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1dwj

study on radiation damage on a cryocooled crystal. Refined part 6: structure after a radiation dose of 54*10e15 photons/mm2

Method: X-RAY DIFFRACTION D_max: 77.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dwj
deposition_date	1999-12-05
title	study on radiation damage on a cryocooled crystal. Refined part 6: structure after a radiation dose of 54*10e15 photons/mm2
keywords	GLYCOSIDASE, RADIATION DAMAGE, RADIOLYSIS, CRYO-COOLED, HYDROLASE; HYDROLASE
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	23.89 Å
rg_electron	22.47 Å
i0	65394700.00
molecular_weight	62145.0 kDa
excluded_volume	76981 Å³
envelope_volume	88442 Å³
shell_volume	31158 Å³
envelope_diameter	78.6 Å
shell_rg	30.80 Å
envelope_rg	22.92 Å
shape_rg	22.38 Å
total_rg	23.56 Å
total_atoms	4366
n_residues	499
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	77.1 Å
rg_real	23.70 Å
rg_real_error	0.39 Å
i0_real	6.5390e+07
i0_real_error	8.7140e+05
rg_reciprocal	23.74 Å
i0_reciprocal	65400000.0000
total_estimate	0.8819
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.3 Å
skewness	0.112
kurtosis	-0.397
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	13790000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	MYROSINASE MA1
formula_weight	56848.1 kDa
ec_number	3.2.1.147
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M
atom_count	5220

EITCQENLPFTCGNTDALNSSSFSSDFIFGVASSAYQIEGTIGRGLNIWDGFTHRYPNKSGPDHGNGDTTCDSFSYWQKDIDVLDELNATGYRFSIAWSRIIPRGKRSRGVNEKGIDYYHGLISGLIKKGITPFVTLFHWDLPQTLQDEYEGFLDPQIIDDFKDYADLCFEEFGDSVKYWLTINQLYSVPTRGYGSALDAPGRCSPTVDPSCYAGNSSTEPYIVAHHQLLAHAKVVDLYRKNYTHQGGKIGPTMITRWFLPYNDTDRHSIAATERMKEFFLGWFMGPLTNGTYPQIMIDTVGERLPSFSPEESNLVKGSYDFLGLNYYFTQYAQPSPNPVNSTNHTAMMDAGAKLTYINASGHYIGPLFEKDKADSTDNIYYYPKGIYSVMDYFKNKYYNPLIYVTENGISTPGDENRNQSMLDYTRIDYLCSHLCFLNKVIKEKDVNVKGYLAWALGDNYEFNKGFTVRFGLSYIDWNNVTDRDLKKSGQWYQTFISP

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 3 branched

description	;beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	864.8 kDa
src_method	man
entity_count	1

Entity 4 branched

description	;beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1189.1 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	6

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	8

Entity 8 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	788

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6. Citations (2)

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length_a	134.300 Å
length_b	136.400 Å
length_c	80.300 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.400 Å
resolution_low	15.000 Å
r_factor	0.1860
r_work	0.1860
r_free	0.2450

fit	/app/data/saxs_computation/dw/1dwj/1dwj.fit
pddf	/app/data/pr_computation/dw/1dwj/1dwj.pr.out
profile	/app/data/saxs_computation/dw/1dwj/1dwj.dat