

Method: X-RAY DIFFRACTION D_max: 105.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9sfa
deposition_date	2025-08-19
title	Cyclic nucleotide binding transcription factor Bd2879 - apo form
keywords	Cyclic nucleotide binding, Transcription factor, Dimer, Complex, Helix-turn-helix, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.36 Å
rg_electron	30.87 Å
i0	88873400.00
molecular_weight	75680.0 kDa
excluded_volume	95451 Å³
envelope_volume	129410 Å³
shell_volume	35931 Å³
envelope_diameter	107.5 Å
shell_rg	36.85 Å
envelope_rg	30.97 Å
shape_rg	30.86 Å
total_rg	31.46 Å
total_atoms	5314
n_residues	667
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

▼

3. P(r) Analysis (GNOM)

dmax	105.1 Å
rg_real	31.36 Å
rg_real_error	0.76 Å
i0_real	8.8870e+07
i0_real_error	1.2890e+06
rg_reciprocal	31.36 Å
i0_reciprocal	88870000.0000
total_estimate	0.8863
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.1 Å
skewness	0.324
kurtosis	-0.344
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	20950000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.920

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (1)

▶

6. Citations (1)

▶

length_a	86.912 Å
length_b	100.016 Å
length_c	198.918 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.880 Å
resolution_low	48.500 Å
r_factor	0.2388
r_work	0.2370
r_free	0.2731

description	Putative regulatory protein
formula_weight	43589.2 kDa
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	5314

Cyclic nucleotide binding transcription factor Bd2879 - apo form

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

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Bdellovibrio bacteriovorus HD100
ncbi_taxonomy_id	264462
host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/sf/9sfa/9sfa.fit
pddf	/app/data/pr_computation/sf/9sfa/9sfa.pr.out
profile	/app/data/saxs_computation/sf/9sfa/9sfa.dat