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Crystal structure of exopolyphosphatase (PPX) mutant E137A from Zymomonas mobilis in complex with magnesium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GTY 8GTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 50 mM Tris pH 8.0, 500 mM NaCl, 5% glycerol
0.2 M magnesium chloride hexahydrate, 0.1 M Tris pH 6.5, 25%(w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.74 α = 90 b = 47.901 β = 126.53 c = 94.892 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 ADSC QUANTUM 270 2015-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.98 SSRF BL17U1
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 1.56 50 99.6 0.043 0.051 0.028 9.9 3.3 63367
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 1.56 1.59 98.2 0.308 0.375 0.212 0.872 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8GTY 1.56 42.55 1.36 63220 3212 99.23 0.1718 0.1701 0.1705 0.2037 0.2023 18.2207
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3600 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing