☰ Navigation Tabs
Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose
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: 2 uL 40 mg/mL protein, 2 uL reservoir solution (16% PEG 3350, 450 mM lithium citrate and 10 mM magnesium chloride) and 0.5 uL 1:10^3 dilution of seed stock prepared according to the Seed Bead protocol. Crystals were transferred to a drop containing 35% PEG 3350, 166 mM lithium citrate, 166 mM magnesium chloride, 10% ethylene glycol and 50 mM trehalose for 30 minutes prior to cryocooling.
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.767 α = 90 b = 52.955 β = 100.61 c = 108.762 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 PIXEL DECTRIS EIGER X 16M 2017-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97919 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 2.05 106.9 98.6 0.084 0.098 0.051 0.997 9.4 3.6 32534 40.4
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 2.05 2.11 88.8 0.859 1.007 0.519 0.577 3.6
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 6upb 2.052 53.451 1.36 32483 2016 98.4 0.221 0.2182 0.2202 0.2615 0.2609 48.6048
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 139 Heterogen Atoms 50
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction