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Structure of Plasmodium falciparum Transketolase in complex with Oxythiamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8R3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.2M potassium citrate diabasic monohydrate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.388 α = 90 b = 142.81 β = 90 c = 176.185 γ = 90
Symmetry Space Group P 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 2025-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 1.81 110.942 99.19 0.995 7.1 13.7 260015
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 1.813 1.884 0.395
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 NONE 1.813 110.942 258211 12987 99.191 0.183 0.1809 0.1931 0.217 0.2274 21.444
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] -1.393 1.883 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_4_deg 16.715 r_dihedral_angle_3_deg 14.317 r_dihedral_angle_1_deg 6.898 r_lrange_it 4.986 r_lrange_other 4.986 r_scangle_it 3.842 r_scangle_other 3.842 r_scbond_it 2.461 r_scbond_other 2.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_4_deg 16.715 r_dihedral_angle_3_deg 14.317 r_dihedral_angle_1_deg 6.898 r_lrange_it 4.986 r_lrange_other 4.986 r_scangle_it 3.842 r_scangle_other 3.842 r_scbond_it 2.461 r_scbond_other 2.461 r_mcangle_it 2.002 r_mcangle_other 2.002 r_angle_refined_deg 1.516 r_mcbond_it 1.419 r_mcbond_other 1.419 r_angle_other_deg 1.399 r_symmetry_xyhbond_nbd_other 0.219 r_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.198 r_nbd_other 0.178 r_symmetry_nbd_other 0.175 r_xyhbond_nbd_refined 0.174 r_symmetry_nbd_refined 0.173 r_nbtor_refined 0.169 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.078 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 21136 Nucleic Acid Atoms Solvent Atoms 1981 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling REFMAC phasing