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Crystal Structure of Transketolase contains cysteinesufonic acid 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 60.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.267 α = 90 b = 185.551 β = 90 c = 98.878 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 2017-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 0.9900 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 1.3 30 99.9 0.05 28.4 8.1 224909
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 1.3 30 201479 10449 93.9 0.13737 0.13652 0.1365 0.15368 0.1542 RANDOM 16.034
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] -0.11 0.17 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.926 r_sphericity_free 21.112 r_dihedral_angle_4_deg 16.113 r_dihedral_angle_3_deg 12.298 r_dihedral_angle_1_deg 5.926 r_sphericity_bonded 5.491 r_rigid_bond_restr 3.15 r_long_range_B_other 2.228 r_long_range_B_refined 2.227 r_scangle_other 1.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.926 r_sphericity_free 21.112 r_dihedral_angle_4_deg 16.113 r_dihedral_angle_3_deg 12.298 r_dihedral_angle_1_deg 5.926 r_sphericity_bonded 5.491 r_rigid_bond_restr 3.15 r_long_range_B_other 2.228 r_long_range_B_refined 2.227 r_scangle_other 1.702 r_scbond_it 1.515 r_scbond_other 1.514 r_angle_refined_deg 1.455 r_mcangle_it 1.283 r_mcangle_other 1.283 r_mcbond_it 1.018 r_mcbond_other 1.017 r_angle_other_deg 0.989 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 5133 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling