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Crystal Structure of Transketolase in complex with TPP_V 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 3.05 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.869 α = 90 b = 183.423 β = 90 c = 98.841 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 2012-05-26 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 1.4 30 100 0.071 25.2 5.9 178636
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 1.4 1.45 100 0.534 3.4 5.4
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 1.4 30 169669 8933 99.87 0.12166 0.12081 0.1209 0.13824 0.1383 RANDOM 12.786
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 0.46 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.869 r_sphericity_free 32.649 r_dihedral_angle_4_deg 15.25 r_dihedral_angle_3_deg 11.694 r_dihedral_angle_1_deg 5.948 r_sphericity_bonded 5.861 r_rigid_bond_restr 4.644 r_long_range_B_refined 3.31 r_long_range_B_other 3.31 r_angle_refined_deg 1.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.869 r_sphericity_free 32.649 r_dihedral_angle_4_deg 15.25 r_dihedral_angle_3_deg 11.694 r_dihedral_angle_1_deg 5.948 r_sphericity_bonded 5.861 r_rigid_bond_restr 4.644 r_long_range_B_refined 3.31 r_long_range_B_other 3.31 r_angle_refined_deg 1.551 r_angle_other_deg 1.299 r_scangle_other 1.196 r_scbond_it 1.047 r_scbond_other 1.047 r_mcangle_it 0.814 r_mcangle_other 0.814 r_mcbond_it 0.627 r_mcbond_other 0.625 r_chiral_restr 0.14 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 5130 Nucleic Acid Atoms Solvent Atoms 926 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data reduction HKL-2000 data scaling