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CRYSTAL STRUCTURE OF NU-CLASS GLUTATHIONE TRANSFERASE YGHU FROM Streptococcus sanguinis SK36, COMPLEX WITH GLUTATHIONE DISULFIDE, TARGET EFI-507286
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C8E PDB ENTRY 3C8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.1M Malonic Acid, 0.15M Ammonium Citrate Tribasic, 0.072M Succinic Acid, 0.18M DL-Malic Acid, 0.24M Sodium Acetate, 0.3M Sodium Formate, 0.096M Ammonium Tartrate Dibasic, pH 7.0, 5MM GSH, PROTEIN IN 10MM HEPES, PH 7.5, 150MM SODIUM CHLORIDE, 5% GLYCEROL, CRYOPROTECTANT: NONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.075 α = 90 b = 88.075 β = 90 c = 163.373 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 ADSC QUANTUM 315 MIRRORS 2013-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 50 99.3 0.075 9.8 13.2 47570 -5
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 1.95 1.98 100 0.76 3.5 13.5
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 3C8E 1.95 50 45722 1476 99.02 0.15288 0.15154 0.1657 0.19383 0.2009 RANDOM 40.471
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] 0.9 0.9 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.859 r_dihedral_angle_4_deg 17.436 r_scangle_other 13.846 r_dihedral_angle_3_deg 13.456 r_long_range_B_refined 13.05 r_long_range_B_other 13.034 r_scbond_it 12.613 r_scbond_other 12.611 r_mcangle_other 10.339 r_mcangle_it 10.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.859 r_dihedral_angle_4_deg 17.436 r_scangle_other 13.846 r_dihedral_angle_3_deg 13.456 r_long_range_B_refined 13.05 r_long_range_B_other 13.034 r_scbond_it 12.613 r_scbond_other 12.611 r_mcangle_other 10.339 r_mcangle_it 10.331 r_mcbond_it 9.17 r_mcbond_other 9.014 r_dihedral_angle_1_deg 5.482 r_angle_refined_deg 1.223 r_angle_other_deg 0.752 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 4169 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 84
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling