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Crystal structure of glutathione transferase SMc00097 from Sinorhizobium meliloti, target EFI-507275, with one glutathione bound per one protein subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LSZ PDB ENTRY 3LSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG3350, 0.1M bis-tris pH 6.5, 0.2M ammonium acetate, 5 mM GSH, cryoprotectant: none, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.306 α = 87.34 b = 62.504 β = 79.73 c = 84.426 γ = 82.04
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 315 MIRRORS 2013-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 50 96.1 0.047 10.6 2 62866 -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 2 2.03 83.6 0.6 1.1 1.8
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 3LSZ 2 50 60645 1906 96.18 0.17437 0.1728 0.22553 0.2473 RANDOM 62.183
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] 0.56 -0.59 -2.71 -0.23 -0.2 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.68 r_dihedral_angle_4_deg 17.834 r_dihedral_angle_3_deg 16.037 r_long_range_B_other 13.739 r_long_range_B_refined 13.738 r_scangle_other 13.244 r_scbond_it 12.175 r_scbond_other 12.17 r_mcangle_other 10.915 r_mcangle_it 10.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.68 r_dihedral_angle_4_deg 17.834 r_dihedral_angle_3_deg 16.037 r_long_range_B_other 13.739 r_long_range_B_refined 13.738 r_scangle_other 13.244 r_scbond_it 12.175 r_scbond_other 12.17 r_mcangle_other 10.915 r_mcangle_it 10.914 r_mcbond_it 9.523 r_mcbond_other 9.511 r_dihedral_angle_1_deg 5.284 r_angle_refined_deg 1.149 r_angle_other_deg 0.743 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6712 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 80
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling