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Crystal Structure of Transketolase in complex with xylulose-5-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 59.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.709 α = 90 b = 183.724 β = 90 c = 98.856 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 2015-09-01 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 1.12 30 99.6 0.04 30.2 7.8 312132
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 1.12 1.14 99.9 0.602 2.9 7.2
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 1.12 30 312132 16024 94.29 0.12305 0.12252 0.1236 0.13352 0.1348 RANDOM 17.951
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] 0.31 -0.15 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.945 r_sphericity_free 25.218 r_dihedral_angle_4_deg 16.582 r_dihedral_angle_3_deg 11.347 r_sphericity_bonded 6.015 r_dihedral_angle_1_deg 5.977 r_long_range_B_refined 2.544 r_rigid_bond_restr 2.37 r_long_range_B_other 2.076 r_scangle_other 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.945 r_sphericity_free 25.218 r_dihedral_angle_4_deg 16.582 r_dihedral_angle_3_deg 11.347 r_sphericity_bonded 6.015 r_dihedral_angle_1_deg 5.977 r_long_range_B_refined 2.544 r_rigid_bond_restr 2.37 r_long_range_B_other 2.076 r_scangle_other 1.56 r_angle_refined_deg 1.451 r_scbond_it 1.318 r_scbond_other 1.317 r_mcangle_it 1.128 r_mcangle_other 1.128 r_angle_other_deg 1.059 r_mcbond_it 0.872 r_mcbond_other 0.871 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 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 756 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data reduction HKL-2000 data scaling