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9r2v

De novo designed M16 protein fold

Method: X-RAY DIFFRACTION D_max: 111.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r2v
deposition_date	2025-05-01
title	De novo designed M16 protein fold
keywords	dark fold, de novo, unnatural, DE NOVO PROTEIN; DE NOVO 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	34.79 Å
rg_electron	33.78 Å
i0	311258000.00
molecular_weight	145730.0 kDa
excluded_volume	184050 Å³
envelope_volume	242120 Å³
shell_volume	57556 Å³
envelope_diameter	120.7 Å
shell_rg	42.05 Å
envelope_rg	33.57 Å
shape_rg	33.76 Å
total_rg	34.49 Å
total_atoms	10246
n_residues	1198
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	111.8 Å
rg_real	34.60 Å
rg_real_error	0.71 Å
i0_real	3.1130e+08
i0_real_error	4.5510e+06
rg_reciprocal	34.72 Å
i0_reciprocal	311300000.0000
total_estimate	0.8898
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.7 Å
skewness	0.165
kurtosis	-0.408
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	50760000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	M16
formula_weight	19752.1 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	10258

MSESKKLIEEAKKEFDKQLAEGKKEIDIEIEYPKKKYDENYKEALEFIKLNSELRVEYVKKSREAGVEKLTIKTKVKLEPTENSDHKLDYEYEEEMSKKALEKTDEKEYKEKLEKEYKKIEETVESNKDYEYEEEYEDKETGYKYKKKVEIKGGSGGSHHHHHH

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	nat
entity_count	8

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	14

Entity 4 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	12

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6. Citations (2)

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length_a	61.250 Å
length_b	82.110 Å
length_c	111.420 Å
angle_alpha	90.00 °
angle_beta	92.45 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.490 Å
resolution_low	61.190 Å
r_factor	0.2374
r_work	0.2345
r_free	0.2904

fit	/app/data/saxs_computation/r2/9r2v/9r2v.fit
pddf	/app/data/pr_computation/r2/9r2v/9r2v.pr.out
profile	/app/data/saxs_computation/r2/9r2v/9r2v.dat