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9t0k

Catalase CryoEM Structure from Human erythrocyte at 1.87A resolution

Method: ELECTRON MICROSCOPY D_max: 89.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t0k
deposition_date	2025-10-17
title	Catalase CryoEM Structure from Human erythrocyte at 1.87A resolution
keywords	Catalase, NADPH, Heme B, Protoporphyrin IX with Fe, OXIDOREDUCTASE; OXIDOREDUCTASE
method	ELECTRON MICROSCOPY

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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	26.35 Å
rg_electron	25.51 Å
i0	58298600.00
molecular_weight	58180.0 kDa
excluded_volume	72172 Å³
envelope_volume	94300 Å³
shell_volume	30741 Å³
envelope_diameter	92.2 Å
shell_rg	32.68 Å
envelope_rg	26.71 Å
shape_rg	25.47 Å
total_rg	26.41 Å
total_atoms	7925
n_residues	500
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	89.3 Å
rg_real	26.35 Å
rg_real_error	0.64 Å
i0_real	5.8300e+07
i0_real_error	8.5840e+05
rg_reciprocal	26.35 Å
i0_reciprocal	58300000.0000
total_estimate	0.8730
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.8 Å
skewness	0.399
kurtosis	-0.182
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	8283000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Catalase
formula_weight	59837.0 kDa
ec_number	1.11.1.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8406

MADSRDPASDQMQHWKEQRAAQKADVLTTGAGNPVGDKLNVITVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITKYSKAKVFEHIGKKTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLSQEDPDYGIRDLFNAIATGKYPSWTFYIQVMTFNQAETFPFNPFDLTKVWPHKDYPLIPVGKLVLNRNPVNYFAEVEQIAFDPSNMPPGIEASPDKMLQGRLFAYPDTHRHRLGPNYLHIPVNCPYRARVANYQRDGPMCMQDNQGGAPNYYPNSFGAPEQQPSALEHSIQYSGEVRRFNTANDDNVTQVRAFYVNVLNEEQRKRLCENIAGHLKDAQIFIQKKAVKNFTEVHPDYGSHIQALLDKYNAEKPKNAIHTFVQSGSHLAAREKANL

Entity 2 non-polymer

description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	745.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	397

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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	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.87 Å
resolution_method	—
num_particles	1070801

fit	/app/data/saxs_computation/t0/9t0k/9t0k.fit
pddf	/app/data/pr_computation/t0/9t0k/9t0k.pr.out
profile	/app/data/saxs_computation/t0/9t0k/9t0k.dat