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L-threonine dehydrogenase from Trypanosoma brucei with NAD and the inhibitor pyruvate bound.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5, 20 % w/v PEG 10K; TDH 2.0 mg/ml, 1 mM NAD(+), 30 mM pyruvate.
Crystal Properties Matthews coefficient Solvent content 2.2 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.04 α = 90 b = 276.49 β = 90 c = 55.74 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 CCD ADSC QUANTUM 315r 2009-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.074 ESRF ID29
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 2.1 95.5 97.3 0.145 11.4 7.5 117204 21.2
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 2.1 2.2 81.9 0.525 3.2 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5L9A 2.1 95.5 111527 5563 97.33 0.14952 0.14654 0.1565 0.20763 0.2138 RANDOM 22.767
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] 0.01 0.76 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.188 r_dihedral_angle_4_deg 18.605 r_dihedral_angle_3_deg 15.461 r_long_range_B_refined 7.489 r_long_range_B_other 7.124 r_dihedral_angle_1_deg 6.874 r_scangle_other 4.601 r_scbond_it 2.986 r_scbond_other 2.986 r_mcangle_other 2.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.188 r_dihedral_angle_4_deg 18.605 r_dihedral_angle_3_deg 15.461 r_long_range_B_refined 7.489 r_long_range_B_other 7.124 r_dihedral_angle_1_deg 6.874 r_scangle_other 4.601 r_scbond_it 2.986 r_scbond_other 2.986 r_mcangle_other 2.675 r_mcangle_it 2.674 r_angle_refined_deg 1.794 r_mcbond_it 1.753 r_mcbond_other 1.752 r_angle_other_deg 1.035 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15010 Nucleic Acid Atoms Solvent Atoms 1962 Heterogen Atoms 326
Software Software Software Name Purpose MOSFLM data reduction MOLREP phasing REFMAC refinement