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1dy5

Deamidated derivative of bovine pancreatic ribonuclease

Method: X-RAY DIFFRACTION D_max: 70.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dy5
deposition_date	2000-01-27
title	Deamidated derivative of bovine pancreatic ribonuclease
keywords	HYDROLASE, RIBONUCLEASE, DEAMIDATION; 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	21.78 Å
rg_electron	21.29 Å
i0	16745300.00
molecular_weight	28274.0 kDa
excluded_volume	34255 Å³
envelope_volume	42641 Å³
shell_volume	17481 Å³
envelope_diameter	69.5 Å
shell_rg	26.60 Å
envelope_rg	21.23 Å
shape_rg	21.28 Å
total_rg	22.01 Å
total_atoms	3735
n_residues	246
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	70.2 Å
rg_real	21.80 Å
rg_real_error	0.48 Å
i0_real	1.6750e+07
i0_real_error	2.3400e+05
rg_reciprocal	21.80 Å
i0_reciprocal	16750000.0000
total_estimate	0.9000
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.9 Å
skewness	0.285
kurtosis	-0.590
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	3596000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.902; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	RIBONUCLEASE A
formula_weight	13709.3 kDa
ec_number	3.1.27.5
mutation	YES
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4437

KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKDGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	ISOPROPYL ALCOHOL
formula_weight	60.1 kDa
src_method	syn
entity_count	8

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	381

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6. Citations (2)

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length_a	61.314 Å
length_b	37.470 Å
length_c	44.915 Å
angle_alpha	90.00 °
angle_beta	94.55 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	0.870 Å
resolution_low	61.000 Å
r_factor	0.1009
r_work	—
r_free	0.1198

fit	/app/data/saxs_computation/dy/1dy5/1dy5.fit
pddf	/app/data/pr_computation/dy/1dy5/1dy5.pr.out
profile	/app/data/saxs_computation/dy/1dy5/1dy5.dat

Deamidated derivative of bovine pancreatic ribonuclease

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