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Crystal structure of glutathione S-transferase complexed and modified with glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M Bis-Tris, 0.4M Ammonium acetate, 26% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.51 51.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.708 α = 90 b = 93.708 β = 90 c = 57.609 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 95 PIXEL DECTRIS PILATUS3 S 2M 2018-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.5 50 97.2 0.188 0.192 0.039 1 16.2 22.3 40217 22.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 100 0.708 0.742 0.215 0.858 2.6 11.2
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 1UA5 1.5 50 37812 1999 96.04 0.19242 0.1908 0.1904 0.2237 0.2226 RANDOM 16.48
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.383 r_dihedral_angle_4_deg 15.122 r_dihedral_angle_3_deg 11.242 r_long_range_B_refined 5.531 r_long_range_B_other 5.531 r_dihedral_angle_1_deg 5.394 r_scangle_other 2.268 r_mcangle_it 1.523 r_mcangle_other 1.523 r_angle_refined_deg 1.467
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.383 r_dihedral_angle_4_deg 15.122 r_dihedral_angle_3_deg 11.242 r_long_range_B_refined 5.531 r_long_range_B_other 5.531 r_dihedral_angle_1_deg 5.394 r_scangle_other 2.268 r_mcangle_it 1.523 r_mcangle_other 1.523 r_angle_refined_deg 1.467 r_scbond_it 1.414 r_scbond_other 1.413 r_mcbond_it 0.918 r_mcbond_other 0.912 r_angle_other_deg 0.844 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 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 1770 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing