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Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii with evidence of substrate binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D91 5D91,4O6M experimental model PDB 4O6M 5D91,4O6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.1 295 100 mM NaCl, 100 mM Sodium Citrate, pH 6.1, 40 mM MgCl2, 29% PEG 400, 500 uM L-myo-inositol-1-phosphate (prepared in house), 2.5 mM CDP (Sigma) (precipitant). Concentrated protein at 30-35 mg/ml was mixed with monoolein at a 1:1.5 protein to lipid ratio
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.089 α = 90 b = 60.857 β = 90.74 c = 85.417 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 PIXEL DECTRIS EIGER X 16M MD2 diffractometer 2018-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.142 78.083 58.72 0.07329 0.1036 0.07329 0.995 9.78 2 26006 41.06
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 2.142 2.221 1.57 0.4034 0.5705 0.4034 0.594 1.73 2
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 5D91,4O6M 2.142 78.083 1.37 25995 1297 58.53 0.2252 0.2228 0.2261 0.2695 0.268 45.381
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 5013 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 268
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing STARANISO data scaling PARROT phasing PHENIX refinement Coot model building PDB_EXTRACT data extraction