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Crystal Structure of apo human Glutathione Synthetase Y270E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 HEPES, PEG400, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.834 α = 90 b = 94.051 β = 92.522 c = 125.122 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 2M 2022-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.59 47.07 98.6 0.093 0.106 0.066 0.996 10.1 4.3 123489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.63 0.687 0.778 0.359 0.74 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.59 47.07 123427 6675 98.42 0.161 0.1599 0.1727 0.1888 0.2005 20.175
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] 1.139 0.073 -0.899 -0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.596 r_dihedral_angle_4_deg 17.62 r_dihedral_angle_3_deg 12.644 r_lrange_it 7.894 r_lrange_other 7.672 r_scangle_it 6.37 r_scangle_other 6.369 r_dihedral_angle_1_deg 6.128 r_scbond_it 4.33 r_scbond_other 4.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.596 r_dihedral_angle_4_deg 17.62 r_dihedral_angle_3_deg 12.644 r_lrange_it 7.894 r_lrange_other 7.672 r_scangle_it 6.37 r_scangle_other 6.369 r_dihedral_angle_1_deg 6.128 r_scbond_it 4.33 r_scbond_other 4.33 r_mcangle_other 2.96 r_mcangle_it 2.958 r_mcbond_it 2.136 r_mcbond_other 2.131 r_angle_other_deg 1.375 r_angle_refined_deg 1.357 r_symmetry_nbd_refined 0.239 r_nbd_refined 0.196 r_nbd_other 0.185 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.077 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7186 Nucleic Acid Atoms Solvent Atoms 1046 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing