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Crystal Structure Of glutathione transferase YghU from Streptococcus pneumoniae ATCC 700669, complexed with glutathione, Target EFI-507284
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MZW PDB ENTRY 4MZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 273 0.2 M sodium tartrate dibasic, 20% w/v PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.36 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.033 α = 90 b = 59.887 β = 90 c = 170.126 γ = 90
Symmetry Space Group I 2 2 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 2014-02-07 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 1.708 85.063 98.8 0.083 11.5 6.8 30558 30529
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 1.708 1.8 97.5 1.363 2 6 4317
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 4MZW 1.708 85.06 28946 1545 98.34 0.1894 0.18694 0.1998 0.23678 0.2451 RANDOM 24.741
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] -0.36 -2.07 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.185 r_dihedral_angle_4_deg 15.605 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 6.204 r_long_range_B_refined 5.514 r_long_range_B_other 5.513 r_scangle_other 4.295 r_mcangle_it 3.093 r_mcangle_other 3.093 r_scbond_it 2.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.185 r_dihedral_angle_4_deg 15.605 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 6.204 r_long_range_B_refined 5.514 r_long_range_B_other 5.513 r_scangle_other 4.295 r_mcangle_it 3.093 r_mcangle_other 3.093 r_scbond_it 2.793 r_scbond_other 2.792 r_mcbond_it 2.112 r_mcbond_other 2.107 r_angle_refined_deg 1.814 r_angle_other_deg 0.91 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 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 2078 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 40
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALA data scaling