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Crystal structure of glutathione transferase BBTA-3750 from Bradyrhizobium sp., Target EFI-507290, with one glutathione bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MF7 PDB ENTRY 4MF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG4000, 0.1M TRIS-HCl pH 8.5, 0.2M calcium acetate, 5 mM GSH, cryoprotectant: 20% glycerol, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.998 α = 89.98 b = 99.359 β = 89.97 c = 108.734 γ = 89.99
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 2013-09-18 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 1.9 50 97.2 0.047 8.8 2 309970 -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 1.9 1.93 95.1 0.35 2.5 2
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 4MF7 1.901 50 303683 6282 97.03 0.18658 0.18577 0.1989 0.22542 0.236 RANDOM 31.684
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] 5.43 0.21 0.05 -2.95 0.06 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.669 r_dihedral_angle_3_deg 13.158 r_dihedral_angle_4_deg 12.236 r_long_range_B_other 10.659 r_long_range_B_refined 10.639 r_scangle_other 10.173 r_scbond_it 9.518 r_scbond_other 9.512 r_mcangle_other 5.65 r_mcangle_it 5.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.669 r_dihedral_angle_3_deg 13.158 r_dihedral_angle_4_deg 12.236 r_long_range_B_other 10.659 r_long_range_B_refined 10.639 r_scangle_other 10.173 r_scbond_it 9.518 r_scbond_other 9.512 r_mcangle_other 5.65 r_mcangle_it 5.649 r_dihedral_angle_1_deg 5.502 r_mcbond_it 5.16 r_mcbond_other 5.157 r_angle_refined_deg 1.381 r_angle_other_deg 0.811 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 29909 Nucleic Acid Atoms Solvent Atoms 2214 Heterogen Atoms 314
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling