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HIV gp41 six-helix bundle composed of a chimeric alpha+alpha/beta-peptide analogue of the CHR domain in complex with an NHR domain alpha-peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F4Y PDB entries 3F4Y, 3F50 experimental model PDB 3F50 PDB entries 3F4Y, 3F50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.4 M lithium sulfate, 12% w/v PEG 8000, 20% v/v glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.39 63.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.043 α = 90 b = 57.043 β = 90 c = 186.314 γ = 120
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 BRUKER SMART 6000 confocal mirrors 2008-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 99.5 0.058 16.8 5.9 3100 3085
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 2.8 2.9 100 0.388 3.7 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 entries 3F4Y, 3F50 2.8 25 2947 132 99.58 0.25425 0.25177 0.2503 0.31083 0.3255 RANDOM 32.413
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] 3.54 1.77 3.54 -5.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.576 r_dihedral_angle_3_deg 21.476 r_dihedral_angle_4_deg 14.274 r_mcangle_it 7.709 r_scangle_it 7.095 r_mcbond_it 5.461 r_dihedral_angle_1_deg 5.362 r_scbond_it 4.422 r_mcbond_other 2.261 r_angle_refined_deg 1.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.576 r_dihedral_angle_3_deg 21.476 r_dihedral_angle_4_deg 14.274 r_mcangle_it 7.709 r_scangle_it 7.095 r_mcbond_it 5.461 r_dihedral_angle_1_deg 5.362 r_scbond_it 4.422 r_mcbond_other 2.261 r_angle_refined_deg 1.751 r_angle_other_deg 0.97 r_chiral_restr 0.081 r_bond_refined_d 0.018 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 574 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 27
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling