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Crystal structure of B. subtilis glucose-1-phosphate uridylyltransferase YngB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2M potassium citrate tribasic monohydrate, 0.05M lithium citrate tribasic tetrahydrate, 0.1M sodium phosphate monobasic monohydrate, 25% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.94 58.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.91 α = 90 b = 158.61 β = 90 c = 179.5 γ = 90
Symmetry Space Group I 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2020-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9794 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.8 55.98 99.8 0.095 0.067 5.6 1.9 19457
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 0.661 0.468
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.8 51.09 18416 937 99.21 0.1932 0.1906 0.2006 0.2443 0.2053 RANDOM 82.119
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] 5.13 -6.74 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.249 r_dihedral_angle_3_deg 24.063 r_dihedral_angle_4_deg 20.821 r_dihedral_angle_1_deg 8.372 r_angle_refined_deg 1.792 r_chiral_restr 0.14 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4378 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data scaling SHELXDE phasing PDB_EXTRACT data extraction XDS data reduction