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L-Threonine Dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFV PDB entry 2DFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.05 M sodium citrate, 2.4 M ammonium sulfate, 0.1 M sodium/potassium tartrate, 5%(v/v) glycerol and 0.1 mM zinc chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.44 64.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.481 α = 90 b = 124.481 β = 90 c = 271.143 γ = 90
Symmetry Space Group P 43 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 4r mirrors 2007-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 2.4 73.92 100 0.146 84056 42.6
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) 2.4 2.5 100 0.59 2.7 9511
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 PDB entry 2DFV 2.4 73.92 79730 4215 100 0.22039 0.21737 0.2175 0.27659 0.2749 RANDOM 38.704
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] 0.07 0.07 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.661 r_dihedral_angle_3_deg 20.023 r_dihedral_angle_4_deg 18.49 r_dihedral_angle_1_deg 9.359 r_scangle_it 5.416 r_scbond_it 3.719 r_angle_refined_deg 2.772 r_mcangle_it 2.545 r_mcbond_it 1.559 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.661 r_dihedral_angle_3_deg 20.023 r_dihedral_angle_4_deg 18.49 r_dihedral_angle_1_deg 9.359 r_scangle_it 5.416 r_scbond_it 3.719 r_angle_refined_deg 2.772 r_mcangle_it 2.545 r_mcbond_it 1.559 r_nbtor_refined 0.325 r_nbd_refined 0.251 r_symmetry_vdw_refined 0.25 r_symmetry_hbond_refined 0.242 r_xyhbond_nbd_refined 0.217 r_chiral_restr 0.19 r_bond_refined_d 0.034 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10672 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 226
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling