☰ Navigation Tabs
Trimeric helix bundle formed by an alpha/beta-peptide derivative of the HIV gp41 CHR domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F4Y PDB entry 3F4Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.5 M ammonium sulfate, 0.1 M HEPES-Na pH 7.5, 30% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.24 62.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.335 α = 90 b = 43.989 β = 105.4 c = 58.142 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 MARMOSAIC 300 mm CCD 2008-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 2.1 50 99.8 0.067 16.1 3.5 10494
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) 2.1 2.18 99.8 0.356 3.5 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3F4Y 2.1 25 9769 496 99.81 0.20606 0.20391 0.24864 0.2681 RANDOM 30.328
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] 1.11 0.62 2.07 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.519 r_dihedral_angle_4_deg 15.294 r_dihedral_angle_3_deg 13.498 r_scangle_it 4.551 r_dihedral_angle_1_deg 4.244 r_scbond_it 2.629 r_angle_refined_deg 1.978 r_mcangle_it 1.785 r_angle_other_deg 1.306 r_mcbond_it 0.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.519 r_dihedral_angle_4_deg 15.294 r_dihedral_angle_3_deg 13.498 r_scangle_it 4.551 r_dihedral_angle_1_deg 4.244 r_scbond_it 2.629 r_angle_refined_deg 1.978 r_mcangle_it 1.785 r_angle_other_deg 1.306 r_mcbond_it 0.923 r_mcbond_other 0.196 r_chiral_restr 0.131 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 1793 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 176
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling