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human glyoxalase I (with C-ter His tag) in complex with licochalcone B, form 1
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 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.258 α = 90 b = 66.149 β = 99.688 c = 42.068 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 2.08 19.88 100 0.11 0.989 13.8 3.4 22600
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 2.08 2.12 100 0.296 0.886 3.6
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 2.08 19.875 22583 1063 99.854 0.17 0.1663 0.1669 0.2338 0.2342 27.738
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] -0.582 0.547 -2.289 2.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.275 r_dihedral_angle_3_deg 16.066 r_dihedral_angle_6_deg 14.866 r_lrange_it 8.427 r_lrange_other 8.422 r_dihedral_angle_1_deg 7.383 r_scangle_it 7.017 r_scangle_other 7.015 r_scbond_other 4.893 r_scbond_it 4.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.275 r_dihedral_angle_3_deg 16.066 r_dihedral_angle_6_deg 14.866 r_lrange_it 8.427 r_lrange_other 8.422 r_dihedral_angle_1_deg 7.383 r_scangle_it 7.017 r_scangle_other 7.015 r_scbond_other 4.893 r_scbond_it 4.892 r_mcangle_other 4.856 r_mcangle_it 4.855 r_mcbond_it 3.6 r_mcbond_other 3.592 r_angle_refined_deg 2.464 r_angle_other_deg 0.796 r_nbd_refined 0.228 r_symmetry_nbd_refined 0.224 r_nbd_other 0.215 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.148 r_chiral_restr 0.114 r_metal_ion_refined 0.102 r_symmetry_nbtor_other 0.09 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2789 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing