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- PDB-8dkf: Antibody DH1030.1 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 8dkf
TitleAntibody DH1030.1 Fab fragment
Components
  • DH1030.1 Heavy chain
  • DH1030.1 Light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab fragment
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsGobeil, S. / Acharya, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: DH1030.1 glycan reactive Ab
Authors: Gobeil, S.M. / Williams, W. / Henderson, R.C. / Janowska, K. / Speakman, M. / Huang, X. / Beaudoin, E. / Martin, M. / Stalls, V. / Manne, K. / Mansouri, K. / Edwards, R.J. / Sempowski, G. / ...Authors: Gobeil, S.M. / Williams, W. / Henderson, R.C. / Janowska, K. / Speakman, M. / Huang, X. / Beaudoin, E. / Martin, M. / Stalls, V. / Manne, K. / Mansouri, K. / Edwards, R.J. / Sempowski, G. / Saunders, K. / Wiehe, K. / Haynes, B.F. / Acharya, P.
History
DepositionJul 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: DH1030.1 Heavy chain
L: DH1030.1 Light chain
A: DH1030.1 Heavy chain
B: DH1030.1 Light chain


Theoretical massNumber of molelcules
Total (without water)97,9974
Polymers97,9974
Non-polymers00
Water7,728429
1
H: DH1030.1 Heavy chain
L: DH1030.1 Light chain


Theoretical massNumber of molelcules
Total (without water)48,9992
Polymers48,9992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-18 kcal/mol
Surface area20120 Å2
MethodPISA
2
A: DH1030.1 Heavy chain
B: DH1030.1 Light chain


Theoretical massNumber of molelcules
Total (without water)48,9992
Polymers48,9992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-18 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.190, 103.120, 109.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody DH1030.1 Heavy chain


Mass: 24947.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody DH1030.1 Light chain


Mass: 24050.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 30% (v/v) MPD 100 mM Sodium acetate/ Acetic acid pH 4.5 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 85926 / % possible obs: 99.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.043 / Rrim(I) all: 0.129 / Χ2: 3.182 / Net I/σ(I): 36.67
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 4207 / CC1/2: 0.93 / CC star: 0.982 / Rpim(I) all: 0.308 / Rrim(I) all: 0.902 / Χ2: 0.542 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PDU

6pdu


Resolution: 1.79→43.52 Å / SU ML: 0.258 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.4945
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2737 1990 2.33 %
Rwork0.2389 83478 -
obs0.2397 85468 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.39 Å2
Refinement stepCycle: LAST / Resolution: 1.79→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 0 0 429 7225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796973
X-RAY DIFFRACTIONf_angle_d0.88779498
X-RAY DIFFRACTIONf_chiral_restr0.0511050
X-RAY DIFFRACTIONf_plane_restr0.01621229
X-RAY DIFFRACTIONf_dihedral_angle_d6.7182975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.40471220.39755402X-RAY DIFFRACTION90.19
1.84-1.890.40471480.35895956X-RAY DIFFRACTION99.46
1.89-1.940.36431380.31745968X-RAY DIFFRACTION99.66
1.94-2.010.33061480.29465946X-RAY DIFFRACTION99.62
2.01-2.080.32891400.28765995X-RAY DIFFRACTION99.66
2.08-2.160.30421410.27945983X-RAY DIFFRACTION99.56
2.16-2.260.31721420.27365991X-RAY DIFFRACTION99.45
2.26-2.380.33961420.25916010X-RAY DIFFRACTION99.64
2.38-2.530.28421480.25165992X-RAY DIFFRACTION99.59
2.53-2.720.25861400.25596022X-RAY DIFFRACTION99.39
2.72-30.32461480.24466055X-RAY DIFFRACTION99.68
3-3.430.29311390.22236039X-RAY DIFFRACTION98.75
3.43-4.320.24191500.19716020X-RAY DIFFRACTION98
4.32-43.520.19771440.2036099X-RAY DIFFRACTION95.55

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