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HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, 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 8.3% PEG 8000, 7.4% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.98 58.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.31 α = 90 b = 87.018 β = 90 c = 196.078 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 2005-04-18 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 2.8 50 92.5 0.151 4.8 3.4 30838 28525 -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 2.8 2.9 65 0.581 2.6
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 2.8 42.37 31422 23560 1188 78.76 0.1959 0.19199 0.19 0.27577 0.2716 RANDOM 51.499
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] -4.3 2.12 2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.956 r_dihedral_angle_3_deg 16.702 r_dihedral_angle_4_deg 14.507 r_dihedral_angle_1_deg 5.283 r_mcangle_it 2.281 r_scangle_it 1.962 r_mcbond_it 1.336 r_scbond_it 1.245 r_angle_refined_deg 1.032 r_nbtor_refined 0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.956 r_dihedral_angle_3_deg 16.702 r_dihedral_angle_4_deg 14.507 r_dihedral_angle_1_deg 5.283 r_mcangle_it 2.281 r_scangle_it 1.962 r_mcbond_it 1.336 r_scbond_it 1.245 r_angle_refined_deg 1.032 r_nbtor_refined 0.341 r_symmetry_vdw_refined 0.31 r_nbd_refined 0.302 r_xyhbond_nbd_refined 0.278 r_symmetry_hbond_refined 0.258 r_chiral_restr 0.079 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 7082 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 135
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