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9vid

cryo-EM structure of alligator haemoglobin in the R conformation

Method: ELECTRON MICROSCOPY D_max: 60.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vid
deposition_date	2025-06-18
last_revision	2025-07-23
title	cryo-EM structure of alligator haemoglobin in the R conformation
keywords	haemoglobin, OXYGEN BINDING; OXYGEN BINDING
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	20.70 Å
rg_electron	19.35 Å
i0	18864800.00
molecular_weight	33633.0 kDa
excluded_volume	42310 Å³
envelope_volume	48484 Å³
shell_volume	20737 Å³
envelope_diameter	60.3 Å
shell_rg	25.72 Å
envelope_rg	19.45 Å
shape_rg	19.33 Å
total_rg	20.28 Å
total_atoms	2373
n_residues	287
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	60.4 Å
rg_real	20.56 Å
rg_real_error	0.27 Å
i0_real	1.8860e+07
i0_real_error	2.0590e+05
rg_reciprocal	20.59 Å
i0_reciprocal	18870000.0000
total_estimate	0.9171
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.088
kurtosis	-0.599
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	3428000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.993

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Hemoglobin subunit alpha
formula_weight	15891.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2373

MVLSMEDKSNVKAIWGKASGHLEEYGAEALERMFCAYPQTKIYFPHFDMSHNSAQIRAHGKKVFSALHEAVNHIDDLPGALCRLSELHAHSLRVDPVNFKFLAHCVLVVFAIHHPSALSPEIHASLDKFLCAVSAVLTSKYR

Entity 2 polymer

description	Hemoglobin subunit beta
formula_weight	16641.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

ASFDAHERKFIVDLWAKVDVAQCGADALSRMLIVYPWKRRYFEHFGKMCNAHDILHNSKVQEHGKKVLASFGEAVKHLDNIKGHFANLSKLHCEKFHVDPENFKLLGDIIIIVLAAHHPEDFSVECHAAFQKLVRQVAAALAAEYH

Entity 3 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CARBON MONOXIDE
formula_weight	28.0 kDa
src_method	syn
entity_count	2

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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	2.220 Å
resolution_low	2.220 Å
r_factor	0.3217
r_work	0.3217
r_free	—

resolution	2.22 Å
resolution_method	—
num_particles	371597

fit	/app/data/saxs_computation/vi/9vid/9vid.fit
pddf	/app/data/pr_computation/vi/9vid/9vid.pr.out
profile	/app/data/saxs_computation/vi/9vid/9vid.dat

cryo-EM structure of alligator haemoglobin in the R conformation

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

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)