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human glyoxalase I (with C-ter His tag) in complex with licochalcone B and GSH, form 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M Sodium chloride, 0.1 M Bis-Tris, 25%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.831 α = 90 b = 65.883 β = 101.044 c = 41.3 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 4M 2024-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.018 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.72 19.6 99.1 0.056 0.935 24.5 3.5 38189
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 95.1 0.294 0.896 3.3
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 1.72 19.596 38134 1922 98.882 0.158 0.1564 0.1572 0.1926 0.194 23.043
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] -0.591 0.057 -0.495 0.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.443 r_dihedral_angle_6_deg 14.896 r_dihedral_angle_3_deg 13.603 r_lrange_it 8.128 r_lrange_other 8.125 r_dihedral_angle_1_deg 6.822 r_scangle_it 6.521 r_scangle_other 6.52 r_scbond_it 4.538 r_scbond_other 4.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.443 r_dihedral_angle_6_deg 14.896 r_dihedral_angle_3_deg 13.603 r_lrange_it 8.128 r_lrange_other 8.125 r_dihedral_angle_1_deg 6.822 r_scangle_it 6.521 r_scangle_other 6.52 r_scbond_it 4.538 r_scbond_other 4.536 r_mcangle_it 3.764 r_mcangle_other 3.764 r_mcbond_it 2.898 r_mcbond_other 2.897 r_angle_refined_deg 2.245 r_angle_other_deg 0.773 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.233 r_nbd_other 0.208 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.142 r_chiral_restr 0.122 r_xyhbond_nbd_refined 0.121 r_symmetry_xyhbond_nbd_other 0.115 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2782 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing