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Crystal structure of a glutathione transferase from Gordonia bronchialis DSM 43247, target EFI-507405
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M1G PDB ENTRY 3M1G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 273 0.1 M sodium acetate/acetic acid, pH 4.5, 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.87 α = 90 b = 75.475 β = 90 c = 193.71 γ = 90
Symmetry Space Group P 21 21 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 2014-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.83 193.71 99.9 0.16 12.3 7 19214 19193
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 2.83 2.99 100 0.498 4.1 7.1 2750
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 3M1G 2.83 96.86 18147 981 99.77 0.20234 0.19993 0.2058 0.24764 0.2469 RANDOM 28.256
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] 7.64 -3.4 -4.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.255 r_dihedral_angle_4_deg 19.495 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 6.808 r_long_range_B_refined 5.094 r_long_range_B_other 5.094 r_scangle_other 3.406 r_mcangle_it 2.878 r_mcangle_other 2.877 r_scbond_it 1.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.255 r_dihedral_angle_4_deg 19.495 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 6.808 r_long_range_B_refined 5.094 r_long_range_B_other 5.094 r_scangle_other 3.406 r_mcangle_it 2.878 r_mcangle_other 2.877 r_scbond_it 1.972 r_scbond_other 1.97 r_mcbond_it 1.672 r_mcbond_other 1.672 r_angle_refined_deg 1.47 r_angle_other_deg 0.985 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 5139 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction SCALA data scaling