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HIV-1 gp120 Envelope Glycoprotein (T123C, T257S, S334A, S375W, G431C) Complexed with CD4 and Antibody 17b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GC1 pdb entry 1GC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 7.2% PEG 8000, 7.8% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.98 58.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.605 α = 90 b = 88.024 β = 90 c = 196.016 γ = 90
Symmetry Space Group P 2 2 21
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 2005-03-03 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 50 99.3 0.082 9.1 3.7 84379 83788 -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 2.07 94.4 0.374 3.4
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 entry 1GC1 2 42.84 84461 75855 4062 94.62 0.19526 0.19379 0.2088 0.22296 0.2307 RANDOM 40.166
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] -0.06 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_dihedral_angle_4_deg 14.81 r_dihedral_angle_3_deg 12.812 r_dihedral_angle_1_deg 5.068 r_mcangle_it 1.232 r_scangle_it 0.969 r_angle_refined_deg 0.911 r_mcbond_it 0.715 r_scbond_it 0.597 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_dihedral_angle_4_deg 14.81 r_dihedral_angle_3_deg 12.812 r_dihedral_angle_1_deg 5.068 r_mcangle_it 1.232 r_scangle_it 0.969 r_angle_refined_deg 0.911 r_mcbond_it 0.715 r_scbond_it 0.597 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.318 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.199 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.059 r_bond_refined_d 0.005 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 7084 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 193
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 CNS phasing