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Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia vietnamiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 BuviA.00046.b.B1.PS02329 at 24.6 mg/mL with 2.5% glycerol, 3 mM UDP and 3 mM MgCl2 against JCSG+ screen condition D7 0.2 M Li2SO4, 0.1 M Tris pH 8.5, 40% MPD, crystal tracking ID 261935d7
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.17 α = 90 b = 103.02 β = 96.42 c = 218.47 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 MARMOSAIC 300 mm CCD 2015-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 50 98.9 0.063 0.998 11.76 3.2 186193 -3 39.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.7 0.455 0.835 2.62 3.2 13778
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 2WTX 2.3 46.536 1.34 186127 2000 98.91 0.1789 0.1784 0.1811 0.2245 0.2268 59.9142
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 15.262 f_angle_d 0.865 f_chiral_restr 0.054 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27774 Nucleic Acid Atoms Solvent Atoms 790 Heterogen Atoms 281
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction BALBES phasing XDS data reduction