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X-ray structure of Thermus thermophilus HB8 transketorase in complex with TPP and MES
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, N-acetyl-D-glucosamine
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.72 α = 72.564 b = 88.84 β = 88.743 c = 117.61 γ = 73.74
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 2018-05-16 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 2.01 46.67 97.7 0.997 17.6 3.5 175041
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 2.01 2.06 0.732
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 2.01 46.67 175041 8735 97.751 0.199 0.1977 0.2038 0.2284 0.2333 43.074
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] 0.088 -0.94 2.01 -0.478 -0.47 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.116 r_dihedral_angle_4_deg 18.411 r_dihedral_angle_3_deg 16.474 r_dihedral_angle_1_deg 7.391 r_lrange_other 7.041 r_lrange_it 7.04 r_scangle_it 5.372 r_scangle_other 5.372 r_mcangle_it 4.651 r_mcangle_other 4.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.116 r_dihedral_angle_4_deg 18.411 r_dihedral_angle_3_deg 16.474 r_dihedral_angle_1_deg 7.391 r_lrange_other 7.041 r_lrange_it 7.04 r_scangle_it 5.372 r_scangle_other 5.372 r_mcangle_it 4.651 r_mcangle_other 4.651 r_scbond_it 3.69 r_scbond_other 3.686 r_mcbond_it 3.471 r_mcbond_other 3.471 r_angle_refined_deg 1.611 r_angle_other_deg 1.35 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.191 r_metal_ion_refined 0.191 r_nbd_other 0.184 r_nbtor_refined 0.168 r_xyhbond_nbd_other 0.167 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.132 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 525 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing