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Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with magnesium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 50 mM Tris-HCl, 25 mM MgCl2, 18% PEG 3350, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.43 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.989 α = 90 b = 85.989 β = 90 c = 126.151 γ = 90
Symmetry Space Group P 41 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 MARMOSAIC 225 mm CCD 2013-06-21 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) Rpim 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 2.04 42.2 100 0.074 0.075 0.014 9.1 28.4 30831 41.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.12 100 0.923 0.94 0.176 0.925 27.4 3024
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5EQD 2.04 40.696 30056 1498 97.45 0.1763 0.1731 0.1783 0.2396 0.2386 52.1184
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 14.088 f_angle_d 1.063 f_chiral_restr 0.044 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3179 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction