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Crystal structure of a tartrate dehydratase from azospirillum, target efi-502395, with bound mg and a putative acrylate ion, ordered active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DW7 PDB ENTRY 2DW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 298 Protein (30 mM NaCl, 2% glycerol, 200 mM MesoTartrate); Reservoir (100 mM Hepes pH 7.6, 20 mM Mg, 20% PolyAcrylic Acid NaSalt 5100); Cryoprotection (reservoir + 20% glycerol), sitting drop vapor diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.167 α = 90 b = 82.925 β = 100.86 c = 103.266 γ = 90
Symmetry Space Group P 1 21 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 MX225HE MIRRORS 2013-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 1.3 100 93.5 0.11 0.11 7.6 3.7 189451 189451
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 1.3 1.37 56.2 0.596 0.596 2.2 3.7
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 2DW7 1.3 21.399 189399 189399 9474 93.1 0.1655 0.1655 0.1644 0.1657 0.1859 0.1865 RANDOM 13.0523
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 12.088 f_angle_d 1.229 f_chiral_restr 0.071 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6046 Nucleic Acid Atoms Solvent Atoms 1221 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction AMoRE phasing