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Crystal Structure of Transketolase in complex with TPP intermediate III 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 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.916 α = 90 b = 184.139 β = 90 c = 98.86 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 2015-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.7 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.92 30 97.6 22.6 8.8 615127
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.92 0.95 96 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5HYV 0.918 26.221 1.33 615018 31393 97.23 0.1378 0.1373 0.1372 0.1475 0.1476
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.786 f_angle_d 1.241 f_chiral_restr 0.096 f_bond_d 0.01 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5130 Nucleic Acid Atoms Solvent Atoms 1106 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement HKL-2000 data processing HKL-2000 data reduction HKL-2000 data scaling