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

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Entry
Database: PDB / ID: 6ehw
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 / MIR / Resolution: 2.19 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 16, 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

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Assembly

Deposited unit
B: 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)26,8921
Polymers26,8921
Non-polymers00
Water1,820101
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 area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.396, 70.033, 78.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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: 26891.822 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.: 101 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: NaCl, Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.19→27.73 Å / Num. obs: 12599 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 34.01 Å2 / Net I/σ(I): 5

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.19→27.73 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.324 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.248 628 4.98 %RANDOM
Rwork0.212 ---
obs0.214 12599 93.9 %-
Displacement parametersBiso mean: 45.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.0368 Å20 Å20 Å2
2--0.3691 Å20 Å2
3----0.4059 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.19→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 0 101 1940
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011889HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.192566HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d618SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes279HARMONIC5
X-RAY DIFFRACTIONt_it1889HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion20.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
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_contact2138SEMIHARMONIC4
LS refinement shellResolution: 2.19→2.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 131 5.46 %
Rwork0.307 2268 -
all0.309 2399 -
obs--76.1 %

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