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Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria in complex with UTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VCT native structure, 5vct
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.07 290 Optimization screen around RigakuReagents JCSG B9: 100mM Sodium citrate / citric acid pH 5.07, 18.73% PEG 6000, BuamA.00118.a.B1.PS37963 at 45.5 mg/ml + 3mM GTP (BSI1746) + 3mM Glucose-1-phosphate (BSI 1952) + 3mM MgCl2, tray 289280h3: cryo: 25% EG in 3 steps: puck kzj0-7.
Crystal Properties Matthews coefficient Solvent content 3.21 63.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.25 α = 90 b = 108.48 β = 90 c = 124.51 γ = 90
Symmetry Space Group I 2 2 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 RIGAKU SATURN 944+ 2017-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.3 50 99.3 0.064 0.069 0.999 20.79 7.055 19325 -3 31.88
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 2.3 2.36 94.2 0.308 0.333 0.984 7.51 7.159
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE native structure, 5vct 2.3 39.092 1.34 19315 1932 99.31 0.1817 0.1775 0.2213 0.2134 0, random 40.4692
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 13.953 f_angle_d 0.892 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 2149 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHENIX phasing Coot model building