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

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Basic information

Entry
Database: PDB / ID: 6ehx
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
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 2.0Oct 16, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy
Revision 2.1Oct 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
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)25,5351
Polymers25,5351
Non-polymers00
Water4,900272
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 area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.559, 81.559, 116.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-485-

HOH

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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: 25534.531 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.: 272 / 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: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7.5 / Details: NaCl 1.5M, Na Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→116 Å / Num. obs: 20644 / % possible obs: 100 % / Redundancy: 25.7 % / Biso Wilson estimate: 40.76 Å2 / Net I/σ(I): 35.9

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.2→51.68 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.926 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.166
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1056 5.13 %RANDOM
Rwork0.207 ---
obs0.209 20597 99.9 %-
Displacement parametersBiso mean: 36.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.3149 Å20 Å20 Å2
2---0.3149 Å20 Å2
3---0.6298 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.2→51.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 0 272 2019
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011794HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.12433HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d586SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes265HARMONIC5
X-RAY DIFFRACTIONt_it1794HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion230SEMIHARMONIC5
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_contact2099SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.295 161 5.52 %
Rwork0.242 2758 -
all0.245 2919 -
obs--99.69 %

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