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Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate(pyranose form) and magnesium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 .2 M NaCl
30% Peg 400
0.1 M HEPES
10 mM RP5, 10 mM TPP, 1mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.337 α = 90 b = 70.955 β = 109.4 c = 69.189 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r mirrors 2010-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.75 40 97.5 0.094 12.7 3.2 59272 57827 2 2 34.3
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 1.75 1.78 99.9 0.415 3.2 2.9 2940
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3M34 1.75 40 2 2 57816 54908 2908 96.76 0.194 0.17121 0.16711 0.1678 0.21076 0.2085 RANDOM 23.719
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] -0.54 0.96 1.03 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.646 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 13.709 r_dihedral_angle_1_deg 6.101 r_scangle_it 5.043 r_scbond_it 3.136 r_mcangle_it 1.893 r_angle_refined_deg 1.858 r_mcbond_it 1.11 r_angle_other_deg 1.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.646 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 13.709 r_dihedral_angle_1_deg 6.101 r_scangle_it 5.043 r_scbond_it 3.136 r_mcangle_it 1.893 r_angle_refined_deg 1.858 r_mcbond_it 1.11 r_angle_other_deg 1.024 r_mcbond_other 0.367 r_chiral_restr 0.114 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4901 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 45
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing Coot model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling CCP4 phasing