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Crystal structure of alpha,alpha-trehalose 6-phosphate sythase from Burkholderia multivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 Morpheus screen, H6: 0.1 M MOPs/HEPES-Na pH 7.5, 10% PEG 8000, 20% ethylene glycol, 0.02 M NaGlu, Ala, Gly, Lys, and Ser: BumuA.00046.b.B1.PS37880 at 18.6 mg/ml: direct cryo: tray 272185 well H6, puck omx7-10
Crystal Properties Matthews coefficient Solvent content 3.03 59.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.58 α = 90 b = 128.92 β = 90 c = 85.96 γ = 90
Symmetry Space Group P 21 21 2
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 RAYONIX MX-300 2016-06-22 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) Rrim 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 1.7 50 98.8 0.086 0.094 0.997 14.26 6.217 142053 -3 15.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 97.7 0.544 0.593 0.904 3.45 6.312
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 FREE R-VALUE 5HXA 1.7 50 1.35 141991 2055 98.75 0.1582 0.1578 0.1586 0.1853 0.1842 23.8782
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 13.5 f_angle_d 0.8 f_chiral_restr 0.054 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7226 Nucleic Acid Atoms Solvent Atoms 1237 Heterogen Atoms 170
Software Software Software Name Purpose XSCALE data scaling Coot model building PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing