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Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate and calcium 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 6.2 291 0.2 M NaCl, 20 % PEG 1000,
0.1 M Na/K phosphate,
10mM TPP, 10 mM R5P, 1mM CaCl2, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.924 α = 90 b = 71.462 β = 109.48 c = 69.617 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 1.59 40 94.8 0.085 19 3.8 80420 76588 1.9 2 27
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 1.59 1.63 72.1 0.74 1.9 3.4 2898
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.59 40 1.9 76498 72677 3821 94.28 0.18 0.16173 0.15968 0.1678 0.20086 0.2043 RANDOM 15.947
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] -0.52 1.83 1.06 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.2 r_dihedral_angle_4_deg 14.355 r_dihedral_angle_3_deg 14.111 r_dihedral_angle_1_deg 6.065 r_scangle_it 5.794 r_scbond_it 3.709 r_mcangle_it 2.241 r_angle_refined_deg 2.17 r_mcbond_it 1.404 r_angle_other_deg 1.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.2 r_dihedral_angle_4_deg 14.355 r_dihedral_angle_3_deg 14.111 r_dihedral_angle_1_deg 6.065 r_scangle_it 5.794 r_scbond_it 3.709 r_mcangle_it 2.241 r_angle_refined_deg 2.17 r_mcbond_it 1.404 r_angle_other_deg 1.122 r_mcbond_other 0.486 r_chiral_restr 0.14 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 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 565 Heterogen Atoms 56
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing Coot model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling