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The structure of human Transketolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QGD PDB ENTRY 1QGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 298 Crystallization trials revealed a reservoir mixture of 13.5-15 % PEG 6000
(w/v), 4% PEG 400 (v/v) and 2% glycerol (v/v) in 50 mM glycyl-glycine (pH
7.9) optimal for reproducible crystallization of single crystals. To
induce crystallization 3 l protein solution (8-12 mg/ml, 0.6 mM ThDP, 5 mM
CaCl2 in 50 mM glycyl-glycine (pH 7.9)) were mixed with 3 l of the reservoir
solution at room temperature.
, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.63 α = 90 b = 85.33 β = 125.69 c = 72.74 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 93 IMAGE PLATE RIGAKU RAXIS IV++ Varimax HR 2008-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 20 98 0.05 0.063 14.78 2.5 57086 55932 2.8 -3 27.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.85 96.2 0.394 0.494 2.8 2.4 8724
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 1QGD 1.75 20 55932 55928 2796 98.41 0.164 0.164 0.162 0.1636 0.206 0.1606 RANDOM 21.521
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] -0.77 0.36 0.48 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.287 r_dihedral_angle_4_deg 18.51 r_dihedral_angle_3_deg 14.264 r_dihedral_angle_1_deg 6.5 r_scangle_it 4.686 r_scbond_it 2.998 r_angle_refined_deg 1.995 r_mcangle_it 1.819 r_mcbond_it 1.182 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.287 r_dihedral_angle_4_deg 18.51 r_dihedral_angle_3_deg 14.264 r_dihedral_angle_1_deg 6.5 r_scangle_it 4.686 r_scbond_it 2.998 r_angle_refined_deg 1.995 r_mcangle_it 1.819 r_mcbond_it 1.182 r_chiral_restr 0.146 r_bond_refined_d 0.024 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4715 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 68
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction