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Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium inhibited by 4-n-octylphenyl alpha-D-glucopyranoside-6-sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 Drop contained: 1.5 uL 40 mg/mL protein, 2 uL reservoir solution (15% PEG 3350, 400 mM lithium citrate, 30 mM magnesium chloride, 40 mM mixture of MES, MOPS, and TAPS at pH 7.5), and 0.5 uL 1:10^3 dilution of seed stock prepared according to Seed Bead protocol. Crystals were transferred to drop containing 18% PEG 3350, 400mM lithium citrate, 40 mM magnesium chloride, 10% ethylene glycol, and 1mM OGS for 24 prior to cryocooling
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.159 α = 90 b = 52.419 β = 100.58 c = 108.615 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 290 CCD MARMOSAIC 325 mm CCD 2016-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.378 SSRL BL14-1
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 2.24 50 99.3 0.107 0.123 0.06 0.978 9.3 4 24547 37.51
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 2.24 2.28 90.6 0.422 0.505 0.273 0.84 3.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6UPB 2.244 37.402 1.35 24528 2009 99.28 0.19 0.1862 0.232 0.2237 43.978
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 3772 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction