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9r45

Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Xylose isomerase (apo state)

Method: X-RAY DIFFRACTION D_max: 84.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r45
deposition_date	2025-05-07
last_revision	2025-12-03
title	Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Xylose isomerase (apo state)
keywords	Xylose isomerase, 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	24.45 Å
rg_electron	23.33 Å
i0	33328100.00
molecular_weight	42901.0 kDa
excluded_volume	53075 Å³
envelope_volume	68319 Å³
shell_volume	24947 Å³
envelope_diameter	87.6 Å
shell_rg	29.57 Å
envelope_rg	24.25 Å
shape_rg	23.32 Å
total_rg	24.13 Å
total_atoms	3031
n_residues	385
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	84.3 Å
rg_real	24.55 Å
rg_real_error	0.59 Å
i0_real	3.3330e+07
i0_real_error	4.5190e+05
rg_reciprocal	24.53 Å
i0_reciprocal	33330000.0000
total_estimate	0.8572
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.8 Å
skewness	0.499
kurtosis	-0.087
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	5988000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	3268

MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG

Source

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

Entity 2 non-polymer

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

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	221

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6. Citations (1)

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length_a	85.498 Å
length_b	93.723 Å
length_c	98.033 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	1.790 Å
resolution_low	67.740 Å
r_factor	0.1983
r_work	0.1957
r_free	0.2444

fit	/app/data/saxs_computation/r4/9r45/9r45.fit
pddf	/app/data/pr_computation/r4/9r45/9r45.pr.out
profile	/app/data/saxs_computation/r4/9r45/9r45.dat

Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Xylose isomerase (apo state)

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

Diffraction