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9qme

McCP in complex with photocaged nitric oxide, 20 ms, 12.9 microjoule, SFX

Method: X-RAY DIFFRACTION D_max: 71.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qme
deposition_date	2025-03-23
title	McCP in complex with photocaged nitric oxide, 20 ms, 12.9 microjoule, SFX
keywords	McCP, heme, gas binding, METAL BINDING PROTEIN, NO; METAL BINDING PROTEIN
method	X-RAY DIFFRACTION

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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	20.65 Å
rg_electron	19.65 Å
i0	18306100.00
molecular_weight	31755.0 kDa
excluded_volume	39352 Å³
envelope_volume	45693 Å³
shell_volume	19698 Å³
envelope_diameter	67.3 Å
shell_rg	25.74 Å
envelope_rg	19.95 Å
shape_rg	19.61 Å
total_rg	20.61 Å
total_atoms	2241
n_residues	272
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	71.2 Å
rg_real	20.62 Å
rg_real_error	0.62 Å
i0_real	1.8310e+07
i0_real_error	2.6110e+05
rg_reciprocal	20.63 Å
i0_reciprocal	18310000.0000
total_estimate	0.7568
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	19.6 Å
skewness	0.338
kurtosis	-0.372
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	5596000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.678; Stabil: 0.940; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Cytochrome c
formula_weight	17370.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2278

MNKPSFLLVGLLVVSGVLGAAETKVKYPDGFRSWYHVKSMVIQPGHPLENPFGGIHHVYANAEAIQGLRGGNYPDGAVLVFDLFDYQEDNHALVEGKRKLIGVMERDAKRFSATGGWGYEGFGEGKPDKRLVTDGGQGCFGCHAAQKESQYVFSRLRD

Source

organism	Methylococcus capsulatus str. Bath
ncbi_taxonomy_id	243233
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	NITRIC OXIDE
formula_weight	30.0 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	22

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6. Citations (1)

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length_a	107.766 Å
length_b	107.766 Å
length_c	107.766 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 21 3
int_tables_number	198
crystal_system	—

resolution	2.250 Å
resolution_low	29.907 Å
r_factor	—
r_work	0.1902
r_free	0.2228

fit	/app/data/saxs_computation/qm/9qme/9qme.fit
pddf	/app/data/pr_computation/qm/9qme/9qme.pr.out
profile	/app/data/saxs_computation/qm/9qme/9qme.dat