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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 5 295 2.8M 1,6-hexanediol, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.967 α = 90 b = 33.967 β = 90 c = 191.331 γ = 120
Symmetry Space Group P 31 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 4 2004-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9795 NSLS X4A
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 1.7 29.41 98.9 0.061 16.2 5.3 14906 14906 20.8
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 1.7 1.76 98.8 0.142 10.5 4.5 1422
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 1.7 29.41 14906 14906 752 98.9 0.20647 0.20647 0.20528 0.2067 0.22805 0.2399 RANDOM 23.359
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] 0.33 0.16 0.33 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.16 r_dihedral_angle_4_deg 20.524 r_dihedral_angle_3_deg 12.421 r_scangle_it 3.766 r_dihedral_angle_1_deg 3.363 r_scbond_it 2.764 r_mcangle_it 1.536 r_angle_refined_deg 1.34 r_mcbond_it 0.972 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.16 r_dihedral_angle_4_deg 20.524 r_dihedral_angle_3_deg 12.421 r_scangle_it 3.766 r_dihedral_angle_1_deg 3.363 r_scbond_it 2.764 r_mcangle_it 1.536 r_angle_refined_deg 1.34 r_mcbond_it 0.972 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.096 r_symmetry_hbond_refined 0.084 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 862 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 64
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling