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Crystal structure of glutathione transferase BgramDRAFT_1843 from Burkholderia graminis, Target EFI-507289, with traces of one GSH bound
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 7 298 protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 3.5 M sodium formate, pH 7.0, cryoprotectant: 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.088 α = 90 b = 84.088 β = 90 c = 78.017 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 1.11 50 99.1 0.091 0.091 7.3 13.9 109376 -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 1.11 1.13 81.4 2.6 11.7
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 1.11 50 105992 3274 99.91 0.11369 0.11326 0.1147 0.12736 0.1296 RANDOM 16.564
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] -0.07 -0.07 0.13
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 52.39 r_dihedral_angle_2_deg 35.135 r_dihedral_angle_3_deg 12.404 r_sphericity_bonded 11.685 r_rigid_bond_restr 10.6 r_dihedral_angle_4_deg 9.283 r_dihedral_angle_1_deg 5.486 r_long_range_B_refined 5.485 r_long_range_B_other 5.484 r_scangle_other 3.89
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 52.39 r_dihedral_angle_2_deg 35.135 r_dihedral_angle_3_deg 12.404 r_sphericity_bonded 11.685 r_rigid_bond_restr 10.6 r_dihedral_angle_4_deg 9.283 r_dihedral_angle_1_deg 5.486 r_long_range_B_refined 5.485 r_long_range_B_other 5.484 r_scangle_other 3.89 r_scbond_other 3.461 r_scbond_it 3.46 r_mcangle_other 3.051 r_mcangle_it 2.96 r_mcbond_it 2.15 r_mcbond_other 2.149 r_angle_refined_deg 1.517 r_angle_other_deg 0.852 r_chiral_restr 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.007 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 1888 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 20
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling