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Crystal Structure of Transketolase in complex with erythrose-4-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, PEG400
Crystal Properties Matthews coefficient Solvent content 3.18 61.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.149 α = 90 b = 185.246 β = 90 c = 98.71 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 2016-10-11 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) R Sym 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 1.07 92.62 99.9 0.058 0.07 20.7 7.9 403372
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.07 0.73
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5HYV 1.07 92.62 368116 19091 95.73 0.11919 0.11854 0.13154 0.1504 RANDOM 19.413
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] -0.22 -0.41 0.63
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.028 r_dihedral_angle_2_deg 34.781 r_dihedral_angle_4_deg 16.863 r_sphericity_bonded 11.958 r_dihedral_angle_3_deg 11.562 r_dihedral_angle_1_deg 6.046 r_long_range_B_refined 4.308 r_long_range_B_other 4.308 r_rigid_bond_restr 4.078 r_scangle_other 3.359
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.028 r_dihedral_angle_2_deg 34.781 r_dihedral_angle_4_deg 16.863 r_sphericity_bonded 11.958 r_dihedral_angle_3_deg 11.562 r_dihedral_angle_1_deg 6.046 r_long_range_B_refined 4.308 r_long_range_B_other 4.308 r_rigid_bond_restr 4.078 r_scangle_other 3.359 r_mcangle_it 3.263 r_mcangle_other 3.263 r_mcbond_it 3.04 r_mcbond_other 3.04 r_scbond_it 2.872 r_scbond_other 2.872 r_angle_refined_deg 1.515 r_angle_other_deg 1.286 r_chiral_restr 0.095 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 948 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling