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Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-galactose and UTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H5R PDB entry 1H5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M sodium cacodylate, 2.0M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.83 56.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.788 α = 90 b = 90.763 β = 125.2 c = 87.702 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r mirrors 2011-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 30 99.6 0.042 22.4 4.1 67790
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 1.8 1.86 99.7 0.214 4.1 6776
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1H5R 1.8 30 67775 3441 99.59 0.1734 0.1714 0.1715 0.2115 0.2089 RANDOM 25.9325
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] -0.97 -1.16 1.15 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.123 r_dihedral_angle_4_deg 22.236 r_dihedral_angle_3_deg 16.008 r_dihedral_angle_1_deg 7.052 r_scangle_it 6.805 r_scbond_it 4.287 r_mcangle_it 2.708 r_mcbond_it 1.645 r_angle_refined_deg 1.455 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.123 r_dihedral_angle_4_deg 22.236 r_dihedral_angle_3_deg 16.008 r_dihedral_angle_1_deg 7.052 r_scangle_it 6.805 r_scbond_it 4.287 r_mcangle_it 2.708 r_mcbond_it 1.645 r_angle_refined_deg 1.455 r_chiral_restr 0.131 r_bond_refined_d 0.02 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4557 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 175
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing