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human Glyoxalase I with an N-hydroxypyridone inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VW9 PDB ENTRY 3VW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 25% (w/v) PEG 2000 MME, 10%(v/v) Glycerol, 0.1M Na-HEPES (pH 7.0), vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.17 α = 90 b = 67.38 β = 90 c = 68.48 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII Osmic VariMax mirrors 2009-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.695 31.82 99.9 0.061 19.1 6.8 44934 44934
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 99.7 0.56 0.56 0.612 0.245 1.4 6 3269
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3VW9 1.7 31.82 44893 2264 99.87 0.2159 0.2145 0.2423 0.2403 RANDOM 19.375
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] 0.8 -0.93 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.638 r_dihedral_angle_3_deg 13.007 r_dihedral_angle_4_deg 9.296 r_dihedral_angle_1_deg 5.877 r_mcangle_it 1.654 r_angle_refined_deg 1.234 r_scbond_it 1.214 r_mcbond_it 0.985 r_chiral_restr 0.091 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.638 r_dihedral_angle_3_deg 13.007 r_dihedral_angle_4_deg 9.296 r_dihedral_angle_1_deg 5.877 r_mcangle_it 1.654 r_angle_refined_deg 1.234 r_scbond_it 1.214 r_mcbond_it 0.985 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2757 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 62
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction