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Structure of the C-terminal Domain of a Putative HIV-1 gp41 Fusion Intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GWO PDB ENTRY 3GWO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 295 3% PEG8000, 0.1M Tris-HCl, 0.1M cesium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.39 71.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.764 α = 90 b = 47.499 β = 128.32 c = 74.824 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315 2005-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1000 NSLS X25
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 2.2 40.1 93.7 0.044 18.7 3 16151 16151 46.5
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 2.28 76.2 0.269 3.1 2.5 1309
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 (All) 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 3GWO 2.2 40.1 16151 16151 807 93.7 0.21403 0.21403 0.2118 0.2249 0.25526 0.2333 RANDOM 37.058
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] 3.09 -25.75 -15.13 12.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.212 r_dihedral_angle_3_deg 21.074 r_dihedral_angle_1_deg 8.337 r_scangle_it 5.933 r_scbond_it 3.834 r_angle_refined_deg 2.406 r_mcangle_it 2.218 r_mcbond_it 1.368 r_chiral_restr 0.177 r_bond_refined_d 0.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.212 r_dihedral_angle_3_deg 21.074 r_dihedral_angle_1_deg 8.337 r_scangle_it 5.933 r_scbond_it 3.834 r_angle_refined_deg 2.406 r_mcangle_it 2.218 r_mcbond_it 1.368 r_chiral_restr 0.177 r_bond_refined_d 0.029 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1309 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling