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Crystal Structure of Transketolase in complex with ribose-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 3.08 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.093 α = 90 b = 184.78 β = 90 c = 99.015 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) 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 1.14 30 96.6 0.051 16.9 4.6 305278
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 1.14 1.18 96 2.2 3.7
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 1.14 30 305278 16025 96.49 0.13007 0.12949 0.1299 0.14121 0.1414 RANDOM 9.189
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] -0.15 0.3 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.812 r_sphericity_free 26.793 r_dihedral_angle_4_deg 15.151 r_dihedral_angle_3_deg 11.241 r_dihedral_angle_1_deg 5.968 r_sphericity_bonded 5.679 r_rigid_bond_restr 4.209 r_long_range_B_refined 2.786 r_long_range_B_other 2.786 r_angle_refined_deg 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.812 r_sphericity_free 26.793 r_dihedral_angle_4_deg 15.151 r_dihedral_angle_3_deg 11.241 r_dihedral_angle_1_deg 5.968 r_sphericity_bonded 5.679 r_rigid_bond_restr 4.209 r_long_range_B_refined 2.786 r_long_range_B_other 2.786 r_angle_refined_deg 1.45 r_scangle_other 1.032 r_angle_other_deg 0.999 r_scbond_other 0.916 r_scbond_it 0.915 r_mcangle_other 0.731 r_mcangle_it 0.73 r_mcbond_it 0.518 r_mcbond_other 0.517 r_chiral_restr 0.083 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 1027 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data reduction HKL-2000 data scaling