SAXSdb — 1dgf

▼

1. Structure Basics

entry_id	1dgf
deposition_date	1999-11-24
title	HUMAN ERYTHROCYTE CATALASE
keywords	CATALASE, HEME, NADPH, HYDROGEN PEROXIDE, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.48 Å
rg_electron	35.76 Å
i0	813536000.00
molecular_weight	230390.0 kDa
excluded_volume	286330 Å³
envelope_volume	333690 Å³
shell_volume	72095 Å³
envelope_diameter	116.1 Å
shell_rg	45.95 Å
envelope_rg	35.78 Å
shape_rg	35.75 Å
total_rg	36.34 Å
total_atoms	16292
n_residues	1988
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	111.4 Å
rg_real	36.24 Å
rg_real_error	0.64 Å
i0_real	8.1350e+08
i0_real_error	1.1980e+07
rg_reciprocal	36.39 Å
i0_reciprocal	813700000.0000
total_estimate	0.8977
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.6 Å
skewness	0.132
kurtosis	-0.516
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	284100000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.908

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	CATALASE
formula_weight	56626.4 kDa
ec_number	1.11.1.6
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	18675

RDPASDQMQHWKEQRAAQKADVLTTGAGNPVGDKLNVITVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITKYSKAKVFEHIGKKTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLSQEDPDYGIRDLFNAIATGKYPSWTFYIQVMTFNQAETFPFNPFDLTKVWPHKDYPLIPVGKLVLNRNPVNYFAEVEQIAFDPSNMPPGIEASPDKMLQGRLFAYPDTHRHRLGPNYLHIPVNCPYRARVANYQRDGPMCMQDNQGGAPNYYPNSFGAPEQQPSALEHSIQYSGEVRRFNTANDDNVTQVRAFYVNVLNEEQRKRLCENIAGHLKDAQIFIQKKAVKNFTEVHPDYGSHIQALLDKYN

Entity 2 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	745.4 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2299

▶

6. Citations (1)

▶

length_a	83.717 Å
length_b	142.505 Å
length_c	232.066 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	—

resolution	1.500 Å
resolution_low	20.000 Å
r_factor	0.1740
r_work	0.1720
r_free	0.1920

fit	/app/data/saxs_computation/dg/1dgf/1dgf.fit
pddf	/app/data/pr_computation/dg/1dgf/1dgf.pr.out
profile	/app/data/saxs_computation/dg/1dgf/1dgf.dat

HUMAN ERYTHROCYTE CATALASE

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