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Crystal structure of a probable lactoylglutathione lyase from Brucella melitensis in complex with glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Molecular Dimensions, Morpheus e4: 30mM each: Di-Ethyleneglycol, Tri-Ethyleneglycol, TetraEthyleneglycol, Penta-Ethyleneglycol; 100mM Imidazole/MES pH 6.5; 12.5% each MPD (racemic), PEG 1K, PEG 3350; BrabA.17481.b.B1.PS02324 at 21.7mg/ml with 8mM Gluathione; Cryo: direct; tray 261781e4; puck epp4-1
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.63 α = 90 b = 39.5 β = 116.29 c = 41.7 γ = 90
Symmetry Space Group C 1 2 1
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 RAYONIX MX-225 2015-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.45 50 98.4 0.034 0.04 20.5 3.96 21619 21264 -3 15.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.49 89.1 0.308 0.383 2.97 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4QB5 1.45 20.622 1.35 21256 1082 98.67 0.1351 0.1337 0.136 0.1611 0.1628 Random selectiob 25.2326
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 f_dihedral_angle_d 12.687 f_angle_d 1.02 f_chiral_restr 0.066 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 933 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 37
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing BALBES phasing PHENIX model building Coot model building PHENIX refinement PDB_EXTRACT data extraction