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1dzb

Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme

Method: X-RAY DIFFRACTION D_max: 117.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dzb
deposition_date	2000-02-23
title	Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme
keywords	;IMMUNE SYSTEM, COMPLEX (ANTIBODY ANTIGEN), SINGLE-DOMAIN ANTIBODY, TURKEY EGG-WHITE LYSOZYME, ANTIBODY- PROTEIN COMPLEX, SINGLE-CHAIN FV FRAGMENT ;; IMMUNE SYSTEM
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	34.02 Å
rg_electron	33.58 Å
i0	101680000.00
molecular_weight	77431.0 kDa
excluded_volume	95560 Å³
envelope_volume	122780 Å³
shell_volume	32241 Å³
envelope_diameter	116.5 Å
shell_rg	38.02 Å
envelope_rg	33.16 Å
shape_rg	33.52 Å
total_rg	34.10 Å
total_atoms	5442
n_residues	706
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	117.2 Å
rg_real	34.26 Å
rg_real_error	1.02 Å
i0_real	1.0170e+08
i0_real_error	1.6660e+06
rg_reciprocal	34.11 Å
i0_reciprocal	101700000.0000
total_estimate	0.7647
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.9 Å
skewness	0.474
kurtosis	-0.455
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	10330000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.640; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	SCFV FRAGMENT 1F9
formula_weight	27253.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5709

QVKLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCARWDWYFDVWGQGTTVTVSSGGGGSGGGGSGGGGSDIELTQSPSSMYTSLGERVTITCKASQDINSYLRWFQQKPGKSPKTLIYYATSLADGVPSRFSGSGSGQDYSLTISSLESDDTTTYYCLQHGESPYTFGGGTKLEIKRAAAEQKLISEEDLN

Entity 2 polymer

description	TURKEY EGG-WHITE LYSOZYME C
formula_weight	14228.1 kDa
ec_number	3.2.1.17
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	X,Y

KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDVHAWIRGCRL

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	260

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6. Citations (2)

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length_a	38.710 Å
length_b	112.440 Å
length_c	80.000 Å
angle_alpha	90.00 °
angle_beta	97.67 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2250
r_free	0.3060

fit	/app/data/saxs_computation/dz/1dzb/1dzb.fit
pddf	/app/data/pr_computation/dz/1dzb/1dzb.pr.out
profile	/app/data/saxs_computation/dz/1dzb/1dzb.dat

Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme

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

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)