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Crystal structure of L-threonine transaldolase from Pseudomonas fluorescens in internal aldimine state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OT8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 N-His-ObiH at 30 mg/ml was dissolved in 10 mM Tris pH 8.5. Two microliter of protein solution was mixed with two microliter of reservoir solution, 0.1 M Bis-Tris pH 6.75 - 7.0, 1.8 - 2.0 M ammonium sulfate and equilibrated against the reservoir at 21 C (294K)
Crystal Properties Matthews coefficient Solvent content 2.27 45.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.613 α = 90 b = 118.613 β = 90 c = 129.976 γ = 90
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 PILATUS3 X 6M 2018-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03321 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.66 118.6 100 0.216 0.083 0.996 6.9 13.4 211275
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.7 100 0.45 13.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4OT8 1.66 50.005 210898 10401 99.849 0.214 0.2127 0.219 0.2423 0.2466 Random selection 27.211
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] 0.239 0.239 -0.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_4_deg 9.902 r_dihedral_angle_1_deg 6.493 r_lrange_it 4.632 r_lrange_other 4.562 r_angle_refined_deg 1.269 r_angle_other_deg 1.265 r_mcangle_it 0.518 r_mcangle_other 0.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_4_deg 9.902 r_dihedral_angle_1_deg 6.493 r_lrange_it 4.632 r_lrange_other 4.562 r_angle_refined_deg 1.269 r_angle_other_deg 1.265 r_mcangle_it 0.518 r_mcangle_other 0.518 r_scangle_it 0.488 r_scangle_other 0.478 r_scbond_it 0.303 r_mcbond_it 0.295 r_mcbond_other 0.295 r_scbond_other 0.288 r_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.182 r_nbd_other 0.177 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.114 r_symmetry_nbd_refined 0.11 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.055 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13407 Nucleic Acid Atoms Solvent Atoms 919 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing