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9r46

Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Xylose isomerase bound with glucose (25 ms soaking)

Method: X-RAY DIFFRACTION D_max: 84.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r46
deposition_date	2025-05-07
last_revision	2025-12-03
title	Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Xylose isomerase bound with glucose (25 ms soaking)
keywords	Xylose isomerase, glucose, Spitrobot-2, ISOMERASE; ISOMERASE
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	24.42 Å
rg_electron	23.28 Å
i0	33962600.00
molecular_weight	43262.0 kDa
excluded_volume	53496 Å³
envelope_volume	68625 Å³
shell_volume	25004 Å³
envelope_diameter	87.5 Å
shell_rg	29.64 Å
envelope_rg	24.33 Å
shape_rg	23.27 Å
total_rg	24.08 Å
total_atoms	3055
n_residues	386
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	84.2 Å
rg_real	24.52 Å
rg_real_error	0.61 Å
i0_real	3.3960e+07
i0_real_error	4.9600e+05
rg_reciprocal	24.50 Å
i0_reciprocal	33960000.0000
total_estimate	0.8578
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.7 Å
skewness	0.498
kurtosis	-0.096
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	6069000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Xylose isomerase
formula_weight	43283.3 kDa
ec_number	5.3.1.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3333

MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG

Source

organism	Streptomyces rubiginosus
ncbi_taxonomy_id	1929
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	beta-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	262

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6. Citations (1)

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length_a	85.680 Å
length_b	93.760 Å
length_c	98.070 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	orthorhombic

resolution	2.100 Å
resolution_low	64.520 Å
r_factor	0.1895
r_work	0.1869
r_free	0.2426

fit	/app/data/saxs_computation/r4/9r46/9r46.fit
pddf	/app/data/pr_computation/r4/9r46/9r46.pr.out
profile	/app/data/saxs_computation/r4/9r46/9r46.dat