3MOA

Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced Fab) with 17 aa gp41 MPER-derived peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TJI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.6298Reservoir; Hampton Research Crystal Screen 40 = 20% isopropanol, 20% PEG 4000, 100 mM Na citrate pH 5.6. Drop: 0.5 uL protein + 0.35 uL reservoir. Reservoir was NOT supplemented with 100 mM NaCl as in Ofek et al. 2004., VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.362.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.82α = 90
b = 65.229β = 90
c = 174.205γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.343.71000.06215.47.3306783067822

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1TJI2.343.6830.1930459198699.470.18620.18390.2193
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
2.46530.1352-2.6005
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.999
f_angle_d1.348
f_chiral_restr0.142
f_bond_d0.027
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3506
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing