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Crystal structure of Threonine Synthase from Arabidopsis thaliana in complex with its cofactor pyridoxal phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E5X PDB ENTRY 1E5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1 M LICL, 13% (W/V) PEG 6000, 5 MM DTT, 0.1 M MES-KOH, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.33 46.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.626 α = 108.96 b = 61.014 β = 102 c = 76.678 γ = 107.36
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2000-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.6 20 95.5 0.05 6.8 2 25774
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 2.61 2.75 93.5 0.29 2.5 2
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 1E5X 2.61 20.63 24429 1311 100 0.191 0.187 0.1876 0.264 0.2638 RANDOM 20.6
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] 2.69 1.89 0.74 0.29 -0.8 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.89 r_dihedral_angle_4_deg 7.553 r_dihedral_angle_3_deg 7.134 r_scangle_it 3.451 r_angle_refined_deg 2.708 r_scbond_it 2.308 r_mcangle_it 1.552 r_dihedral_angle_1_deg 1.046 r_mcbond_it 0.885 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.89 r_dihedral_angle_4_deg 7.553 r_dihedral_angle_3_deg 7.134 r_scangle_it 3.451 r_angle_refined_deg 2.708 r_scbond_it 2.308 r_mcangle_it 1.552 r_dihedral_angle_1_deg 1.046 r_mcbond_it 0.885 r_nbtor_refined 0.332 r_nbd_refined 0.271 r_symmetry_vdw_refined 0.263 r_chiral_restr 0.203 r_xyhbond_nbd_refined 0.189 r_symmetry_hbond_refined 0.184 r_bond_refined_d 0.022 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6864 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling