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- PDB-3gk8: X-ray crystal structure of the Fab from MAb 14, mouse antibody ag... -

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Basic information

Entry
Database: PDB / ID: 3gk8
TitleX-ray crystal structure of the Fab from MAb 14, mouse antibody against Canine Parvovirus
Components
  • Fab 14 Heavy ChainFragment antigen-binding
  • Fab 14 Light ChainFragment antigen-binding
KeywordsIMMUNE SYSTEM / antibody fragment from neutralizing monoclonal antibody against canine parvovirus
Specimen sourceMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 2 Å resolution
AuthorsHafenstein, S. / Bowman, V. / Sun, T. / Nelson, C. / Palermo, L. / Chipman, P. / Battisti, A. / Parrish, C.
CitationJournal: J. Virol. / Year: 2009
Title: Structural comparison of different antibodies interacting with parvovirus capsids.
Authors: Susan Hafenstein / Valorie D Bowman / Tao Sun / Christian D S Nelson / Laura M Palermo / Paul R Chipman / Anthony J Battisti / Colin R Parrish / Michael G Rossmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 10, 2009 / Release: Jun 16, 2009
RevisionDateData content typeGroupCategoryProviderType
1.0Jun 16, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Sep 25, 2013Structure modelDatabase references
1.3Nov 1, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab 14 Light Chain
H: Fab 14 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)46,6112
Polyers46,6112
Non-polymers00
Water2,036113
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3580
ΔGint (kcal/M)-25
Surface area (Å2)19320
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)168.604, 39.885, 70.745
Angle α, β, γ (deg.)90.000, 94.579, 90.000
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Protein/peptide Fab 14 Light Chain / Fragment antigen-binding


Mass: 23261.770 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma
#2: Protein/peptide Fab 14 Heavy Chain / Fragment antigen-binding


Mass: 23349.105 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Formula: H2O / Water

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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: 2.54 / Density percent sol: 51.64 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 5000, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

SourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorCollection date: May 2, 2005
RadiationDiffraction protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv sigmaI over netI: 25.82 / Number: 147415 / Rmerge I obs: 0.061 / Chi squared: 1.39 / Highest resolution: 1.85 Å / Lowest resolution: 5 Å / Number obs: 40514 / Percent possible obs: 99.8 / Redundancy: 3.6 %
Diffraction reflection shell

Id: 1

Highest resolutionLowest resolutionRmerge I obsChi squaredPercent possible obsRedundancy
3.9950.000.0211.39398.303.50
3.163.990.0271.396100.003.70
2.763.160.0501.33999.903.70
2.512.760.0891.348100.003.70
2.332.510.1401.38599.903.70
2.192.330.2001.406100.003.70
2.082.190.2571.39599.903.60
1.992.080.3621.38499.903.60
1.921.990.5341.427100.003.70
1.851.920.9021.419100.003.60
ReflectionD resolution high: 1.85 Å / D resolution low: 5 Å / Number obs: 40514 / Rmerge I obs: 0.061 / Chi squared: 1.389 / NetI over sigmaI: 25.819 / Redundancy: 3.6 % / Percent possible obs: 99.8
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible all
0.9021.851.9240351.4193.60100.00
0.5341.921.9940261.4273.70100.00
0.3621.992.0840161.3843.6099.90
0.2572.082.1940241.3953.6099.90
0.2002.192.3340221.4063.70100.00
0.1402.332.5140301.3853.7099.90
0.0892.512.7640431.3483.70100.00
0.0502.763.1640601.3393.7099.90
0.0273.163.9941281.3963.70100.00
0.0213.9950.0041301.3933.5098.30

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Phasing

PhasingMethod: molecular replacement
Phasing MRR factor: 0.447 / Correlation coeff Fo to Fc: 0.449 / D res high translation: 4 / D res low translation: 8

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Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeLanguageDate
DENZOdata reductionZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
SCALEPACKdata scalingZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
AMoREphasingJorge Navazaccp4[at]ccp4.ac.ukhttp://www.ccp4.ac.uk/programFortran_77
CNSrefinementAxel T. Brungeraxel.brunger[at]yale.eduhttp://cns-online.org/packageFortran_77
PDB_EXTRACT3.006data extractionPDBhelp[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packageC++June 11, 2008
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Occupancy max: 1 / Occupancy min: 1 / Overall FOM work R set: 0.756
Displacement parametersB iso max: 99.13 Å2 / B iso mean: 41.161 Å2 / B iso min: 1.89 Å2 / Aniso B11: -3.358 Å2 / Aniso B12: 0 Å2 / Aniso B13: 6.723 Å2 / Aniso B22: -0.676 Å2 / Aniso B23: 0 Å2 / Aniso B33: 4.035 Å2
Least-squares processR factor R free: 0.306 / R factor R work: 0.266 / Highest resolution: 2 Å / Lowest resolution: 42.02 Å / Number reflection R free: 934 / Number reflection obs: 30479
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 42.02 Å
Number of atoms included #LASTProtein: 3283 / Nucleic acid: 0 / Ligand: 0 / Solvent: 113 / Total: 3396
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.391.50
X-RAY DIFFRACTIONc_mcangle_it2.212.00
X-RAY DIFFRACTIONc_scbond_it1.952.00
X-RAY DIFFRACTIONc_scangle_it2.732.50

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