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Crystal structure of glutathione transferase iota 1 from Synechocystis sp. PCC 6803 in complex with FMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 277 30% PEG 4000, 200 mM LiSO4, 100 mM Tris
Crystal Properties Matthews coefficient Solvent content 3.71 66.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.313 α = 90 b = 173.927 β = 90 c = 318.382 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 9M 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.71 48.791 99.2 1 22.3 14 92848
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.71 2.78 0.83 1.6
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 FREE R-VALUE 2.71 48.791 92753 4658 99.796 0.21 0.2084 0.2084 0.2417 0.2418 76.239
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] 2.031 2.758 -4.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.947 r_lrange_it 16.222 r_dihedral_angle_6_deg 15.327 r_scangle_it 13.836 r_mcangle_it 12.948 r_scbond_it 10.211 r_mcbond_it 9.208 r_dihedral_angle_2_deg 8.475 r_dihedral_angle_1_deg 6.744 r_angle_refined_deg 1.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.947 r_lrange_it 16.222 r_dihedral_angle_6_deg 15.327 r_scangle_it 13.836 r_mcangle_it 12.948 r_scbond_it 10.211 r_mcbond_it 9.208 r_dihedral_angle_2_deg 8.475 r_dihedral_angle_1_deg 6.744 r_angle_refined_deg 1.904 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.235 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.138 r_metal_ion_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.083 r_ncsr_local_group_6 0.05 r_ncsr_local_group_10 0.049 r_ncsr_local_group_7 0.046 r_ncsr_local_group_3 0.045 r_ncsr_local_group_8 0.045 r_ncsr_local_group_5 0.043 r_ncsr_local_group_9 0.042 r_ncsr_local_group_4 0.041 r_ncsr_local_group_1 0.04 r_ncsr_local_group_2 0.04 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16190 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing