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X-ray structure ofThermus thermophilus HB8 transketorase demonstrate in complex with TPP and D-erythrose-4-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 100mM imidazole/MES buffer pH 6.5, 20%(v/v) ethylene glycol, 10% (w/v) PEG 8000, 24mM of D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, and N-acetyl-D-glucosamine
Crystal Properties Matthews coefficient Solvent content 2.33 47.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.68 α = 72.308 b = 88.86 β = 88.696 c = 117.37 γ = 73.459
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 PILATUS3 6M 2019-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 41.86 98.1 0.998 18.6 3.5 124659
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.31 0.839
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2E6K 2.25 41.86 124659 6251 98.152 0.205 0.202 0.2074 0.254 0.2543 55.66
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] -0.409 -0.111 0.005 0.057 -0.084 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.727 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 17.407 r_lrange_it 9.752 r_lrange_other 9.752 r_dihedral_angle_1_deg 7.712 r_mcangle_it 7.239 r_mcangle_other 7.239 r_scangle_it 7.237 r_scangle_other 7.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.727 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 17.407 r_lrange_it 9.752 r_lrange_other 9.752 r_dihedral_angle_1_deg 7.712 r_mcangle_it 7.239 r_mcangle_other 7.239 r_scangle_it 7.237 r_scangle_other 7.237 r_mcbond_it 5.185 r_mcbond_other 5.185 r_scbond_it 5.013 r_scbond_other 5.013 r_angle_refined_deg 1.642 r_angle_other_deg 1.256 r_nbd_refined 0.212 r_symmetry_nbd_other 0.187 r_symmetry_xyhbond_nbd_refined 0.183 r_metal_ion_refined 0.174 r_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.166 r_nbd_other 0.161 r_symmetry_nbd_refined 0.111 r_symmetry_xyhbond_nbd_other 0.104 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20280 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing