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9qzt

Room temperature structure of Glycine max phyA in Pfr/Pr ensemble

Method: X-RAY DIFFRACTION D_max: 87.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qzt
deposition_date	2025-04-24
title	Room temperature structure of Glycine max phyA in Pfr/Pr ensemble
keywords	phytochrome, phyA, Glycine max, PLANT PROTEIN; PLANT 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	28.28 Å
rg_electron	27.01 Å
i0	73850800.00
molecular_weight	69726.0 kDa
excluded_volume	88447 Å³
envelope_volume	109010 Å³
shell_volume	33204 Å³
envelope_diameter	85.4 Å
shell_rg	34.82 Å
envelope_rg	26.93 Å
shape_rg	27.03 Å
total_rg	27.82 Å
total_atoms	4889
n_residues	615
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	87.3 Å
rg_real	28.16 Å
rg_real_error	0.45 Å
i0_real	7.3850e+07
i0_real_error	9.5880e+05
rg_reciprocal	28.20 Å
i0_reciprocal	73850000.0000
total_estimate	0.9133
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	32.8 Å
skewness	0.162
kurtosis	-0.660
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	36480000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Phytochrome A-2
formula_weight	40026.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9893

MISGTADGVNQPRHDKVTTAYLHHMQKGKMIQPFGCLLALDEKTCKVIAYSENAPEMLTMVSHAVPSVGDHPALGIGTDIKTLFTAPSASALQKALGFAEVLLLNPVLIHCKTSGKPFYAIIHRVTGSMIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMVQEVFELTGYDRVMAYKFHEDDHGEVIAEITKPGLEPYLGLHYPATDIPQASRFLFMKNKVRMIVDCHAKHVRVLQDEKLPFDLTLCGSTLRAPHSCHAQYMANMDSIASLVMAVVVNDNEEDGDTDAIQPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKEIELHHHHHH

Source

organism	Glycine max
common_name	soybean
ncbi_taxonomy_id	3847
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PHYCOCYANOBILIN
formula_weight	588.7 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	138

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6. Citations (2)

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length_a	56.450 Å
length_b	115.050 Å
length_c	69.800 Å
angle_alpha	90.00 °
angle_beta	92.68 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.200 Å
resolution_low	20.480 Å
r_factor	0.1929
r_work	0.1907
r_free	0.2314

fit	/app/data/saxs_computation/qz/9qzt/9qzt.fit
pddf	/app/data/pr_computation/qz/9qzt/9qzt.pr.out
profile	/app/data/saxs_computation/qz/9qzt/9qzt.dat

Room temperature structure of Glycine max phyA in Pfr/Pr ensemble

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