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Crystal structure of the Leishmania infantum glyoxalase II with D-Lactate at the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P18 pdb entry 2P18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288 30% PEG 8K, 0.2M MgCl2, 0.1M ammonium acetate - soaked 30 min in 40% PEG 8K, 0.2M MgCl2, 0.1M ammonium acetate, 10mM S-D-lactoyltrypanothione, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 1.87 34.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.172 α = 90 b = 89.121 β = 90 c = 85.98 γ = 90
Symmetry Space Group C 2 2 21
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 QUANTUM 315 Undulator 2006-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 53.642 100 0.087 0.087 5.1 13.8 20715 20715 24.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.488 0.488 1.5 14.1 2983
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2P18 1.9 53.61 20692 20692 1060 99.97 0.261 0.183 0.181 0.1808 0.22 0.2208 RANDOM 26.204
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] -0.37 0.06 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.251 r_dihedral_angle_4_deg 17.365 r_dihedral_angle_3_deg 13.517 r_dihedral_angle_1_deg 8.724 r_scangle_it 3.139 r_scbond_it 2.242 r_angle_refined_deg 1.54 r_mcangle_it 1.22 r_mcbond_it 0.831 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.251 r_dihedral_angle_4_deg 17.365 r_dihedral_angle_3_deg 13.517 r_dihedral_angle_1_deg 8.724 r_scangle_it 3.139 r_scbond_it 2.242 r_angle_refined_deg 1.54 r_mcangle_it 1.22 r_mcbond_it 0.831 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.23 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.116 r_metal_ion_refined 0.024 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2129 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection MOSFLM data reduction