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L-threonine dehydrogenase from trypanosoma brucei.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YY7
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
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.985 α = 72.46 b = 57.722 β = 70.38 c = 70.074 γ = 73.2
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 MARRESEARCH 2009-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 1.45 53.82 95 0.089 10.4 3.8 109054 11.9
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 1.45 1.53 82.1 0.398 2.7 2.3
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 2yy7 1.45 46.82 103550 5491 95.03 0.10254 0.09969 0.0993 0.15643 0.1561 RANDOM 16.591
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] -0.04 -0.03 0.01 0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.177 r_dihedral_angle_2_deg 35.633 r_dihedral_angle_4_deg 14.77 r_dihedral_angle_3_deg 13.769 r_sphericity_bonded 11.902 r_dihedral_angle_1_deg 6.466 r_long_range_B_refined 5.313 r_rigid_bond_restr 4.414 r_long_range_B_other 4.115 r_scangle_other 3.8
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.177 r_dihedral_angle_2_deg 35.633 r_dihedral_angle_4_deg 14.77 r_dihedral_angle_3_deg 13.769 r_sphericity_bonded 11.902 r_dihedral_angle_1_deg 6.466 r_long_range_B_refined 5.313 r_rigid_bond_restr 4.414 r_long_range_B_other 4.115 r_scangle_other 3.8 r_scbond_it 3.286 r_scbond_other 3.286 r_angle_refined_deg 2.07 r_mcangle_it 1.837 r_mcangle_other 1.837 r_mcbond_it 1.525 r_mcbond_other 1.491 r_angle_other_deg 1.325 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5011 Nucleic Acid Atoms Solvent Atoms 1335 Heterogen Atoms 8
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement