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Specificity of the Trypanothione-dependednt Leishmania major Glyoxalase I: Structure and biochemical comparison with the human enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FA8 PDB ENTRY 1FA8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 62% (V/V) MPD, 100MM TRIS-HCL PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.24 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.193 α = 90 b = 148.957 β = 90 c = 50.698 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 CCD ADSC CCD TOROIDAL MIRROR 2004-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2 60 99.8 0.05 17.7 4.2 67613 28.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99.5 0.3 4.9 4
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 PDB ENTRY 1FA8 2 129.1 64010 3378 99.6 0.157 0.155 0.1663 0.201 0.2096 RANDOM 34.53
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] -0.82 -0.3 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.439 r_dihedral_angle_4_deg 15.845 r_dihedral_angle_3_deg 14.28 r_dihedral_angle_1_deg 5.992 r_scangle_it 2.351 r_scbond_it 1.529 r_angle_refined_deg 1.248 r_mcangle_it 0.875 r_angle_other_deg 0.758 r_mcbond_it 0.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.439 r_dihedral_angle_4_deg 15.845 r_dihedral_angle_3_deg 14.28 r_dihedral_angle_1_deg 5.992 r_scangle_it 2.351 r_scbond_it 1.529 r_angle_refined_deg 1.248 r_mcangle_it 0.875 r_angle_other_deg 0.758 r_mcbond_it 0.491 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.178 r_nbtor_refined 0.177 r_nbd_other 0.176 r_symmetry_vdw_other 0.174 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.141 r_nbtor_other 0.08 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6768 Nucleic Acid Atoms Solvent Atoms 839 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing