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Crystal Structure of Transketolase in complex with TPP_III and fructose-6-phosphate from Pichia Stipitis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HYV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M MES, 0.1M NaCl, PEG 400
Crystal Properties Matthews coefficient Solvent content 3.09 60.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.269 α = 90 b = 185.284 β = 90 c = 98.932 γ = 90
Symmetry Space Group C 2 2 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 CCD RAYONIX MX300HE 2015-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 0.97 30 99 0.1 19.9 10.7 542392
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 0.97 1 0.66
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 5HYV 0.97 30 514761 27497 99.66 0.13708 0.13661 0.1427 0.14568 0.1503 RANDOM 10.945
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] -0.19 0.41 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.592 r_sphericity_free 26.213 r_dihedral_angle_4_deg 16.024 r_rigid_bond_restr 11.801 r_dihedral_angle_3_deg 11.764 r_sphericity_bonded 6.202 r_dihedral_angle_1_deg 5.976 r_long_range_B_refined 2.843 r_long_range_B_other 2.843 r_angle_other_deg 1.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.592 r_sphericity_free 26.213 r_dihedral_angle_4_deg 16.024 r_rigid_bond_restr 11.801 r_dihedral_angle_3_deg 11.764 r_sphericity_bonded 6.202 r_dihedral_angle_1_deg 5.976 r_long_range_B_refined 2.843 r_long_range_B_other 2.843 r_angle_other_deg 1.976 r_scangle_other 1.897 r_angle_refined_deg 1.68 r_scbond_it 1.577 r_scbond_other 1.577 r_mcangle_it 1.016 r_mcangle_other 1.016 r_mcbond_it 0.785 r_mcbond_other 0.784 r_chiral_restr 0.112 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5133 Nucleic Acid Atoms Solvent Atoms 785 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling