3QEG

Crystal structure of human N12-i2 Fab, an ADCC and neutralizing anti-HIV-1 Env antibody


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RZ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52940.01 M Ni (II) chloride hexahydrate, 0.1 M Tris HCl, pH 8.5, 20% Polyethylene glycol monomethyl ether 2,000, , VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.8857.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.906α = 90
b = 78.906β = 90
c = 315.147γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.979464SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.9568.335990.0940.0654020.2436464361312
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0299.70.7950.6182.515.24255

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RZ81.95202294641215218999.590.204830.204830.203160.23612RANDOM41.489
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]
1.740.871.74-2.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.929
r_dihedral_angle_4_deg19.33
r_dihedral_angle_3_deg15.239
r_dihedral_angle_1_deg7.099
r_scangle_it4.658
r_scbond_it3.01
r_mcangle_it1.849
r_angle_refined_deg1.794
r_mcbond_it1.053
r_chiral_restr0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.929
r_dihedral_angle_4_deg19.33
r_dihedral_angle_3_deg15.239
r_dihedral_angle_1_deg7.099
r_scangle_it4.658
r_scbond_it3.01
r_mcangle_it1.849
r_angle_refined_deg1.794
r_mcbond_it1.053
r_chiral_restr0.143
r_bond_refined_d0.02
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3261
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling