☰ Navigation Tabs
Structural basis for the binding of the anti-cancer compound 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX) to human glutathione S-transferases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GSS PDB ENTRY 6GSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 1.8M AMMONIUM SULFATE, 100MM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 52.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.869 α = 90 b = 89.535 β = 98.04 c = 68.916 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 4r mirrors 2009-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 29.21 99.1 0.058 0.058 17.4 4 42435 42435 1 1 16.5
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 1.8 1.86 99 0.178 8.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 6GSS 1.8 29.21 2 42435 40294 2132 98.49 0.18042 0.18042 0.17887 0.1785 0.20938 0.2064 RANDOM 14.588
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] 1.33 -0.12 -1.24 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.161 r_dihedral_angle_4_deg 15.726 r_dihedral_angle_3_deg 10.959 r_dihedral_angle_1_deg 4.538 r_angle_refined_deg 1.373 r_scangle_it 1.116 r_scbond_it 0.726 r_mcangle_it 0.517 r_mcbond_it 0.317 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.161 r_dihedral_angle_4_deg 15.726 r_dihedral_angle_3_deg 10.959 r_dihedral_angle_1_deg 4.538 r_angle_refined_deg 1.373 r_scangle_it 1.116 r_scbond_it 0.726 r_mcangle_it 0.517 r_mcbond_it 0.317 r_nbtor_refined 0.299 r_nbd_refined 0.177 r_chiral_restr 0.153 r_symmetry_vdw_refined 0.104 r_symmetry_hbond_refined 0.093 r_xyhbond_nbd_refined 0.085 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3263 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 104
Software Software Software Name Purpose ADSC data collection FFT model building REFMAC refinement DENZO data reduction SCALEPACK data scaling FFT phasing