5WB9

Crystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E strain 93TH057 gp120 core


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NGB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.1M MOPS pH 7.5, ).1M Magnesium acetate hexahydrate
Crystal Properties
Matthews coefficientSolvent content
2.7455.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.562α = 90
b = 68.567β = 111.36
c = 119.356γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2016-01-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL14-10.979SSRLBL14-1

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
12.38501000.169.73.638617
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)
12.382.43990.9081.22.9

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 REPLACEMENTTHROUGHOUT3NGB2.437.3335668188199.650.215740.213470.25763RANDOM44.972
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]
-0.74-0.03-0.761.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.055
r_dihedral_angle_4_deg20.597
r_dihedral_angle_3_deg18.851
r_dihedral_angle_1_deg8.87
r_long_range_B_refined6.886
r_long_range_B_other6.876
r_scangle_other2.357
r_angle_refined_deg1.937
r_mcangle_it1.611
r_mcangle_other1.611
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.055
r_dihedral_angle_4_deg20.597
r_dihedral_angle_3_deg18.851
r_dihedral_angle_1_deg8.87
r_long_range_B_refined6.886
r_long_range_B_other6.876
r_scangle_other2.357
r_angle_refined_deg1.937
r_mcangle_it1.611
r_mcangle_other1.611
r_scbond_it1.353
r_scbond_other1.352
r_angle_other_deg1.097
r_mcbond_other0.935
r_mcbond_it0.934
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms5893
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms133

Software

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