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Crystal structure of glutathione transferase BBTA-3750 from Bradyrhizobium sp., Target EFI-507290
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IKH PDB ENTRY 4IKH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 298 protein in 10 MM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 0.2 M potassium nitrate, pH 6.9, 20% PEG3350, cryoprotectant: 20% diethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.526 α = 90 b = 88.951 β = 90 c = 78.127 γ = 90
Symmetry Space Group C 2 2 21
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 RAYONIX MX225HE mirrors 2013-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 1.8 50 99.9 0.071 0.071 13.8 7.4 25702 -5
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 1.8 1.83 100 0.8 0.8 2.8 7.4
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 4IKH 1.8 50 24850 829 99.85 0.17821 0.17693 0.1906 0.21858 0.2282 RANDOM 40.306
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] -1.1 1.29 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.819 r_dihedral_angle_3_deg 13.692 r_long_range_B_other 12.671 r_long_range_B_refined 12.525 r_scangle_other 12.409 r_scbond_other 11.816 r_scbond_it 11.796 r_dihedral_angle_4_deg 8.033 r_mcangle_it 7.621 r_mcangle_other 7.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.819 r_dihedral_angle_3_deg 13.692 r_long_range_B_other 12.671 r_long_range_B_refined 12.525 r_scangle_other 12.409 r_scbond_other 11.816 r_scbond_it 11.796 r_dihedral_angle_4_deg 8.033 r_mcangle_it 7.621 r_mcangle_other 7.618 r_mcbond_it 7.6 r_mcbond_other 7.596 r_dihedral_angle_1_deg 5.83 r_angle_refined_deg 1.361 r_angle_other_deg 0.838 r_chiral_restr 0.081 r_bond_refined_d 0.011 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 1627 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling