SPERM WHALE MYOGLOBIN D122N METHYL ISOCYANIDE AT PH 9.0

Method: X-RAY DIFFRACTION D_max: 50.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	110m
deposition_date	1997-12-23
title	SPERM WHALE MYOGLOBIN D122N METHYL ISOCYANIDE AT PH 9.0
keywords	LIGAND BINDING, OXYGEN STORAGE, OXYGEN BINDING, HEME, OXYGEN TRANSPORT; OXYGEN TRANSPORT
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	16.62 Å
rg_electron	15.21 Å
i0	5821760.00
molecular_weight	18087.0 kDa
excluded_volume	22909 Å³
envelope_volume	25230 Å³
shell_volume	14069 Å³
envelope_diameter	51.4 Å
shell_rg	20.96 Å
envelope_rg	15.39 Å
shape_rg	15.17 Å
total_rg	16.39 Å
total_atoms	1276
n_residues	154
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	50.8 Å
rg_real	16.50 Å
rg_real_error	0.25 Å
i0_real	5.8220e+06
i0_real_error	5.6790e+04
rg_reciprocal	16.51 Å
i0_reciprocal	5822000.0000
total_estimate	0.9028
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	21.1 Å
skewness	0.087
kurtosis	-0.468
angular_range	— – 0.4800 Å⁻¹
current_alpha	0.0000
highest_alpha	863000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.968

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	MYOGLOBIN
formula_weight	17365.2 kDa
mutation	INS(M0), D122N
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1455

MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG

Source

organism	Physeter catodon
common_name	sperm whale
ncbi_taxonomy_id	9755
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 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 non-polymer

description	METHYL ISOCYANIDE
formula_weight	41.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	179

▶

6. Citations (1)

▶

length_a	91.442 Å
length_b	91.442 Å
length_c	45.843 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 6
int_tables_number	168
crystal_system	—

resolution	1.770 Å
resolution_low	5.000 Å
r_factor	0.1570
r_work	0.1570
r_free	0.2140

fit	/app/data/saxs_computation/10/110m/110m.fit
pddf	/app/data/pr_computation/10/110m/110m.pr.out
profile	/app/data/saxs_computation/10/110m/110m.dat