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Structure of HIV-1 gp120 (core with V3) in Complex with CD4-Binding-Site Antibody F105
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BBD PDB ENTRIES 1BBD, 1BBJ experimental model PDB 1BBJ PDB ENTRIES 1BBD, 1BBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 16% PEG 6000, 8% 2-PROPANOL, 0.2M AMMONIUM SULFATE, 0.1M HEPES, PH 7.5, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.08 69.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 412.403 α = 90 b = 412.403 β = 90 c = 83.206 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2005-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.9 50 0.123 0.085 13.1 4.4 48590
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) Redundancy Number Unique Reflections (All) 1 2.9 2.98 0.456 0.413 1.21 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 1BBD, 1BBJ 2.9 43.48 42563 2247 75.5 0.204 0.202 0.2084 0.243 0.2445 RANDOM 119.9
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] 1.02 0.51 1.02 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.958 r_dihedral_angle_4_deg 17.851 r_dihedral_angle_3_deg 15.623 r_dihedral_angle_1_deg 6.085 r_mcangle_it 2.445 r_mcbond_it 1.371 r_scangle_it 1.213 r_angle_refined_deg 1.154 r_scbond_it 0.71 r_nbtor_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.958 r_dihedral_angle_4_deg 17.851 r_dihedral_angle_3_deg 15.623 r_dihedral_angle_1_deg 6.085 r_mcangle_it 2.445 r_mcbond_it 1.371 r_scangle_it 1.213 r_angle_refined_deg 1.154 r_scbond_it 0.71 r_nbtor_refined 0.336 r_nbd_refined 0.259 r_symmetry_vdw_refined 0.251 r_symmetry_hbond_refined 0.215 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 11214 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 378
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling