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Crystal structure of transketolase in complex with thiamin diphosphate and calcium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 0.1 M Ches ph 9.5 30 % PEG 400 10 mM TPP, 1mm CaCl2. Sitting drop, vapor
diffusion method
Temp 293 K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.13 42.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.35 α = 90 b = 70.819 β = 109.92 c = 69.236 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 2009-02-11 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 1.65 40 99.4 0.08 17.6 3.6 70630 70590 2 2 31.4
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 1.65 1.68 99.9 0.61 2.2 3.5 3508
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 3L84 1.65 40 2 2 70600 67019 3566 99.24 0.17 0.15294 0.15141 0.1514 0.18186 0.1823 RANDOM 19.448
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] 0.46 0.11 0.56 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.025 r_dihedral_angle_3_deg 12.905 r_dihedral_angle_4_deg 12.636 r_dihedral_angle_1_deg 6.041 r_scangle_it 5.023 r_scbond_it 3.064 r_angle_refined_deg 1.809 r_mcangle_it 1.793 r_mcbond_it 1.037 r_angle_other_deg 0.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.025 r_dihedral_angle_3_deg 12.905 r_dihedral_angle_4_deg 12.636 r_dihedral_angle_1_deg 6.041 r_scangle_it 5.023 r_scbond_it 3.064 r_angle_refined_deg 1.809 r_mcangle_it 1.793 r_mcbond_it 1.037 r_angle_other_deg 0.976 r_mcbond_other 0.345 r_chiral_restr 0.161 r_bond_refined_d 0.02 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 420 Heterogen Atoms 43
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling