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HIV-1 gp120 Envelope Glycoprotein (T257S, S334A, S375W) Complexed with CD4 and Antibody 17b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G9C pdb entry 1G9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 7.5% PEG 4000, 8.5% MPD, 100 mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.03 59.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.915 α = 90 b = 88.126 β = 90 c = 197.685 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 MAR CCD 225 mm 2003-02-13 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 2.04 50 92.2 0.114 5.7 4.5 80471 74195 -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 2.04 2.12 68.2 0.505 2.1
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 1G9C 2.04 35.38 80742 66733 3578 87.08 0.20821 0.20629 0.2017 0.24425 0.2397 RANDOM 25.41
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] 0.44 -0.33 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.93 r_dihedral_angle_4_deg 16.279 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 5.28 r_scangle_it 1.803 r_scbond_it 1.058 r_angle_refined_deg 0.997 r_mcangle_it 0.688 r_mcbond_it 0.39 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.93 r_dihedral_angle_4_deg 16.279 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 5.28 r_scangle_it 1.803 r_scbond_it 1.058 r_angle_refined_deg 0.997 r_mcangle_it 0.688 r_mcbond_it 0.39 r_nbtor_refined 0.32 r_symmetry_hbond_refined 0.285 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.204 r_symmetry_vdw_refined 0.162 r_chiral_restr 0.063 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 7105 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 229
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 CNS phasing