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Crystal structure of a putative glyoxalase i (lmof2365_0426) from listeria monocytogenes str. 4b f2365 at 2.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 1.1M sodium citrate, 0.15M sodium chloride, 0.1M TRIS pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 5.42 77.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.59 α = 90 b = 123.59 β = 90 c = 123.59 γ = 90
Symmetry Space Group I 21 3
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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.7 29.136 99.7 0.051 22.2 8775 -3 103.91
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 2.7 2.8 98.8 0.991 2.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.7 29.136 8766 416 99.8 0.173 0.172 0.1783 0.198 0.1915 RANDOM 57.474
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.224 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 12.377 r_scangle_it 5.127 r_dihedral_angle_1_deg 4.031 r_scbond_it 3.973 r_mcangle_it 2.134 r_angle_refined_deg 1.657 r_mcbond_it 1.373 r_angle_other_deg 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.224 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 12.377 r_scangle_it 5.127 r_dihedral_angle_1_deg 4.031 r_scbond_it 3.973 r_mcangle_it 2.134 r_angle_refined_deg 1.657 r_mcbond_it 1.373 r_angle_other_deg 0.959 r_xyhbond_nbd_refined 0.376 r_mcbond_other 0.243 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.216 r_symmetry_vdw_other 0.206 r_nbtor_refined 0.188 r_nbd_other 0.185 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.095 r_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 996 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing