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

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Entry
Database: PDB / ID: 6ehv
TitlescFv AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in drug discovery
ComponentsscFv AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in drug discovery
KeywordsIMMUNE SYSTEM / scFv / AbVance / Pistoia Alliance
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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 1.2Nov 13, 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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Assembly

Deposited unit
X: scFv AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in drug discovery


Theoretical massNumber of molelcules
Total (without water)27,4941
Polymers27,4941
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.899, 132.899, 80.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Antibody scFv AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in drug discovery


Mass: 27494.418 Da / Num. of mol.: 1
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.: 72 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.54→40.37 Å / Num. obs: 12186 / % possible obs: 99.6 % / Redundancy: 11 % / Biso Wilson estimate: 72.74 Å2 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→38.84 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.863 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.438 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.459 / SU Rfree Blow DPI: 0.314 / SU Rfree Cruickshank DPI: 0.312
RfactorNum. reflection% reflectionSelection details
Rfree0.314 598 4.94 %RANDOM
Rwork0.275 ---
obs0.276 12108 99 %-
Displacement parametersBiso mean: 61.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.3366 Å20 Å20 Å2
2--0.3366 Å20 Å2
3----0.6733 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: 1 / Resolution: 2.54→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 0 72 1848
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011822HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.32475HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d605SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes269HARMONIC5
X-RAY DIFFRACTIONt_it1822HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion23.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion236SEMIHARMONIC5
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_contact2037SEMIHARMONIC4
LS refinement shellResolution: 2.54→2.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 159 5.59 %
Rwork0.303 2685 -
all0.306 2844 -
obs--99.03 %

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