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HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HZH pdb entries 1HZH, 1GC1 experimental model PDB 1GC1 pdb entries 1HZH, 1GC1
Crystallization Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.955 α = 90 b = 101.955 β = 90 c = 298.294 γ = 120
Symmetry Space Group P 65 2 2
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 2003-10-13 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) 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 2.3 50 97.2 0.096 9.8 8.8 41973 40798 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 77.5 0.755 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1HZH, 1GC1 2.3 49.45 40751 36114 1890 93.26 0.19601 0.19291 0.1919 0.25503 0.253 RANDOM 62.345
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] 0.04 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.691 r_dihedral_angle_4_deg 17.829 r_dihedral_angle_3_deg 14.657 r_scangle_it 7.281 r_scbond_it 5.296 r_dihedral_angle_1_deg 5.18 r_mcangle_it 3.235 r_mcbond_it 2.174 r_angle_refined_deg 0.852 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.691 r_dihedral_angle_4_deg 17.829 r_dihedral_angle_3_deg 14.657 r_scangle_it 7.281 r_scbond_it 5.296 r_dihedral_angle_1_deg 5.18 r_mcangle_it 3.235 r_mcbond_it 2.174 r_angle_refined_deg 0.852 r_nbtor_refined 0.325 r_xyhbond_nbd_refined 0.238 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.205 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 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 5687 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 182
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing