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Structure of human Glutathione Transferase Pi class in complex with Ethacraplatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 100mM MES, pH 5.5, pH 6.0, 28% (w/v) PEG 8000, 20mM CaCl2 10mM DTT, 3mM EACPT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.806 α = 90 b = 89.994 β = 98.24 c = 68.87 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 2006-12-05 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 1.85 20.28 99.8 0.06 0.06 16.9 3.7 39483 39483 21.98
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 1.85 1.95 99.6 0.4 0.4 1.9 3.6 5695
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 Difference Fourier THROUGHOUT 5GSS 1.85 20.28 39483 2026 99.89 0.18 0.178 0.1769 0.218 0.2177 RANDOM 20.291
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] 1.56 -0.68 -0.79 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.294 r_dihedral_angle_4_deg 14.826 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_1_deg 5.352 r_scangle_it 3.135 r_scbond_it 2.107 r_angle_refined_deg 1.554 r_mcangle_it 1.276 r_mcbond_it 0.873 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.294 r_dihedral_angle_4_deg 14.826 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_1_deg 5.352 r_scangle_it 3.135 r_scbond_it 2.107 r_angle_refined_deg 1.554 r_mcangle_it 1.276 r_mcbond_it 0.873 r_nbtor_refined 0.302 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.163 r_symmetry_vdw_refined 0.154 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.138 r_metal_ion_refined 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3262 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 67
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction