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- PDB-6ehy: scFv AbVance: increasing our knowledge of antibody structural spa... -

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Basic information

Entry
Database: PDB / ID: 6ehy
TitlescFv AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in drug discovery
ComponentsscFv antibody fragment
KeywordsIMMUNE SYSTEM / scFv / AbVance / Pistoia Alliance
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.25 Å
AuthorsHargreaves, D.
CitationJournal: To Be Published
Title: scFv AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in drug discovery
Authors: Hargreaves, D.
History
DepositionSep 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scFv antibody fragment
B: scFv antibody fragment


Theoretical massNumber of molelcules
Total (without water)53,7092
Polymers53,7092
Non-polymers00
Water3,801211
1
A: scFv antibody fragment


Theoretical massNumber of molelcules
Total (without water)26,8551
Polymers26,8551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: scFv antibody fragment


Theoretical massNumber of molelcules
Total (without water)26,8551
Polymers26,8551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.061, 71.040, 121.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody scFv antibody fragment


Mass: 26854.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 4.5M NaCl 100mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→48.06 Å / Num. obs: 20323 / % possible obs: 99.5 % / Redundancy: 5.59 % / Biso Wilson estimate: 49.16 Å2 / Net I/σ(I): 6.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.25→44.68 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.481 / SU Rfree Blow DPI: 0.279 / SU Rfree Cruickshank DPI: 0.275
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1031 5.11 %RANDOM
Rwork0.228 ---
obs0.231 20191 99.1 %-
Displacement parametersBiso mean: 44.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.4306 Å20 Å20 Å2
2---0.431 Å20 Å2
3----0.9996 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.25→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 0 211 3693
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013574HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.144858HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1156SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes528HARMONIC5
X-RAY DIFFRACTIONt_it3574HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion18.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion472SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4135SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.266 140 4.86 %
Rwork0.23 2738 -
all0.232 2878 -
obs--99.17 %

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