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Crystal structure of the glutathione transferase PI enzyme in complex with the bifunctional inhibitor, etharapta
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 5.5 298 100mM MES BUFFER PH 5.5, 22%(W/V) PEG 8000, 20mM CACL2, 10mM DTT, Small amounts of solid compound were streaked through the drops containing preformed crystals. These were soaked for 48hours., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.93 α = 90 b = 90.33 β = 98.88 c = 68.96 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++ ACXO 2006-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 1.6 19.53 98.3 0.046 0.046 13.2 3.6 62097 61004 21.56
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) 1.6 1.69 96.1 0.554 0.554 1.3 3.5 8643
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 THROUGHOUT 5GSS 1.6 19.53 61004 3095 98.24 0.196 0.195 0.1888 0.227 0.2218 RANDOM 18.15
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] 0.77 -0.37 -0.51 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.947 r_dihedral_angle_4_deg 16.323 r_dihedral_angle_3_deg 11.145 r_dihedral_angle_1_deg 5.945 r_scangle_it 3.231 r_scbond_it 2.206 r_angle_refined_deg 1.539 r_mcangle_it 1.385 r_mcbond_it 0.979 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.947 r_dihedral_angle_4_deg 16.323 r_dihedral_angle_3_deg 11.145 r_dihedral_angle_1_deg 5.945 r_scangle_it 3.231 r_scbond_it 2.206 r_angle_refined_deg 1.539 r_mcangle_it 1.385 r_mcbond_it 0.979 r_nbtor_refined 0.312 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.128 r_metal_ion_refined 0.116 r_chiral_restr 0.103 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3277 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 51
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction