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Structural Determinants of Trimerization Specificity in HIV-1 gp41 Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AIK PDB ENTRY 1AIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 20% Jeffamine M600, 0.1M MES, 25mM Cesium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.17 61.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.308 α = 90 b = 45.308 β = 90 c = 42.16 γ = 120
Symmetry Space Group P 3 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 2005-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9676 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 1.45 42.14 99.8 0.065 9.1 8.8 9173
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 99.8 0.467 6.4 8.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AIK 1.45 42.14 9173 8256 917 99.85 0.19585 0.19191 0.23341 0.2281 RANDOM 26.142
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] 0.62 0.31 0.62 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.213 r_dihedral_angle_3_deg 12.035 r_dihedral_angle_4_deg 7.733 r_dihedral_angle_1_deg 4.226 r_scangle_it 3.846 r_scbond_it 2.362 r_mcangle_it 1.42 r_angle_refined_deg 1.138 r_mcbond_it 0.784 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.213 r_dihedral_angle_3_deg 12.035 r_dihedral_angle_4_deg 7.733 r_dihedral_angle_1_deg 4.226 r_scangle_it 3.846 r_scbond_it 2.362 r_mcangle_it 1.42 r_angle_refined_deg 1.138 r_mcbond_it 0.784 r_nbtor_refined 0.301 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 255 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 13
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling