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Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ and L-allo-threonine refined to 2.23 angstroms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.1M tri-sodium citrate, 30% w/v PEG 4K, 0.2M ammonium acetate, NAD+ (10mM), L-allo-threonine (30mM)
Crystal Properties Matthews coefficient Solvent content 2.23 44.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.03 α = 90 b = 273.06 β = 90 c = 55.8 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2013-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.26 31.09 90.4 0.151 0.862 5.6 1.9 154520
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 2.26 2.34 92.5 0.403 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.26 31.09 91289 4815 99.65 0.211 0.2073 0.2144 0.2808 0.2801 RANDOM 33.758
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] -0.02 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.375 r_dihedral_angle_4_deg 17.896 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_1_deg 7.507 r_mcangle_it 3.387 r_mcbond_it 2.186 r_mcbond_other 2.186 r_angle_refined_deg 1.649 r_angle_other_deg 0.862 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.375 r_dihedral_angle_4_deg 17.896 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_1_deg 7.507 r_mcangle_it 3.387 r_mcbond_it 2.186 r_mcbond_other 2.186 r_angle_refined_deg 1.649 r_angle_other_deg 0.862 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14958 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 344
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOLREP phasing PHASER phasing