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Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia xenovorans in complex with glucose-6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 MORPHEUS G2 (269140g2): 10% w/v PEG8000, 20% v/v EG, 20mM tartarate, citrate, oxamate, acetate, formate, 100mM MES/imidazole pH 6.5: 2mM UDP, 2mM glucose-6-phosphate, 2mM MgCl2: protein conc 22.24mg/mL: dc: wpj5-2
Crystal Properties Matthews coefficient Solvent content 2.77 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.92 α = 91.36 b = 105.95 β = 90.37 c = 135.71 γ = 89.97
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-225 2016-02-11 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 1.95 50 95.7 0.05 0.071 0.997 11.68 1.994 329972 -3 24.74
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 1.95 2 95.3 0.422 0.597 0.713 1.95 1.995
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 4b14 1.95 50 1.97 329927 1982 95.69 0.1555 0.1554 0.1559 0.1777 0.1776 32.7772
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 16.137 f_angle_d 0.856 f_chiral_restr 0.053 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28448 Nucleic Acid Atoms Solvent Atoms 2866 Heterogen Atoms 575
Software Software Software Name Purpose XSCALE data scaling Coot model building PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing