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Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia vietnamiensis in complex with Uridine-5'-diphosphate-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UX8 2ux8, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 MCSG1 screen A4: 2500mM NaCl, 200mM MgCl2, 100mM Tris base/HCl pH 7.0; BuviA.00118.e.B1.PS02498 at 27.5mg/ml + 4mM Glucose-1-phosphate + 4mM UTP + 4mM MgCl2; ; tray: 267283a4, puck sbq8-1, cryo: 20% EG
Crystal Properties Matthews coefficient Solvent content 3.92 68.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.9 α = 90 b = 84.9 β = 90 c = 252.7 γ = 120
Symmetry Space Group P 62 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 RAYONIX MX-225 2015-12-10 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 2.15 50 99.9 0.09 0.998 12.87 6.8 30405 -3 33.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 100 0.542 3.56 7.3
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 2ux8, chain A 2.15 50 1.35 30327 1968 99.9 0.1741 0.172 0.1738 0.2025 0.2026 45.623
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 17.11 f_angle_d 0.889 f_chiral_restr 0.057 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2233 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX model building PHENIX refinement