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1d83

STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN SOLUTION

Method: SOLUTION NMR D_max: 39.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d83
deposition_date	1992-07-22
title	STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN SOLUTION
keywords	DNA, DOUBLE HELIX, CHROMOMYCIN; DNA
method	SOLUTION NMR

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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	12.44 Å
rg_electron	11.58 Å
i0	1867600.00
molecular_weight	7238.0 kDa
excluded_volume	8021 Å³
envelope_volume	9597 Å³
shell_volume	7477 Å³
envelope_diameter	38.0 Å
shell_rg	16.50 Å
envelope_rg	11.90 Å
shape_rg	11.48 Å
total_rg	12.78 Å
total_atoms	835
n_residues	16
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	39.8 Å
rg_real	12.41 Å
rg_real_error	0.24 Å
i0_real	1.8680e+06
i0_real_error	1.9080e+04
rg_reciprocal	12.41 Å
i0_reciprocal	1868000.0000
total_estimate	0.9068
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	14.1 Å
skewness	0.225
kurtosis	-0.457
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	176600.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;DNA (5'-D(APAPGPGPCPCPTPT)-3') ;
formula_weight	2426.6 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	A,B
atom_count	835

AAGGCCTT

Entity 2 branched

description	;3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol ;
formula_weight	432.5 kDa
src_method	man
entity_count	2

Entity 3 branched

description	2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate
formula_weight	318.4 kDa
src_method	man
entity_count	2

Entity 4 non-polymer

description	(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
formula_weight	420.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	—

fit	/app/data/saxs_computation/d8/1d83/1d83.fit
pddf	/app/data/pr_computation/d8/1d83/1d83.pr.out
profile	/app/data/saxs_computation/d8/1d83/1d83.dat

STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN SOLUTION

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 branched

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)