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human glyoxalase I (with C-ter His tag) in complex with TLSC702
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.689 α = 90 b = 81.971 β = 93.85 c = 46.927 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 95 PIXEL DECTRIS EIGER X 16M 2020-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A
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 20 99.4 0.071 0.998 10.7 3.5 27285 30.4
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 2.11 99.3 0.78 0.717 1.6
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 3vw9 2 19.79 24507 2760 99.27 0.1898 0.1863 0.1957 0.2217 0.228 RANDOM 40.919
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] -0.04 0.04 -0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.257 r_dihedral_angle_3_deg 14.763 r_dihedral_angle_4_deg 10.597 r_dihedral_angle_1_deg 7.375 r_angle_refined_deg 1.459 r_angle_other_deg 1.299 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.257 r_dihedral_angle_3_deg 14.763 r_dihedral_angle_4_deg 10.597 r_dihedral_angle_1_deg 7.375 r_angle_refined_deg 1.459 r_angle_other_deg 1.299 r_chiral_restr 0.079 r_bond_refined_d 0.008 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 2916 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing