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Crystal structure of glutathione transferase BgramDRAFT_1843 from Burkholderia graminis, Target EFI-507289, with two glutathione molecules bound per one protein subunit
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 8.5 298 protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 0.1 M Tris-HCl, pH 8.5, 1.4 M ammonium tartrate dibasic, cryoprotectant: 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.175 α = 90 b = 84.175 β = 90 c = 78.597 γ = 90
Symmetry Space Group P 43 21 2
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 1.2 50 100 0.096 0.096 6.3 13.6 88463 -5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 100 2.3 10.7
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 1.2 50 85711 2670 99.99 0.11273 0.11216 0.1143 0.13111 0.1354 RANDOM 16.361
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] 0.09 0.09 -0.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.016 r_dihedral_angle_2_deg 35.073 r_sphericity_bonded 16.848 r_rigid_bond_restr 11.237 r_dihedral_angle_3_deg 10.703 r_dihedral_angle_4_deg 9.016 r_scangle_other 8.189 r_long_range_B_refined 8.046 r_long_range_B_other 8.045 r_scbond_it 7.466
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.016 r_dihedral_angle_2_deg 35.073 r_sphericity_bonded 16.848 r_rigid_bond_restr 11.237 r_dihedral_angle_3_deg 10.703 r_dihedral_angle_4_deg 9.016 r_scangle_other 8.189 r_long_range_B_refined 8.046 r_long_range_B_other 8.045 r_scbond_it 7.466 r_scbond_other 7.462 r_dihedral_angle_1_deg 5.41 r_mcangle_other 4.478 r_mcbond_it 4.436 r_mcbond_other 4.101 r_mcangle_it 4.03 r_angle_refined_deg 1.49 r_angle_other_deg 0.861 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 49
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling