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Maize Transketolase in complex with TPP and hydrolyzed (+)-Cornexistin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ITZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 28 % PEG 3350, 250 mM ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.309 α = 90 b = 135.309 β = 90 c = 201.439 γ = 120
Symmetry Space Group P 31 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 100 CCD OXFORD ONYX CCD 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION NOVA 1.54
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 1.9 23.83 94.4 0.064 19 6.01 157602
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 1.9 2 0.175
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.902 23.727 157559 7754 94.208 0.155 0.1532 0.1646 0.1836 0.1928 11.924
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] 0.127 0.064 0.127 -0.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.725 r_dihedral_angle_4_deg 18.559 r_dihedral_angle_3_deg 13.957 r_dihedral_angle_1_deg 6.691 r_lrange_it 4.267 r_lrange_other 3.903 r_scangle_it 2.638 r_scangle_other 2.638 r_scbond_other 1.711 r_scbond_it 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.725 r_dihedral_angle_4_deg 18.559 r_dihedral_angle_3_deg 13.957 r_dihedral_angle_1_deg 6.691 r_lrange_it 4.267 r_lrange_other 3.903 r_scangle_it 2.638 r_scangle_other 2.638 r_scbond_other 1.711 r_scbond_it 1.71 r_angle_refined_deg 1.544 r_angle_other_deg 1.488 r_mcangle_other 1.347 r_mcangle_it 1.346 r_mcbond_it 0.919 r_mcbond_other 0.915 r_symmetry_nbd_refined 0.255 r_symmetry_xyhbond_nbd_refined 0.245 r_nbd_refined 0.216 r_nbd_other 0.212 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_1 0.052 r_ncsr_local_group_2 0.049 r_ncsr_local_group_3 0.043 r_symmetry_xyhbond_nbd_other 0.027 r_bond_refined_d 0.01 r_metal_ion_refined 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 15246 Nucleic Acid Atoms Solvent Atoms 2014 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction XSCALE data scaling MOLREP phasing