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Crystal Structure of Glutathione Transferase Pi Y108V Mutant in Complex with the Glutathione Conjugate of Ethacrynic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GSS PDB ENTRY 5GSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 133mM Calcium Acetate, 18% PEG8000, 100mM MES, pH5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.384 α = 90 b = 89.375 β = 90.07 c = 69.19 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 IMAGE PLATE RIGAKU RAXIS IV++ AXCO 2008-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.95 37.54 87.2 0.08 0.08 8.56 5.6 29135 16.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 42.2 0.38 0.38 1.9 3.5 2026
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 ENTRY 5GSS 1.95 37.53 29133 1507 87.1 0.16 0.15 0.1547 0.21 0.2093 RANDOM 14.39
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] 1.66 0.01 -0.9 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.859 r_dihedral_angle_4_deg 15.534 r_dihedral_angle_3_deg 12.881 r_dihedral_angle_1_deg 5.615 r_scangle_it 2.789 r_scbond_it 1.903 r_angle_refined_deg 1.356 r_mcangle_it 1.176 r_mcbond_it 0.72 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.859 r_dihedral_angle_4_deg 15.534 r_dihedral_angle_3_deg 12.881 r_dihedral_angle_1_deg 5.615 r_scangle_it 2.789 r_scbond_it 1.903 r_angle_refined_deg 1.356 r_mcangle_it 1.176 r_mcbond_it 0.72 r_nbtor_refined 0.3 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.131 r_metal_ion_refined 0.092 r_chiral_restr 0.091 r_symmetry_metal_ion_refined 0.069 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3264 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 92
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection PHASER phasing