3HI1

Structure of HIV-1 gp120 (core with V3) in Complex with CD4-Binding-Site Antibody F105


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BBDPDB ENTRIES 1BBD, 1BBJ
experimental modelPDB 1BBJPDB ENTRIES 1BBD, 1BBJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529316% PEG 6000, 8% 2-PROPANOL, 0.2M AMMONIUM SULFATE, 0.1M HEPES, PH 7.5, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.0869.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 412.403α = 90
b = 412.403β = 90
c = 83.206γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
12.9500.1230.08513.14.448590
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)
12.92.980.4560.4131.211.5

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 REPLACEMENTTHROUGHOUTPDB ENTRIES 1BBD, 1BBJ2.943.4842563224775.50.2040.2020.243RANDOM119.9
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]
1.020.511.02-1.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.958
r_dihedral_angle_4_deg17.851
r_dihedral_angle_3_deg15.623
r_dihedral_angle_1_deg6.085
r_mcangle_it2.445
r_mcbond_it1.371
r_scangle_it1.213
r_angle_refined_deg1.154
r_scbond_it0.71
r_nbtor_refined0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.958
r_dihedral_angle_4_deg17.851
r_dihedral_angle_3_deg15.623
r_dihedral_angle_1_deg6.085
r_mcangle_it2.445
r_mcbond_it1.371
r_scangle_it1.213
r_angle_refined_deg1.154
r_scbond_it0.71
r_nbtor_refined0.336
r_nbd_refined0.259
r_symmetry_vdw_refined0.251
r_symmetry_hbond_refined0.215
r_xyhbond_nbd_refined0.198
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11214
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms378

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling