6MFP

Crystal Structure of the RV305 C1-C2 specific ADCC potent antibody DH677.3 Fab in complex with HIV-1 clade A/E gp120 and M48U1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TGT3TGT, 6MFJ
experimental modelPDB 6MFJ3TGT, 6MFJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529425% PEG 4000 0.1 M MES pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.4549.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.487α = 84.82
b = 80.093β = 82.33
c = 88.688γ = 82.24
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

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
135089.10.09210.21.930469
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.0590.70.4421.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3TGT, 6MFJ339.628977149288.90.2170.2140.274RANDOM93.95
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]
1.841.48-3.11-0.25-1.24-2.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.977
r_dihedral_angle_3_deg18.934
r_dihedral_angle_4_deg17.044
r_long_range_B_other9.892
r_long_range_B_refined9.891
r_dihedral_angle_1_deg6.981
r_scangle_other4.509
r_mcangle_it4.161
r_mcangle_other4.161
r_scbond_other2.689
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.977
r_dihedral_angle_3_deg18.934
r_dihedral_angle_4_deg17.044
r_long_range_B_other9.892
r_long_range_B_refined9.891
r_dihedral_angle_1_deg6.981
r_scangle_other4.509
r_mcangle_it4.161
r_mcangle_other4.161
r_scbond_other2.689
r_scbond_it2.688
r_mcbond_it2.528
r_mcbond_other2.528
r_angle_refined_deg1.451
r_angle_other_deg1.184
r_chiral_restr0.053
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12342
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms362

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing